Short table format (without abstract)
Alphabetical list of abstract authors
Invited Speaker Abstracts
Number: Invited-1
Authors: Robert B. Russell1
1EMBL, russell@embl.de
Title: A Structural Perspective on Protein Interactions & Complexes
Representative figure:
Short abstract: I will discuss how protein structure information can be used as a tool to interrogate and predict structures for interactions identified by other methods (e.g. two-hybrids), and present approaches for merging experimental interactions, electron microscopy via structural bioinformatics.
Full abstract
Number: Invited-2
Authors: Ron Unger1
1Bar-Ilan University, ron@biocom1.ls.biu.ac.il
Title: Using Accumulated Dot Matrices to Detect RNA and Protein Structures
Representative figure:
Short abstract: We present an approach based on matrix representation of all potential base-pairing of a set of RNA sequences. A proper accumulation of such matrices exposes common structural features, including pseudo-knots. Similar ideas can be extended to analyze aligned protein sequences in order to detect common structural motifs within proteins families.
Full abstract
Number: Invited-3
Authors: Gregorio Fernandez, Christine Kiel, Luis Serrano1
1EMBL, Heidelberg, serrano@EMBL-Heidelberg.DE
Title: In silico Prediction of Protein-Protein Interactions: How and When It Can Work
Full abstract
Number: Invited-4
Authors: Gunnar von Heijne1
1Department of Biochemistry and Biophysics, Stockholm University, gunnar@dbb.su.se
Title: Genome-wide Membrane Protein Topology Predictions
Short abstract: Current estimates are that we can predict the correct topology for 55-60% of all membrane proteins. One way to improve these numbers is to incorporate more experimental data into the predictions. Recent work in our laboratory aiming to produce such data on a genome-wide scale will be presented.
Number: Invited-5
Authors: Florencio Pazos, Michael JE Sternberg1
1Imperial College of Science, Technology and Medicine, m.sternberg@imperial.ac.uk
Title: Automated Prediction of Protein Function from Structure
Representative figure:
Short abstract: An algorithm is presented that predicts protein function based on structure. The approach uses Gene Ontology Classification (GO) to supervise the identification of functionally-important residues from a structural alignment. In a cross-validated benchmark it is significantly superior to functional transfer from the closest sequence homologues in the twilight-zone for functional prediction (sequence ID=~15%).
Full abstract
Number: Invited-7
Authors: Martin Madera1, Julian Gough2, Sarah Kummerfeld, Cyrus Chothia 3
1MRC Laboratory of Molecular Biology, Cambridge, UK, mm238@mrc-lmb.cam.ac.uk 3chc1@mrc-lmb.cam.ac.uk 2gough@gsc.riken.go.jp
Title: The Homology of Genome Sequences: Profile-Profile Sequence Matching and the SUPERFAMILY Database
Representative figure:
Short abstract: We describe: the features and performance of PRofile Comparer (PRC, http://supfam.org/PRC), a new tool for aligning and scoring two profile hidden Markov models; the SUPERFAMILY database (http://supfam.org), which lists for all genomes the homologs to domains of known structure, and the distribution of known protein superfamilies in different genomes.
Full abstract
Number: Invited-8
Authors: Song Yang, Russell Doolittle, Philip E. Bourne1
1University of California San Diego, bourne@sdsc.edu
Title: The Study of Evolution through Protein Domain Structure
Short abstract: Consider two principles: 1. Structure can provide information on distant evolutionary relationships. 2. Nature is comprised of a very limited parts list of protein domain folds, hence for a species to loose or gain a fold is a major event. The use of these principles in phylogenetic analysis is discussed.
Full abstract
Speaker Abstracts
Number: 5
Authors: Rune Linding1, Robert B. Russell, Lars J. Jensen, Francesca Diella, Peer Bork, Toby J. Gibson
1EMBL, linding@embl.de
Title: Intrinsic Protein Disorder - Function, Disease and Structural Proteomics.
Representative figure:
Short abstract: Disordered regions in proteins often contain short linear peptide motifs (e.g. SH3-ligands and targeting signals) that are important for protein function. Avoiding potentially disordered segments in protein expression constructs can ncrease expression, foldability and stability of the expressed protein.
Full abstract
Number: 9
Authors: Barry J. Grant1, Leo S. Caves2, Rob Cross3
1University of York & Marie Curie Research Institut, grant@ysbl.york.ac.uk 2University of York, lsdc1@york.ac.uk 3Marie Curie Research Institute, r.cross@mcri.ac.uk
Title: Stripping down the Kinesin Molecular Motor: a Combined Informatics and Simulation Approach
Representative figure:
Short abstract: Structural informatics and molecular modelling were used to probe sequence-structure-function relationships in the kinesin molecular motor. This study provides information on conformational changes, allosteric modulation, protein-protein interactions and evolutionary relationships. The work illustrates the powerful interplay of informatics and simulation with structural, biochemical and biophysical experiments on this important mechanoenzyme.
Full abstract
Number: 15
Authors: Eran Eyal1, Marvin Edelman, Vladimir Sobolev
1Weizmann Institute of Science, eran.eyal@weizmann.ac.il
Title: The Influence of Crystal Packing on Protein structure
Representative figure:
Short abstract: The crystal environment has a small yet statistically significant influence on the structure of a protein. B-factor values of atoms having crystal contacts are smaller. Associated water molecules tend to change position when the environment is changed; associated hetero-groups, less so. See our tool for crystal contact analysis http://atlantis.weizmann.ac.il/~eyale/cryco
Full abstract
Number: 18
Authors: Andreas Heger1, Liisa Holm2
University of Helsinki, 1andreas.heger@helsinki.fi 2liisa.holm@helsinki.fi
Title: Fast Fold Recognition by Consensus Alignment within Transitive Closure
Representative figure:
Short abstract: Protein structure is more conserved than sequence. Many distant homologues can only be linked by significant sequence similarity using many intermediate sequences. Pre-processing the information in an all-against-all alignment library enables us to instantaneously generate an optimal transitive alignment between any two proteins, no matter how many intermediates separate them.
Full abstract
Number: 22
Authors: Oxana V. Galzitskaya1, Sergiy O. Garbuzynskiy2, Bogdan S. Melnik3, Michail Y. Lobanov, Alexei V. Finkelstein
Institute of Protein Research, 1ogalzit@vega.protres.ru 2S_rgei@mail.ru 3bmelnik@alpha.protres.ru
Title: Comparison of X-ray and NMR Protein Structures
Representative figure:
Short abstract: What is the difference between X-ray and NMR-resolved protein structures? A comparison of structures of 61 proteins determined by both NMR and X-ray show statistically reliable differences in the number of contacts per residue and the number of main-chain hydrogen bonds.
Full abstract
Number: 24
Authors: Sanne Abeln1, Charlotte M. Deane2
Department of Statistics, University of Oxford, 1abeln@stats.ox.ac.uk 2deane@stats.ox.ac.uk
Title: Investigating Protein Structure Evolution by Fold Usage on Genomes
Representative figure:
Short abstract: Here we use different measures of fold usage on completed genomes in order to explore protein structure evolution. We show that there is not a clear relationship between the number of families per fold, the number of fold copies per genome and the number of genomes a fold occurs on.
Full abstract
Number: 28
Authors: Antonio Del Sol1, Paul A. O'Meara2
1Protein Design Group, National Center for Biotechnology and Research and Development Division, Fujirebio Inc., ao-mesa@fujirebio.co.jp 2Research Division, Fujirebio Inc., pl-omeara@fujirebio.co.jp
Title: Small-World Network Approach to Identify Key Residues in Protein-Protein Interaction.
