Short table format (without abstract)
Alphabetical list of abstract authors
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Invited Speaker Abstracts
Number: 72
Authors: Nick V Grishin1
1University of Texas Southwestern Medical Center & HHMI, grishin@chop.swmed.edu
Title: Dramatic Evolutionary Changes in Protein Structures
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Short abstract: Most common molecular events in sequence evolution are point mutations,insertions/deletions and non-homologous recombination. Effects of these events on protein spatial structure will be discussed, and a few examples of significant structural rearrangements that frequently lead to fold change in evolution will be shown.
Full abstract
Number: 77
Authors: Christopher Dupont1, Song Yang2, Brian Palenik3, Philip E. Bourne4
1Scripps Institute of Oceanography, University of California San Diego, cdupont@ucsd.edu 2Dept. of Chemistry and Biochemistry, University of California San Diego, soyang@sdsc.edu 3Scripps Institute of Oceanography, University of California San Diego, bpalenik@ucsd.edu , 4Dept of Pharmacology, University of California San Diego, bourne@sdsc.edu
Title: Modern Proteomes Contain Imprints of Ancient Shifts in Environmental Chemistry
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Short abstract: The Gaia hypothesis states that life fosters and maintains suitable conditions for itself by helping to create an environment on Earth suitable for its continuity. Using structural bioinformatics to explore the metallomes or species across the Superkingdoms we provide data supporting the Gaia hypothesis.
Full abstract
Number: 83
Authors: Wah Chiu1, Matthew L Baker2
1MCMI, Baylor College of Medicine, wah@bcm.edu 2mbaker@bcm.edu
Title: Modeling Protein Components of Biological Nano-Machines in Subnanometer Resolution CryoEM Density Maps
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Full abstract
Number: 86
Authors: Jeffery G Saven1
1University of Pennsylvania, saven@sas.upenn.edu
Title: Theoretical Methods for the Design and Engineering of Proteins
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Short abstract: Recent theoretical methods for identifying the properties of amino acid sequences likely to fold to a given three-dimensional structure will be presented, as will several examples of structures so designed that have been experimentally synthesized and characterized.
Full abstract
Number: 87
Authors: Janet M. Thornton1, Gemma L. Holliday2, Alex Gutteridge, James Torrance, Gail J. Bartlett, Daniel E. Almonacid, Noel M.O'Boyle, Peter Murray-Rust, John B. O. Mitchell
1EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, thornton@ebi.ac.uk 2European Bioinformatics Institute, gemma@ebi.ac.uk
Title: Using the Three Dimensional Structures of Enzymes to Understand Catalysis
Short abstract: Traditionally each enzyme has been studied individually, but as more enzymes are characterised it is now timely to revisit the molecular basis of catalysis, by comparing different enzymes and their mechanisms, and to consider how complex pathways and networks may have evolved.
Full abstract
Speaker Abstracts
Number: 8
Authors: Melissa R Landon1, Spencer C Thiel2, David R. Lancia Jr., Sandor Vajda
1Boston University, mlandon@bu.edu 2cank@bu.edu
Title: Identification of Druggabable “Hot Spots” in Ligand Binding Pockets by Computational Solvent Mapping of Proteins
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Short abstract: Here we describe the application of the CS-Map algorithm to the identification of druggable subsites within a ligand binding pocket. The accuracy of CS-Map results is illustrated on a set of fifty proteins for which both high affinity drug-like compounds have been developed and structural information is available.
Full abstract
Number: 10
Authors: Stefano Lise1, David T Jones, Alice Walker-Taylor
1Department of Biochemistry and Molecular Biology, University College Loondon, lise@biochem.ucl.ac.uk
Title: Docking protein domains in contact space
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Short abstract: We present a novel method that attempts to dock protein domains using a contact map representation. It is based on a scoring function that combines structural, physicochemical and evolutionary information. The method correctly predicts some contacts across the interface and can complement effectively other computational methods.
Full abstract
Number: 15
Authors: Anna CV Johansson1, Erik Lindahl2
Stockholm Bioinformatics Center, 1annj@sbc.su.se 2lindahl@sbc.su.se
Title: Simulation of Amino Acid Solvation Structure in Transmembrane Helices and Implications for Membrane Protein Folding
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Short abstract: We report on extensive molecular dynamics simulations used to quantitativly study the atomic scale structure and dynamics of interactions between hydrophilic residues in transmembrane helices and the bilayer environment. The main conclusion is that hydrophilic residues retain solvation water in amounts that correlate well with experimental hydrophobicity scales.
Full abstract
Number: 17
Authors: Diana K Ekman1, Åsa K Björklund2, Arne Elofsson
1Stockholm Bioinformatics Center, Stockholm University, diaek@sbc.su.se 2asbj@sbc.su.se
Title: Evolutionary History of Multi-Domain Proteins
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Short abstract: A majority of the eukaryotic proteins are multidomain proteins. Here, we present a study of the evolution of new domain architectures through fusion and internal duplication. We found that architectures are created mainly through insertions/deletions of domains at the terminals. Expansion of domain repeats is also an important contribution.