Representative figure:
Short abstract: Protein structures are examples of small-world networks, exhibiting a small number of vertices with many connections corresponding to key residues for protein folding. We have successfully used the small-world network approach to predict experimentally verified and new potential candidates for hot spots involved in different biological cases of protein-protein interaction.
Full abstract
Number: 31
Authors: Maxim Chapovalov1, Roland L. Dunbrack2
Fox Chase Cancer Center, 1Maxim.Chapovalov@fccc.edu 2RL_Dunbrack@fccc.edu
Title: Using Statistical Analysis of Electron Density to Evaluate Protein Side-Chain Conformations and Rotamer Disorder
Representative figure:
Short abstract: Electron density calculations on high-resolution structures demonstrate that non-rotameric side-chain conformations have poor density. Density about chi1 shows that 9% of side-chains exist in more than one chi1 rotamer, with only 2% shown in the PDB entries. These calculations can improve rotamer-libraries and side-chain prediction of single or multiple conformations.
Full abstract
Number: 36
Authors: Maxim Totrov1
1Molsoft, max@molsoft.com
Title: Protein-Protein Docking Simulations with Local Backbone Flexibility
Representative figure:
Short abstract: Induced fit remains principal obstacle to accurate protein-protein docking. ICM methodology was adapted to efficiently handle full flexibility of segment of polypeptide chain and successfully applied to dock unbound chymotrypsin and eglin with fully flexible 9-residue binding loop. The method may allow accurate docking for systems involving highly flexible loop.
Full abstract
Number: 41
Authors: Johannes Soeding1, Andrei N. Lupas2
Max-Planck-Institute for Developmental Biology, Dept Protein Evolution, 1johannes.soeding@tuebingen.mpg.de 2andrei.lupas@tuebingen.mpg.de
Title: Homology Search By HMM-HMM Comparison Detects More Than Three Times As Many Remote Homologs as PSIBLAST or HMMER
Representative figure:
Short abstract: We developed a homology search method based on pairwise comparison of profile HMMs. In an all-against-all benchmark (3691 SCOP 1.63 domains, < 20% sequence identity) the method detects 3-5 times more homologs than PSIBLAST or HMMER and between 25% and 100% more than profile-profile comparison tools COMPASS and PROF_SIM.
Full abstract
Number: 43
Authors: Richard J. Morris1, Abdullah Kahraman2, Rafael Najmanovich, Fabian Glaser, Roman Laskowski, Janet M. Thornton
EBI, 1rjmorris@ebi.ac.uk 2abdullah@ebi.ac.uk
Title: Protein Active Site Identification and Fast Shape Comparison
Representative figure:
Short abstract: Methods are presented to aid protein function prediction from structure. We focus on algorithms to locate and to describe a protein's active site with parameters from a multipole expansion. An active site similarity metric is presented that allows for rapid comparisons against a large signature database.
Full abstract
Number: 45
Authors: Arye Shemesh1, Gil Amitai, Einat Sitbon, Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski
1Weizmann Institute of Science, arye.shemesh@weizmann.ac.il
Title: Structural Analysis of Residue Interaction Graphs
Representative figure:
Short abstract: We present a graph theory approach for studying protein structures. Structures were transformed to residue interaction graphs, where nodes are residues and edges connect interacting residues. Centrality measures of nodes identified various functional sites. Our method analyzes single structures, is independent of conservation, and does not rely on prior training.
Full abstract
Number: 46
Authors: Gestel David1, Ian Humphery-Smith2
Dept. of Pharmaceutical Proteomics, Universiteit Utrecht, 1david.gestel@pharm.uu.nl 2ianhs@hotmail.com
Title: The Binding-Site Diversity of the Entire Non-denatured, Surface-exposed Human Proteome
Representative figure:
Short abstract: Thirty-seven antigen / antibody crystal structures were employed to establish a mean interaction patch radius. A minimalist model corrected with data derived from 680 SCOP domain structures was then employed in association with every Open Reading Frame in the human genome to provide a reliable estimate of potential binding-site diversity.
Full abstract
Number: 47
Authors: Inge Jonassen1, William R. Taylor2
1University of Bergen, inge@ii.uib.no 2National Institute of Medical Research, London, wtaylor@nimr.mrc.ac.uk
Title: SPREK: A Method for Evaluating Structural Models using Structural Patterns
Representative figure:
Short abstract: We propose a novel method for the evaluation of structural models. The captures multiple interactions and rewards models having interaction patterns frequently found in true structures. The method utilises string representations of local neighbourhoods. A comparative evaluation of SPREK demonstrates that it is competetive with state of the art methods.
Full abstract
Number: 53
Authors: Jaspreet S. Sodhi1, Kevin Bryson2, Liam J. McGuffin, Jonathan J. Ward, Lornenz Wernisch, David T. Jones
University College London, 1j.sodhi@cs.ucl.ac.uk 2K.Bryson@cs.ucl.ac.uk
Title: Predicting the Location and Identity of Protein Functional Sites, Application to Genomic Fold Recognition
Representative figure:
Short abstract: We present a fully automatic site detection method, FuncSite, that uses neural network classifiers to predict the location and type of functionally important sites in protein structures. We have shown the method to be robust enough for site detection in low resolution structural models applicable to genomic fold recognition predictions.
Full abstract
Number: 68
Authors: Marialuisa Pellegrini-Calace1, William R. Taylor, David T. Jones
1EMBL, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kin, marial@ebi.ac.uk
Title: FILM2: a Novel Method for the Prediction of Transmembrane Helical Bundles in a Membrane-like Environment
Representative figure:
Short abstract: A novel method for the prediction of helical transmembrane protein structures, FILM2, is presented. The method combines the helix variphobicity, which predicts the exposure of each transmembrane helix to lipids, with a previously developed knowledge-based membrane potential and can predict with reasonable accuracy both helix topologies and the protein folds.
Full abstract
Number: 72
Authors: Qiaojuan Jane Su1, Orit Foord2, Scott Klakamp, Holly Tao, Larry L. Green
1Abgenix, jane.su@abgenix.com 2orit.foord@abgenix.com
Title: Modeling and Simulation of Antibody-Antigen Interaction: An Integrated Approach
Representative figure:
Short abstract: We have built an antibody-epitope docking model that integrates epitope mapping and affinity data. Using this model, we show that structure-based antibody-antigen binding energetics simulations can correlate well with experimental affinity ranking. We propose that a proven docking model might further be applied to perform in silico design to optimize antibody characteristics.
Full abstract
Number: 74
Authors: Joerg Hackermueller1, Nicole-Claudia Meisner2, Manfred Auer, Markus Jaritz
Novartis Institute for Biomedical Research Vienna, 1joerg.hackermueller@pharma.novartis.com 2nicole-claudia.meisner@pharma.novartis.com
Title: mRNA Openers – Computationally Designed Modulators of mRNA Secondary Structure which Manipulate Gene Expression
Representative figure:
Short abstract: Recognition of RNA secondary structure motifs is of central importance for regulatory RNA protein interactions. The presented method allows to explain measured RNA protein affinities by quantitatively describing RNA secondary structure motif availability. Computationally designed secondary structure modulators boost or inhibit regulatory RNA protein interactions as predicted.
Full abstract
Number: 76
Authors: Yuval Inbar1, Haim J. Wolfson2, Ruth Nussinov
Tel Aviv University, 1inbaryuv@tau.ac.il 2wolfson@tau.ac.il
Title: Prediction of Multi-Molecular Assemblies by Multiple Combinatorial Docking.
Representative figure:
Short abstract: We have developed an algorithm that extends the application of docking to multimolecular assemblies. The algorithm should be particularly useful to predict the structures of large macromolecular assemblies, difficult to be determined experimentally. The algorithm well predicted quaternary structures of oligomers and multi-protein complexes, even for a structurally distorted input.
Full abstract
Number: 77
Authors: Matthew L. Baker1, Wah Chiu2
Baylor College of Medicine, 1mbaker@bcm.tmc.edu 2wah@bcm.tmc.edu
Title: Analysis of Intermediate Resolution Structures
Representative figure:
Short abstract: To facilitate the analysis of structures from electron cryomicroscopy, we have developed the Analysis of Intermediate Resolution Structures toolkit (AIRS). AIRS provides a mechanism to localize structures, recognize secondary structure, identify folds and model large macromolecular assemblies. This toolkit has been successfully applied to HSV-1 and RDV.
Full abstract
Laptop Session Abstracts
Number: 1
Authors: Anne Marie Quinn1, Luke Fisher2, Dana Haley-Vicente3
Accelrys, 1aquinn@accelrys.com 2lfisher@accelrys.com 3danaHV@netscape.net
Title: From Gene to Function: In Silico Warfare on the West Nile Virus
Representative figure:
Short abstract: Can we produce reliable structural models of the proteins of the West Nile virus even when sequence identity is low among homologs? Here we show that the DS GeneAtlas pipeline can be used to produce reliable structural and functional annotation of the proteins encoded by the this genome.
Full abstract
Number: 2
Authors: Efrat Ben-Zeev1, Miriam Eisenstein2
1Weizamann Institute of Science, efrat.ben-zeev@weizmann.ac.il 2Weizmann Institute of Science, miriam.eisenstein@weizmann.ac.il
Title: Weighted Geometric Docking with MolFit: Incorporating External Information in the Rotation-Translation Scan
Representative figure:
Short abstract: Weighted-geometric docking incorporates external data from different sources, such as biochemical and biophysical experiments and bioinformatics analyses, in the docking rotation-translation scan. The method is successful even when the weighted portion of the surface corresponded only partially and approximately to the binding site. Implemented in our program MolFit.
Full abstract
Number: 3
Authors: James Bradford1, David Westhead2
1University of Leeds, School of Biochemistry and Molecular Biology, bmbjrb@bmb.leeds.ac.uk 2University of Leeds, School of Biochemistry and Mi, westhead@bmb.leeds.ac.uk
Title: Prediction of Protein-Protein Binding Sites using Support Vector Machines
Representative figure:
Short abstract: We have applied a machine-learning approach, the support vector machine, to the prediction of protein-protein binding sites. Our method classifies surface patches as part of or outside a binding site, and has a high success rate with broad specificity, being able to predict both transient and obligomeric binding sites.
Full abstract
Number: 4
Authors: Kim Henrick1, Tom Oldfield2, Adel Golovin, John Tate, Sameer Velankar, Harry Boutselakis, Dimitris Dimitropoulos, Peter Keller, Eugene Krissinel, Phil McNeil, Jorge Pineda, Abdelkrim Rachedi, Antonio Suarez-Uruena, Jawahar Swaminathan, Mohamed Tagari
European Bioinformatics Institute, 1henrick@ebi.ac.uk 2oldfield@ebi.ac.uk
Title: MSD Relational Database, Search and Visualisation of Queries and Results
Representative figure:
Short abstract: The MSD macromolecular structure database together with search interfaces will be described as an integrated system that includes structure matching through to active site visualisation.
Full abstract
Number: 6
Authors: Sarel J. Fleishman1, Vinzenz M. Unger, Mark Yeager, Nir Ben-Tal
1Tel-Aviv University, sarel@post.tau.ac.il
Title: A Model Structure of the Gap-Junction Transmembrane Domain Specifying C-alpha Positions
Representative figure:
Short abstract: A set of methods for predicting the orientations of transmembrane alpha helices was developed and applied to predicting the gap junction’s structure. The model provides a structural basis for understanding the different physiological effects of almost 30 mutations and polymorphisms, revealing an intimate relationship between molecular structure and disease.
Full abstract
Number: 7
Authors: Thomas Lütteke1, Claus W. von der Lieth2
DKFZ Heidelberg, Central Spectroscopic Department, 1t.luetteke@dkfz.de 2w.vonderlieth@dkfz.de
Title: Towards Deciphering the Structural Features of Glycosylation Sites: Analysis of Carbohydrate-Related Data contained in the Protein Data Bank
Representative figure:
Short abstract: www.glycosciences.de provides several tools to examine carbohydrate 3D structures derived from PDB entries using pdb2linucs: GlyTorsion statistically analyses various torsion angles. GlySeq generates statistics on amino acids around glycosylation sites. Carp performs a Ramachandran-like plot of carbohydrate linkage torsions. Data sets are updated weekly with new PDB entries.
Full abstract
Number: 8
Authors: Wolfgang F. Bluhm1 on behalf of the PDB team
1RCSB Protein Data Bank, wbluhm@sdsc.edu
Title: PDB-in-a-Box
Representative figure:
Short abstract: The Protein Data Bank (http://www.pdb.org/, PDB), maintained by the Research Collaboratory for Structural Biology (RCSB), is completely reengineering its Web site and database. We will demonstrate one product of this reengineering: a stand-alone version of the entire Web site and database on a laptop computer.
Full abstract
Number: 10
Authors: Howard J. Feldman1, Christopher WV Hogue2, Kevin Snyder
The Blueprint Initiative, 1feldman@mshri.on.ca 2hogue@mshri.on.ca
Title: MMDBBIND - Macromolecular Interactions with Atomic Level Detail
Representative figure:
Short abstract: MMDBBIND provides over 18,000 high quality fully annotated, searchable, atomic-level detail molecular interaction records to BIND (Biomolecular Interaction Network Database). Interactions can be viewed with the Cn3D structure viewing software, with interacting residues highlighted. These could be used, for example, to generate empirical protein-protein docking potentials.
Full abstract
Number: 11
Authors: Philip C. Biggin1, Yalini Arinaminpathy2, Mark SP Sansom
Oxford University, 1phil@biop.ox.ac.uk 2pathy@biop.ox.ac.uk
Title: Conformational Dynamics of Glutamate Receptors: Simulation Studies.
Representative figure:
Short abstract: The precise mechanism of partial agonism in ionotropic glutamate receptors remains unclear. We present results from molecular dynamics simulations of the ligand-binding core (S1S2) which suggest how partial agonists can induce single-channel currents of the same magnitude as full agonist but with a reduced frequency as recently observed experimentally.
Full abstract
Number: 12
Authors: Nicola D. Gold1, Richard M. Jackson2
1University of Leeds, n.d.gold@leeds.ac.uk 2jackson@bmb.leeds.ac.uk
Title: A Searchable Database for Comparing Protein-Ligand Binding Sites for the Discovery of Structure-Function Relationships
Representative figure:
Short abstract: It may be possible to infer common functional roles for proteins with similar ligand binding sites. We have therefore developed a web accessible database of ligand binding sites combined with a similarity searching method based on geometric hashing to identify binding sites with similar atomic arrangements and properties.
Full abstract
Number: 13
Authors: Andreas Bohne-Lang1, Claus W. von der Lieth
1German Cancer Research Center, a.bohne@dkfz-heidelberg.de
Title: Glyprot: a Web-tool for in-silico Glycosylation of Proteins
Representative figure:
Short abstract: Over 50% of the proteins are glycosylated. But many of the 3d structures of proteins stored in PDB have no or only a small carbohydrate part. However, our free web-tool is capable to create a 3d protein structure with attached n-glycan –– in–silio.