Full abstract
Number: 19
Authors: Michal J Gajda1, Marta Kaczor, Janusz M Bujnicki2, Anastasia Bakulina, Andrzej Kasperski, Alan M. Friedman, Chris Bailey-Kellogg
International Institute of Molecular and Cell Biology in Warsaw, Poland, 1mgajda@genesilico.pl 2iamb@genesilico.pl
Title: FILTREST3D: a Simple Method for Discrimination of Multiple Structural Models Against Spatial Restraints
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Short abstract: FILTREST3D http://filtrest3d.genesilico.pl/ is a new method for discrimination of alternative models against mixed sets of restraints (e.g. spatial distances) derived from experimental analyses as well as from computational predictions (e.g. solvent accessibility) or arbitrarily defined by the user. It can be used to analyze models of individual proteins and complexes.
Full abstract
Number: 26
Authors: Marcin Pawlowski1, Janusz Bujnicki2, Ryszard Matlak
International Institute of Molecular and Cell Biology in Warsaw, 1marcinp@genesilico.pl 2iamb@genesilico.pl
Title: Meta-MQAP: an SVM-based meta-server for the quality assessment of protein models
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Short abstract: Presented Meta-MQAP uses the results of the five primary MQAPs to predict the absolute deviation (in Angstrom) of C-alpha atoms of all residues in the model from their counterparts in the native structure, without the knowledge of the actual native structure
Full abstract
Number: 30
Authors: Antonio del Sol1, Marcos J. Arauzo-Bravo2, Dolors Amoros, Ruth Nussinov
Fujirebio Inc., 1ao-mesa@fujirebio.co.jp 2ms-arauzo@fujirebio.co.jp
Title: Network Robustness and Modularity of Protein Structures in the Identification of Key Residues for the Allosteric Communications
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Short abstract: We represent protein structures as residue interacting networks in the analysis of several protein families. We identify fold centrally-conserved residues, playing key roles in the allosteric communications. The modular decomposition of these protein networks characterizes different allosteric sites, with the fold centrally-conserved residues participating in the inter-modular interactions.
Full abstract
Number: 34
Authors: Scooter Willis1
1University of Florida-Department of Computer and Information Science and Engineering, willishf@ufl.edu
Title: Predicting co-evolving pairs in Pfam based on Mutual Information of mutation events measured along the phylogenetic tree
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Short abstract: Mutual Information (MI) is used to detect co-evolving pairs in a protein family by re-sampling based on mutation events in the phylogenetic tree. The predictive quality with MI (Z>=4), a sequence distance > 10 and within 12 angstroms using the RPE method is on average 81% in a Pfam family.
Full abstract
Number: 37
Authors: Avner Schlessinger1, Marco Punta2, Burkhard Rost
Columbia University, 1as2067@columbia.edu 2punta@rostlab.org
Title: Identifying Natively Unstructured Proteins Using Residue Contact Predictions
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Short abstract: Recently, increasing attention has been drawn to the study of ‘natively unstructured’ proteins. Here, we combine a position specific contact propensity predictor with an average pairwise energy-like matrix to estimate the energetic contribution of each residue of the protein sequence to the protein foldability. Our novel approach outperforms competing methods.
Full abstract
Number: 43
Authors: Francisco Melo1, Alejandro Panjkovich2, Andrej Sali, Marc A. Marti-Renom,
Catholic University of Chile, 1fmelo@bio.puc.cl 2sasha.panjkovich@gmail.com
Title: Structure Specific Statistical Potentials for Protein Structure Prediction
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Short abstract: We describe a novel approach to derive improved statistical potentials for protein structure prediction, which are specific of a particular fold or structure. The specific potentials take advantage of the known evolutionary record by incorporating homologue sequences that give useful information about kinetics, function and thermodynamics governing protein folding.
Full abstract
Number: 44
Authors: Bingding Huang1, Michael Schroeder2
Biotec, Technical University Dresden, Germany, 1bhuang@biotec.tu-dresden.de 2ms@biotec.tu-dresden.de
Title: Integrate the Degree of Burial and Conservation of Surface Residues into Protein-protein Docking
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Short abstract: The binding sites of enzyme-inhibitor complexes usually involve a very deep buried pocket and are more conserved than the rest of surface. In our docking approach BDOCK, the degree of burial and conservation of surface residues are taken into account, which significantly improves the performance of traditional FFT docking method.
Full abstract
Number: 45
Authors: Sandra Maguid1, Gustavo Parisi2, Sebastian Fernandez-Alberti3, Julian Echave
Universidad Nacional de Quilmes, 1smaguid@unq.edu.ar 2gustavo@unq.edu.ar 3seba@unq.edu.ar
Title: Sequence-structure-flexibility relationship in protein evolution.