Glyprot: http://www.dkfz.de/spec/glyprot/
Full abstract
Number: 14
Authors: Vladimir Potapov1, Vladimir Sobolev2, Marvin Edelman, Alexander Kister, Israel Gelfand
Weizmann Institute of Science, 1vladimir.potapov@weizmann.ac.il 2vladimir.sobolev@weizmann.ac.il
Title: Interface Cores in Sandwich-like Proteins
Representative figure:
Short abstract: We define protein-protein interface and domain cores for immunoglobulins containing about half the residues and surface areas of the full interfaces. Residues of the two cores are structurally connected, imparting rigidity at the interface core. The rule of positional connectivity extends generally to sandwich-like proteins interacting in a sheet-sheet fashion.
Full abstract
Number: 16
Authors: Eran Eyal1, Vladimir Sobolev, Rafael Najmanovich, Brendan J. McConkey, Marvin Edelman
1Weizmann Institute of Science, Rehovot, Israel, eyale@wicc.weizmann.ac.il
Title: Modeling Side Chain Conformations using Contact Surfaces and solvent Accessible Surface
Representative figure:
Short abstract: Contact surface area and chemical properties of atoms form the core of a scoring function to concurrently predict conformations of amino acid sidechains. The program (http://sgedg.weizmann.ac.il/sccomp.html) combines accuracy and speed. Most atoms prefer intramolecular surface contact over solvent contact. This might be the driving force for maximizing protein packing.
Full abstract
Number: 17
Authors: Gail J. Bartlett1, James W. Torrance2, Craig T. Porter, Jonathan A. Barker, Alex Gutteridge, Malcolm W. MacArthur, Janet M. Thornton
1Imperial College London, Centre for Bioinformatics, g.bartlett@imperial.ac.uk 2European Bioinformatics Institute
Title: Generation of 3D Templates for Enzymes in the Catalytic Site Atlas: Analysis of Catalytic Residue Geometry and Utility of Automatically-generated templates for Function Prediction from 3D Structure
Representative figure:
Short abstract: 3D active site templates were automatically generated from enzyme structures in a database of catalytic sites. Templates were used to analyse catalytic residue geometry within homologous enzyme families, and also to test a template-based active site recognition method. Template effectiveness was measured using RMSD and statistical significance scores.
Full abstract
Number: 19
Authors: Andreas Prlic1, Thomas A. Down, Tim JP. Hubbard
1The Wellcome Trust Sanger Institute, ap3@sanger.ac.uk
Title: Protein DAS, Distributed Annotation System for Proteins
Representative figure:
Short abstract: DAS,the distributed annotation system, provides a communication protocol used to exchange annotations between decentralized data sources. We give an overview of extensions to the original DAS protocol in order to provide a client which displays DNA data like SNPs, or Intron and Exon borders, projected onto protein sequences and
structures.
Full abstract
Number: 20
Authors: Ingolf E. Sommer1, Joerg Rahnenfuehrer2, Francisco S. Domingues, Ulrik de Lichtenberg, Thomas Lengauer
Max-Planck-Institute for Informatics, 1sommer@mpi-sb.mpg.de 2rahnenfj@mpi-sb.mpg.de
Title: Predicting Protein Structure Classes from Function Predictions
Representative figure:
Short abstract: We introduce an approach to using sequence-to-function data to recognize protein template classes, a critical step in predicting protein structure. The likelihood of a query sequence to belong to a specific structural family is calculated from probability estimates for different functional categories. The method can be incorporated into existing fold recognition machinery.
Full abstract
Number: 21
Authors: Jean-Luc Pellequer1, Shu-wen W. Chen2, Gilles Imbert, Olivier Pible, Isabelle Vergely
1CEA Valrhô, jlpellequer@cea.fr 2cmft551@yahoo.com
Title: Selecting Non-Redundant Protein Structures from the Protein Data Bank
Representative figure:
Short abstract: Our work aims at developing applications to screen functional properties on a large set of protein structures. To obtain macromolecular structures of high quality and completeness we ssessed the quality of mmCIF files from the PDB, devised programs to repair incomplete structures, and conceived a procedure to select non-redundant structures.
Full abstract
Number: 23
Authors: Samantha L. Kaye1, Mark SP Sansom2, Philip C. Biggin
1University of Oxford, samantha@biop.ox.ac.uk 2mark@biop.ox.ac.uk
Title: Simulation and Modelling studies of the NMDA Receptor
Representative figure:
Short abstract: Ionotropic glutamate receptors (iGluR) are ligand-gated ion channels which mediate excitatory synaptic transmission. Crystal structures of the ligand binding domain of two types of iGluR have been solved. This poster describes the results of 30ns molecular dynamics simulations of one receptor (NR1), in complex with agonists and an antagonist.
Full abstract
Number: 25
Authors: Silke Trissl1, Kristian Rother2, Ulf Leser
1Institute of Informatics, Humboldt-Universität zu Berlin, Berlin, Germany, trissl@informatik.hu-berlin.de 2Institute of Biochemistry, Charitè, Berlin, Germany, kristian.rother@charite.de
Title: COLUMBA - A Database of Annotated Protein Structures
Representative figure:
Short abstract: We present COLUMBA, a database of information on protein structures that integrates data from twelve different biological databases, including the PDB, ENZYME, KEGG, SCOP, CATH, DSSP, and SwissProt. COLUMBA allows for the quick computation of sets of protein structures that share interesting properties according to the different data sources.
Full abstract
Number: 26
Authors: Merridee A. Wouters1, Ken K. Lau, Philip J. Hogg
1Victor Chang Cardiac Research Institute, m.wouters@victorchang.unsw.edu.au
Title: Cross-Strand Disulphides in Cell Entry Proteins: Redox Switches in Protein Nanomachines
Representative figure:
Short abstract: Cross-strand disulphides (CSDs) link adjacent beta-strands. A search for CSDs in a representative set of the PDB showed their dihedral strain energies are higher than disulphides in general. Conspicuously, CSDs are over-represented in molecules involved in cell entry and there is evidence suggesting their involvement in cell entry events.
Full abstract
Number: 27
Authors: Alessandro Pandini1, Giancarlo Mauri2, Laura Bonati
1DISAT - Universita' degli Studi di Milano-Bicocca, alessandro.pandini@unimib.it 2DISCO - Universita' degli Studi di Milano-Bicocca, giancarlo.mauri@unimib.it
Title: BioPySDS: an Object-Oriented Interface to Manage Protein Dynamics in an Evolutionary Framework
Representative figure:
Short abstract: A new approach to computational investigation of protein function is presented: structural, dynamical and evolutionary informations are combined and compared to gain deeper insight in the function of protein superfamilies. BioPySDS, a new object oriented tool is presented: design, implementation and application are detailed.
Full abstract
Number: 29
Authors: Chen Yanover1, Ori Shachar2, Yair Weiss
The Hebrew University of Jerusalem, 1cheny@cs.huji.ac.il 2orish@cs.huji.ac.il
Title: Inference in Graphical Models for Side-chain Prediction
Representative figure:
Short abstract: Inference in graphical models is a widely studied problem in computer science. We apply various inference algorithms to the side chain prediction problem, both for finding the lowest energy configurations and characterizing the variability in configurations, and show excellent results. An extension to protein peptide binding prediction gives promising results.
Full abstract
Number: 30
Authors: Fabrizio Ferre'1, Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich2
1Centre of Molecular Bioinformatics, University of Rome Tor Vergata and Boston College, Boston MA, fabrizio@cbm.bio.uniroma2.it 2Centre of Molecular Bioinformatics, University of Rome Tor Vergata, citterich@uniroma2.it
Title: Large Scale Surface Comparison for the Identification of Functional Similarities in Unrelated Proteins
Representative figure:
Short abstract: A systematic local comparison of protein surfaces is performed aiming at functional annotation based upon stringent shape and residue similarity criteria.Protein surface patches and the results of the comparison are stored in the SURFACE database. Significant similarities are found between proteins sharing low sequence or structural homology (structural genomics).
Full abstract
Number: 32
Authors: Ruchir R. Shah1, Luke Huan2, Deepak Bandyopadhyay, Wei Wang, Alexander Tropsha
University of North Carolina at Chapel Hill, 1ruchir@email.unc.edu 2huan@cs.unc.edu
Title: Structure Based Identification of Protein Family Signatures for Function Annotation
Representative figure:
Short abstract: We present a novel approach to identifying recurrent structure-sequence motifs common to particular protein families. The approach employs Delone tessellation to generate protein graphs and frequent subgraph mining to obtain the motifs. We demonstrate the utility of these motifs for highly accurate annotation of several protein families.
Full abstract
Number: 33
Authors: Ilan Samish1, Eran Goldberg2, Oksana Kerner, Avigdor Scherz
1Weizmann Institute of Science, ilan.samish@weizmann.ac.il 2eran.goldberg@weizmann.ac.il
Title: Centrality of Weak Interhelical H-bonds in Membrane Protein Functional Assembly and Conformational Gating
Representative figure:
Short abstract: We show (see ISMB/ECCB2004 paper 57) that weak, membrane protein backbone-mediated interhelical H-bonds cluster in the conserved, buried protein core. The residue-propensity for these bonds correlates with the packing scale. In-silico and in vivo mutagenesis of such bonds suggests a mechanism for the conformational-gated electron-transfer in photosysnthetic reaction-centers. The results provide insight for structure and function prediction.
Full abstract
Number: 34
Authors: Dmitry S. Kanibolotsky1, Konstantin A. Odynets2, Alexander I. Kornelyuk3
Institute of Molecular Biology & Genetics, Kiev, Ukraine, 1kornelyuk@imbg.org.ua 2odynets@imbg.org.ua 3kornelyuk@imbg.org.ua
Title: Homology Modeling and Molecular Dynamics Simulation Study of Cytokine-like C-terminal Module of Mammalian Tyrosyl-tRNA Synthetase
Representative figure:
Short abstract: Homology modeling of 3D structure and exploration of molecular dynamics of tyrosyl-tRNA synthetase C-module were performed. Our data revealed that 86-92 and 107-117 loops are most flexible parts of protein structure. The dynamics of cytokine motif revealed the increase of Arg8 and Arg12 solvent accessibilities.
Full abstract
Number: 35
Authors: Elmar Krieger1, Tom Darden2, Sander B. Nabuurs, Alexei V. Finkelstein, Gert Vriend
1University of Nijmegen, elmar@cmbi.kun.nl 2NIEHS
Title: Making Optimal Use of Empirical energy Functions: Force Field Parameterization in crystal Space
Representative figure:
Short abstract: Increasingly accurate energy functions are required to improve protein models built by homology, for example during molecular dynamics refinement. By simulating protein crystals and adjusting the AMBER force field parameters to minimize the deviations from experiment, we arrive at the YAMBER force field, which is shown to improve homology models.
Full abstract
Number: 37
Authors: Antonis Koussounadis1, David W Ritchie2, Antonis Koussounadis, Chris J. Secombes
1Department of Computing Science/ Zoology, University of Aberdeen, akoussou@csd.abdn.ac.uk 2Department of Computing Science, University of Aberdeen, dritchie@csd.abdn.ac.uk
Title: Modelling b-Trefoil Proteins Using an Object-Oriented Database
Representative figure:
Short abstract: This presentation describes on-going work using an object-oriented database, P/FDM, to build 3D homology models of b-trefoil proteins, by exploiting existing structural data. The model-building procedure is based on the querying capabilities of P/FDM that allows data access, navigation, computation to be mixed easily in order to formulate structural queries.
Full abstract
Number: 38
Authors: Juan Fernandez-Recio1, Tom L. Blundell2
University of Cambridge, 1juan@cryst.bioc.cam.ac.uk 2tom@cryst.bioc.cam.ac.uk
Title: Computer Simulations of Protein-Protein Interactions: Rigid-Body Docking and Flexible-Link Refinement Applied to Multi-Domain Signalling Complexes
Representative figure:
Short abstract: The ICM-DISCO method for protein-protein docking was recently validated in a blind assessment (CAPRI). The method provides a description of the rigid-body association energy landscape and identifies protein-binding areas on protein surfaces. As a further step, a new flexible-link refinement protocol is applied here to multi-domain signalling complexes.
Full abstract
Number: 39
Authors: Hugh P. Shanahan1, Sue Jones2, Carles Ferrer, Janet M. Thornton
1EBI, Hugh.Shanahan@physics.org 2University of Sussex, S.Jones@sussex.ac.uk
Title: Detecting DNA-binding Proteins using Structural Motifs and Electrostatics
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Short abstract: We present a method for detecting DNA-binding proteins by a structural motif search and a positive electrostatic potential in that region. We demonstrate that this approach has a true positive rate that is comparable to more complicated structural methods of detecting DNA-binding proteins.
Full abstract
Number: 40
Authors: Robert M. MacCallum1
1Stockholm Bioinformatics Center, maccallr@sbc.su.se
Title: Self-Organized Maps of Sequence Profiles for Protein Structure Prediction
Representative figure:
Short abstract: Self-organizing maps have been shown to be useful for visualising the high-dimensional data associated with sequence profile windows and for contact prediction (MacCallum, R.M., ISMB/ECCB 2004 Long paper #45). This laptop session provides an ideal opportunity to discuss the meaning of these results while looking at 3D visualisations in real time.
Full abstract
Number: 42
Authors: Craig J. Lucas1, Andrew Bulpitt2
University of Leeds, 1craigl@comp.leeds.ac.uk 2andyb@comp.leeds.ac.uk
Title: Automatic Identification of Key Patterns Within Multiple Protein Structures
Representative figure:
Short abstract: We present an algorithm that searches for multiple key patterns between protein structures, optimised for comparing multiple structures with common function but different fold. We demonstrate the algorithm running on three proteins, showing that finding patterns by comparing all three together is preferable to comparing two of the three seperately.
Full abstract
Number: 44
Authors: Damien Devos1, Svetlana Dokudovskaya2, Marc A. Marti-Renom, Rosemary Williams, Brian T. Chait, Andrej Sali, Michael P. Rout
1UCSF, damien@salilab.org 2Rockefeller U.
Title: Evidence for A Common Evolutionary Origin of Nuclear Pore Complexes and Coated Vesicles
Representative figure:
Short abstract: We report a structural analysis of the seven proteins that comprise the yNup84/vNup107 subcomplex. Our results suggest a common evolutionary origin for nuclear pore complexes and coated vesicles in an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes.
Full abstract
Number: 48
Authors: Cristina Benros1, Alexandre G. de Brevern2, Serge Hazout
1EBGM, INSERM E0346, benros@ebgm.jussieu.fr 2debrevern@ebgm.jussieu.fr
Title: Predicting Local Structural Candidates from Sequence by the "Hybrid Protein Model" Approach
Representative figure:
Short abstract: We are developing a structural profile-based method for local protein structure prediction from sequence. The aim is to propose long local structural candidates. The prediction scheme is based on a novel clustering method, named "Hybrid Protein Model". The principle of our strategy is to carry out a sequence–structure alignment.
Full abstract
Number: 49
Authors: Abraham Nahmany1, Francesco Strino, Jimmy Rosen, Graham JL. Kemp, Per-Georg Nyholm
Department of Medical Biochemistry, Gothenburg University, 1avi_nahmany@yahoo.se
Title: Prediction of Oligosaccharide Conformations using Genetic Algorithms and Molecular Mechanics MM3
Representative figure:
Short abstract: In the present study, we have implemented a system called GLYGAL for the prediction of oligosaccharides 3D structures. GLYGAL performs conformational searches using a parallel genetic algorithm. The searches are performed in the torsion angle conformational space and energy calculations are performed using the MM3(96) force field.
Full abstract
Number: 50
Authors: Björn Wallner1, Arne Elofsson2
Stockholm Bioinformatics Center, 1bjorn@sbc.su.se 2arne@sbc.su.se
Title: Benchmark of Different Homology Modelling Programs
Representative figure:
Short abstract: In this study we have benchmarked freely available homology modelling programs: Modeller, SWISS-MODEL, SegMod/ENCAD, 3D-JIGSAW and nest. We also included two methods for predicting side-chains: SCWRL and scap. All methods were given the same alignment and the overall quality and stereochemistry of the resulting models were analyzed.
Full abstract
Number: 51
Authors: Patrick May1, Thomas Steinke2, Michael Meyer
Zuse Institute Berlin, 1patrick.may@zib.de 2steinke@zib.de
Title: THESEUS: A Parallel Threading Core
Representative figure:
Short abstract: THESEUS is a parallel implementation of a protein threading algorithm for structure prediction. THESEUS is designed on the basis of a fast branch-and-bound search for the optimal threading through a library of structural templates build on SCOP domains based on a core model and a pairwise scoring function.
Full abstract
Number: 52
Authors: Ermanna Rovida1, Pasqualina D'Ursi2, Paola Fossa, Luciano Milanesi
Institute for Biomedical Technologies - CNR, 1ermanna.rovida@itb.cnr.it 2pasqualina.dursi@itb.cnr.it
Title: Modelling the Interaction of Human Estrogen Receptor alpha with Organic Polychlorinated Compounds
Representative figure:
Short abstract: The organic polychlorinated compounds are endocrine disrupters known to bind and activate estrogen receptors. We present the molecular models of the complexes of the estrogen receptor alpha with DDT and its metabolites (DDD, DDE) and with PCB obtained with docking simulation. Details of the binding interactions are also described.
Full abstract
Number: 54
Authors: Julian Mintseris1, Zhiping Weng2
Boston University, 1julianm@bu.edu 2zhiping@bu.edu
Title: Optimized Protein Representations from Information Theory
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Short abstract: We address the long-standing problem of representing a protein by an alphabet of functionally similar atom/residue groups. Using information theory we can obtain an optimized protein representation from protein monomer or protein interface datasets that are in agreement with each other and with general concepts of protein energetics.
Full abstract
Number: 55
Authors: Nalin C. Goonesekere1, Byungkook Lee2
Bioinformatics & molecular modeling section, Laboratory for Molecular Biology, National Cancer Institute, 1goonesen@pop.nci.nih.gov 2bk@nih.gov
Title: Frequency of Gaps Observed in a Structurally Aligned Protein Pair Database Suggests a SIMPLE GAP PENALTY FUNCTION
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Short abstract: The logarithm of the frequency of gaps observed in a database of structurally aligned protein domain pairs is found to vary linearly with the length of the gap, but with a break at a gap of length 3. These results suggest a modification of the affine gap penalty function.
Full abstract
Number: 56
Authors: Victoria F. Dominguez Del Angel1, Luis Mochan2, Bernard Caudron, Charles Roth
1bbmi - Pole Informatique; Institut Pasteur, victoria@pasteur.fr 2Centro de Ciencias Fisicas, Universidad Nacional Autónoma de México, Cuernavaca, México, mochan@em.fis.unam.mx
Title: PP2A(alpha) Interactions Domains, a Model of 3D Pattern Representation
Representative figure:
Short abstract: The Protein phosphatase-2A is a holoenzyme with pleiotropic functions. Based on analysis in amino-acid composition and 3D representation, we developed a in-silico approache that detects small fragments in proteins that might interact with AC core of this protein phosphatase. This strategie could be extended to detect small binding fragments in other proteins.
Full abstract
Number: 57
Authors: Qingjuan Gu1, William W. Reenstra, John J. Rux2
The Wistar Institute, 1qingjuan@wistar.upenn.edu 2rux@wistar.upenn.edu
Title: MMD: A Macro-Molecular Docking Program for Locating Domain-Domain Interactions
Representative figure:
Short abstract: MMD is a macro-molecular docking program designed to take advantage of distributed computing resources so that multiple docking solutions can be evaluated in parallel on a wide range of hardware. The ready availability of inexpensive PC’s and open-source software makes these types of studies feasible on a limited budget.
Full abstract
Number: 58
Authors: Gianni De Fabritiis1, Rafael Delgado-Buscalioni, P. V. Coveney
University College of London, 1g.defabritiis@ucl.ac.uk
Title: A Minimisation Method for the efficient Insertion of Solvent Water Molecules
Representative figure:
Short abstract: Many molecular dynamic simulations involving open systems require the insertion of solvent water molecules. This work provides a fast algorithm for on-the-fly insertion of water molecules.
Full abstract
Number: 59
Authors: Jim Procter1, Andrew Torda2
1Centre for Bioinformatics, University of Hamburg, procter@zbh.uni-hamburg.de 2torda@zbh.uni-hamburg.de
Title: Protein sequence-structure Alignments for Prediction, Classification, and Visualization
Representative figure:
Short abstract: This poster examines the use of sequence-structure alignments for protein classification, and evaluates the effect that fold conformation and architecture have on the performance of a threading based fold recognition method. The dataset used is also presented as a
VRML based visualization available for browsing at http://www.zbh.uni-hamburg.de/wurst/protspace/
Full abstract
Number: 60
Authors: Alexandra Shulman-Peleg1, Shira Mintz2, Ruth Nussinov, Haim J. Wolfson
1Tel-Aviv University, School of Computer Science, shulmana@post.tau.ac.il 2Tel-Aviv University, Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine
Title: Protein Functional Sites Recognition and Classification
Representative figure:
Short abstract: We present two novel methods for recognition of protein functional sites. While the first method searches the protein surface for regions similar to known functional sites, the second recognizes similar chemical binding organizations shared by protein-protein interfaces. The methods consider the geometrical and physico-chemical properties and are applicable to large-scale searches of the entire PDB.
Full abstract
Number: 61
Authors: Dina Schneidman1, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson
Tel Aviv University, 1duhovka@tau.ac.il
Title: FlexDock: An Algorithm for Flexible Hinge-Bent Docking.
Representative figure:
Short abstract: We present FlexDock, an algorithm for flexible hinge-bent docking. The algorithm allows hinges placement in one of the docked molecules: receptor or ligand. The number of hinges is not limited. The method performs simultaneous docking of all rigid parts, explicitly considering potential hinge-bending motions.
Full abstract
Number: 62
Authors: Meytal Landau1, Sarel J. Fleishman, Nir Ben-Tal2
Tel-Aviv University, 1meytalc@post.tau.ac.il 2NirB@tauex.tau.ac.il
Title: Down-Regulation of the Catalytic Activity of the EGF Receptor via Direct Contact between the Kinase and C-Terminal Domains
Representative figure:
Short abstract: The ErbBs are unique among receptor tyrosine kinases, as the catalytic elements of their kinase domain are constitutively ready for phospho-transfer. The absence of conformational regulation raises a fundamental dilemma: namely, by what mechanism is spurious activation avoided? Our studies, using various computational tools, suggest a novel molecular regulation mechanism.
Full abstract
Number: 63
Authors: Håkan Viklund1, Arne Elofsson2
Stockholm Bioinformatics Center, 1hakanv@sbc.su.se 2arne@sbc.su.se
Title: Profile-profile HMMs for Structure Predictions
Representative figure:
Short abstract: In a Hidden Markov model (HMM) the probability that a single sequence is generated by the model is calculated. Here, we show that extending HMMs to calculate the probability that a profile is generated by the model increase the performance both for fold recognition and for membrane topology predictions.
Full abstract
Number: 64
Authors: Thomas P. Walsh1, Geoffrey J. Barton2
1School of Life Sciences, University of Dundee, tom@compbio.dundee.ac.uk 2geoff@compbio.dundee.ac.uk
Title: A PERL Library for Generating Hierarchical, Tree-based Browser Interfaces for SCOP Database Searches.
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Short abstract: A Perl library has been developed that creates interfaces for displaying the results of SCOP database searches in a tree-based, hierarchical interface that reflects the SCOP classification. The library is designed to be easily extended to generate interfaces for algorithms of interest.
Full abstract
Number: 65
Authors: Jan Reichert1, Kristina Mehliss2, Juergen Suehnel3
Institute of Molecular Biotechnology, Jena Centre for Bioinformatics, Jena / Germany, 1jr@imb-jena.de 2mehliss@imb-jena.de 3jsuehnel@imb-jena.de
Title: The IMB Jena Image Library of Biological Macromolecules - Recent Developments
Representative figure:
Short abstract: The database (http://www.imb-jena.de/IMAGE.html) is aimed at a better dissemination of information on three-dimensional biopolymer structures with an emphasis on visualization, classification and analysis. It provides basic information on the architecture of biological macromolecules and includes an Atlas of Macromolecule Structures with all PDB and NDB entries.
Full abstract
Number: 66
Authors: Liam J. McGuffin1, Stefano A. Street2, David T. Jones3, Soren-Aksel Sorensen
1University College London, l.mcguffin@cs.ucl.ac.uk 2s.street@cs.ucl.ac.uk 3dtj@cs.ucl.ac.uk
Title: The Genomic Threading Database
Representative figure:
Short abstract: The Genomic Threading Database (GTD) currently contains structural assignments for the proteins encoded within the genomes of 174 organisms. Assignments are carried out using a version of GenTHREADER which is distributed using grid technology. The resulting predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD.
Full abstract
Number: 67
Authors: Hannes Ponstingl1, Janet M. Thornton2
European Bioinformatics Institute, EMBL-EBI, 1hpo@ebi.ac.uk 2thornton@ebi.ac.uk
Title: Structure and Sequence Characteristics of Oligomeric Proteins
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Short abstract: The three-dimensional crystal structures of oligomeric proteins are studied with respect to physico-chemical and geometric properties and sequence variation. Feature combinations are evaluated for the prediction of protein-protein interaction sites on the subunit surface.
Full abstract
Number: 69
Authors: Vichetra Sam1, Chin-Hsien (Emily) Tai2, Peter J. Munson3, Jean Garnier, Jean-François Gibrat, Byungkook Lee
MSCL/DCB/CIT/NIH/DHHS, 1vsam@helix.nih.gov 2taic@pop.nci.nih.gov 3munson@helix.nih.gov
Title: Comparison of Protein Structural Comparison Methods, VAST and SHEBA, with the SCOP Classification, using Statistical Methods
Representative figure:
Short abstract: We conducted a comparison of the structural comparison methods VAST and SHEBA with the structural classification SCOP. Higher agreement with SCOP was obtained when combinations of scores from VAST and SHEBA were used. Fold-classification confusions were quantified. In depth visual analysis of the structures of confused folds will be presented.
Full abstract
Number: 70
Authors: Apostol Gramada1, Philip E. Bourne2
University of California San Diego, 1agramada@sdsc.edu 2bourne@sdsc.edu
Title: A Multipole-Based Method for Comparison of Protein Structures
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Short abstract: We present a method for the comparison of protein structures using a hierarchical set of shape descriptors. It is based on the use of a multipolar representation of the quantitative property of interest. Possible functions for protein similarity calculation are discussed and illustrated with test calculations.
Full abstract
Number: 71
Authors: Goran Neshich1, Roberto Higa2, Adauto Mancini, Paula Kuzer, Michel Yamagishi, Renato Fileto
1EMBRAPA / CNPTIA, neshich@cnptia.embrapa.br 2Embrapa / CNPTIA, roberto@cnptia.embrapa.br
Title: Selecting a Set of the Protein Structure Descriptors Uniquely Defining the Active Site Residues
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Short abstract: Is there a set of parameters (protein structure descriptors) which can define UNIQUELY an amino acid ensemble coinciding with the active site of a given protein? Our newly assembled STING_DB allowed us to test and confirm this hypothesis on several protein structures, including HIV-integrase.
Full abstract
Number: 73
Authors: Javier De Las Rivas1, Carlos Prieto, Alberto De Luis
CIC, CSIC-USAL, 1jrivas@usal.es
Title: Exploring Protein Interaction Networks and Functional Relationships at a Genomic Scale with a Agile Browser
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Short abstract: Development of the bioinformatic tool APIN (Agile Protein Interaction Network browser) design to view and browse the nodes and links/edges of protein-protein interaction databases. The interface allos to navigate into complex interactome databases focusing on some areas, or on some specific proteins, by applying restrictions to the queried data.
Full abstract
Number: 75
Authors: Rafael Najmanovich1, Richard J. Morris, Roman Laskowski, Janet M. Thornton
1European Bioinformatics Institute, rafael.najmanovich@ebi.ac.uk
Title: Shape Description of Protein Clefts
Representative figure:
Short abstract: In the present work we describe the utilization of hybrid ellipsoids to model the shape of protein clefts. The small number of parameters describing the hybrid ellipsoid model can be used to assess binding site shape similarities. The method has applications in the prediction of protein function from structure.
Full abstract
Number: 79
Authors: Silvia N. Crivelli1, James Lu2, James Lu, Oliver Kreylos, Nelson Max, and Wes Bethel
Lawrence Berkeley National Laboratory, 1SNCrivelli@lbl.gov 2TLu@lbl.gov
Title: ProteinShop: a Tool for Interactive Protein Manipulation
Representative figure:
Short abstract: We describe ProteinShop, a program that creates and manipulates protein structures interactively. ProteinShop provides unique capabilities that enable its users to apply their accumulated biochemical knowledge and intuition during the interactive manipulation of protein structures.
Full abstract
Number: 80
Authors: Jessica Fong1, Amy Keating2, Mona Singh3
Princeton University, 1jfong@cs.princeton.edu 2keating@mit.edu 3mona@cs.princeton.edu
Title: Large Scale, High-Confidence Predictions of bZIP Protein-Protein Interactions
Representative figure:
Short abstract: We have developed a method for predicting protein-protein interactions
mediated by coiled coils. Testing on interactions among nearly all human bZIP proteins, our method identifies 70% of strong interactions while maintaining that 92% of predictions are correct. Our work demonstrates a structural interaction motif for which large-scale, high-confidence predictions can be made.
Full abstract
Number: 81
Authors: Jessica C. Shapiro1, Douglas L. Brutlag2
Stanford University, 1jessicas@stanford.edu 2brutlag@stanford.edu
Title: Automatic Structural Motif Discovery using FOLDMINER
Representative figure:
Short abstract: FoldMiner, an unsupervised motif discovery algorithm, analyzes high scoring structural superpositions of a query protein with a database of targets and identifies structurally conserved regions of the query. These conserved regions then describe a structural motif shared among the query and its structural neighbors. Web access is provided at http://foldminer.stanford.edu/.
Full abstract
Number: 82
Authors: Deepak Bandyopadhyay1, Luke Huan2, Wei Wang, Jack Snoeyink, Jan Prins, Alexander Tropsha
UNC Chapel Hill, 1debug@cs.unc.edu 2huan@cs.unc.edu
Title: Graph Representations and Algorithms for Protein Family Classification and Functional Annotation
Representative figure:
Short abstract: Protein family-specific fingerprints are residue packing patterns occurring frequently within a structural/functional family and rarely outside it. We compare three graph representations (contact distance, Delaunay and Almost-Delaunay) for finding fingerprints, discuss their biological significance, and use them for protein family classification and functional annotation.
Full abstract
Number: 83
Authors: Agnes Tan1
1Institute of Molecular and Cell Biology, mcbtanlc@imcb.a-star.edu.sg
Title: Automated Contruction of WD40 proteins
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Short abstract: We have written scripts in Sybyl Programming Language to automate construction of models of any beta propeller protein given a template and positions of beta strands, and also for the general case of modeling any protein by direct mutation (with optimization) of a suitable template based on a ClustalW alignment
Full abstract
Number: 84
Authors: Alvin Ng1
1Institute of Molecular and Cell Biology, Singapore, ngyj@imcb.a-star.edu.sg
Title: Homology Model and Substrate Recognition of Yeast Prk1p Kinase
Representative figure:
Short abstract: Prk1p is a serine/threonine kinase involved in actin cytoskeleton organization in yeast Saccharomyces cerevisiae.A homology model was created to further understand the substrate recognition of the LxxQxTG motif.
Full abstract
Number: 85
Authors: Michael L. Sierk1, William R. Pearson2
University of Virginia, 1mls5w@virginia.edu 2wrp@virginia.edu
Title: Benchmarking Protein Structure Alignment Statistics Against the CATH Database
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Short abstract: We present a large-scale analysis of several structure alignment methods and ability to detect homologs in the CATH domain database. The programs vary considerably in their performance, and the statistical estimates reported by the programs overstate the significance matches by orders of magnitude compared to the actual distribution of errors.
Full abstract
Number: 86
Authors: Christina Kiel1, Luis Serrano2, Alfred Wittinghofer, Sabine Wohlgemuth
EMBL Heidelberg, Germany, 1kiel@embl.de 2serrano@embl.de
Title: Recognizing and Defining true Ras Association (RA) Domains based on Protein Sequence and Structure
Representative figure:
Short abstract: We are using homology modelling, and complex stability calculations using Fold-X in order to predict the affinities of Ras association (RA) domains in complex with Ras proteins. Calculated stabilities are compared with experimental data from Isothermal Titration Calorimetry experiments.
Full abstract
Number: 87
Authors: Kay Gottschalk, Hani Neuvirth, Gideon Schreiber1
1Weizmann Institute of Science, bcges@weizmann.ac.il
Title: Docking Protein Complexes from their Predicted Binding Site
Representative figure:
Short abstract: We introduce a docking method which discriminates between the few correct and many wrong results by measuring the tightness of fit of two docked proteins at their predicted binding interface. The location of the binding interface is identified using ProMate (http://bioportal.weizmann.ac.il/promate), a computer algorithm developed by us for this purpose.
Full abstract
Number: 88
Authors: Juliette Martin1, Jean-François Gibrat2, François Rodolphe
1INRA, jumartin@jouy.inra.fr 2Laboratoire Mathématique Informatique et Génome, INRA de Jouy-en-Josas, France, gibrat@jouy.inra.fr
Title: Hidden Markov Model for Protein Secondary Structure
Representative figure:
Short abstract: We present an attempt to predict the secondary structure of proteins with Hidden Markov Models. We designed a 21-states model in which regular secondary structures are described by motifs. With single-sequence information the rate of good prediction of this model is about 65%, and 71% with profile information.
Full abstract
Number: 89
Authors: C. Jayaprabha, N. Santhi1, J. Kamesh2, P. Chitra, N. Bharathi, S. Krishnaveni, S. Valarmathi, S. Sujatha and S. Seethalakshmi
1Dept. of Bioinformatics, Sri Ramakrishna College of Arts & Science for Women, INDIA, santhigowri@rediffmail.com 2Sai's Biosciences Research Institute Pvt.Ltd., INDIA, jkbioinfo@graffiti.net
Title: In Silico Transfer of Neurotransmitter Transporter Motif Between Structurally Analogous Protein (Catechol-O-methyltransferase)
Representative figure:
Short abstract: A homology model for Catechol-O-methyltransferase (COMT) of human was created, enabling us to analyse the active site. To analyse the function, the motif region is transferred from human COMT to rat COMT. The structure of the mutated rat sequence was compared with original rat COMT structure.
Full abstract
Number: 90
Authors: Giacomo De Mori1, Raul Mendez, Didier Croes, Shoshana J. Wodak 1
1SCMBB, Universite Libre de Bruxelles, Belgium, shosh@scmbb.ulb.ac.be, raul@scmbb.ulb.ac.be
Title: Analysis of Conformational Changes on Protein - Protein Complexes.
Representative figure:
Short abstract: An exhaustive analysis of protein - protein conformational changes is presented on protein complex structures deposited at the PDB. Secondary structure elements changing upon association are identified using a non-standard structural alingment method. A detailed description on the different conformational changes over the different protein complexed families is provided.
Full abstract
Number: 91
Authors: YY Cai1, BF Lu2, ZW Fan, and KT Lim
1Nanyang Technological University, myycai@ntu.edu.sg 2mbflu@ntu.edu.sg
Title: 3D Structure Image Generator using Virtual Reality Technology for Protein Immersive Visualization
Representative figure:
Short abstract: We present our low-cost VR technology for interactive visualization and modeling of 3D protein structure. Emphasis will be placed on the affordable solution which integrates commodity hardware available and specialized software we developed. In particular, visual and haptic sensorial channels for immersive interaction with the protein structure will be discussed.
Full abstract
Number: 92
Authors: Dinesh C. Soares1, Paul N. Barlow2, Dietlind L. Gerloff
1Biocomputing Research Unit, University of Edinburgh, D.C.Soares@sms.ed.ac.uk 2Biomolecular NMR Unit, University of Edinburgh, Paul.Barlow@ed.ac.uk
Title: The CCP-Module Model Database - Automated Large-Scale Protein Structure Modelling of Individual Human Complement Control Protein (CCP)-Modules
Representative figure:
Short abstract: A large-scale comparative protein structure modelling procedure was automated and applied to 136 representative individual CCP module sequences, including members of the regulators of complement activation family. Systematic comparisons of surface electrostatics provide new functional insight with respect to potential protein-protein interactions. All models are publicly available at:
http://www.bru.ed.ac.uk/~dinesh/ccp-db.html
Full abstract
Number: 93
Authors: Joaquim Mendes1, Luis Serrano2
EMBL, 1mendes@embl.de 2serrano@embl.de
Title: Incorporating an Accurate Solvation Model into Computational Protein Design
Representative figure:
Short abstract: The Langevin Dipoles solvation model is one of the most accurate quantitative solvation models currently available. Here we describe its incorporation into one of the most successful methods for computational protein design (CPD): the Mean Field method. This work represents a major step forward toward first principle CPD methods.
Full abstract