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Short abstract: We study the evolutionary divergence of protein backbone dynamics by comparing the Cα flexibility profiles for a large dataset of homologous proteins classified into families and superfamilies. Proteins were structurally aligned and for each alignment we calculated sequence similarity, structural dissimilarity and different measures of backbone flexibility similarity.
Full abstract
Number: 55
Authors: Iris Antes1, Thomas Lengauer2
Max-Planck-Institute for Informatics, 1antes@mpi-inf.mpg.de 2lengauer@mpi-inf.mpg.de
Title: DynaDock: Inhibitor based Refinement of Homology Modeled Protein Structures for Molecular Docking
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Short abstract: We present a new refinement strategy and program, DynaDock, for homology modeled protein structures to be used molecular docking. The approach uses an iterative, inhibitor-based refinement protocol and was evaluated on several CYP P450 protein structures and applied during a drug design project searching for inhibitors of CYP11B2.
Full abstract
Number: 59
Authors: Maria S Fornasari1, Gustavo Parisi2
Universidad Nacional de Quilmes, 1silvina@unq.edu.ar 2gustavo@unq.edu.ar
Title: Protein Structure Diversity and Sequence Divergence in Evolution
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Short abstract: Using the Structurally Constrained Protein Evolution model (SCPE), we found that the consideration of the quaternary structure and the different oligomeric states a protein could adopt, enhance the description of the sequence divergence during evolution.
Full abstract
Number: 62
Authors: Ingo Ruczinski1, Kevin W Plaxco2, Tobin R. Sosnick
1Johns Hopkins University, ingo@jhu.edu 2University of California at Santa Barbara, kwp@chem.ucsb.edu
Title: On the Precision of Experimentally Determined Protein Folding Rates and Φ Values
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Short abstract: Φ-values are the most important experimental benchmark by which theoretical models of protein folding are tested. Adressing the significant controversy that has emerged regarding reliability, we show how to derive valid standard errors for Φ estimates, and discuss what determines the precision with which Φ-values can be estimated.
Full abstract
Number: 63
Authors: Elon Portugaly1, Nathan Linial2, Michal Linial
The Hebrew University of Jerusalem, School of Computer Science and Engineering, 1elonp@cs.huji.ac.il 2nati@cs.huji.ac.il
Title: Assessment of Protein Domain Classifications: An Automatic Sequence-based Method and Methods Based on 3D Structures
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Short abstract: EVEREST is an automatic system that identifies and classifies domains within a database of protein sequences. We show that the set of EVEREST families is as similar to the set of CATH families and to the set of SCOP families as the latter two sets are similar to each other.
Full abstract
Number: 66
Authors: Thomas Funkhouser1, Roman Laskowski2, Janet Thornton3
Princeton University, 1funk@cs.princeton.edu 2European Bioinformatics Institute, roman@ebi.ac.uk 3thornton@ebi.ac.uk
Title: Matching Volumetric Models of Protein Active Sites
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Short abstract: This paper investigates the use of a knowledge-based algorithm to build volumetric models of active site cavities from protein structures, a fast rotational matching algorithm to detect similarities in the volumetric models, and a nearest neighbor classifier to predict the type of ligand bound based on similarities in volumetric models.
Full abstract
Number: 69
Authors: Frank P DiMaio1, Jude W Shavlik2, George N. Phillips
University of Wisconsin - Madison, 1dimaio@cs.wisc.edu 2shavlik@cs.wisc.edu
Title: A Probabilistic Approach to Protein Backbone Tracing in Electron Density Maps
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Short abstract: One particularly time-consuming step in x-ray crystallography is interpreting the electron density map. We describe a probabilistic approach to automated backbone tracing in poor-quality density maps using a Markov random field. The model is flexible, considering an almost-infinite number of possible backbone conformations, while ignoring physically impossible ones.
Full abstract
Number: 76
Authors: Ilan Samish1, Oksana Kerner2, David Kaftan, Eran Goldberg, Avigdor Scherz
1Present address: Dept. of Chemistry and Dept. of Biochemistry and Biophysics, University of Pennsylvania, samish@sas.upenn.edu 2Weizmann Institute of Science
Title: Datamining the Fourth Dimension from Crystal Structures: Structure-Function-Entropy Relationships in Membrane Proteins
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Short abstract: Datamining crystal structures, we show how variation in local conformational flexibility, entwined with structural motifs, controlls the dynamic function of membrane proteins. Our experimentally validated analysis explains Biological dynamic mechanisms and provides new simple guidelines for the study of membrane proteins.
Full abstract
Number: 82
Authors: Rafael J Najmanovich1, Richard J Morris2, Janet M. Thornton
European Bioinformatics Institute, 1rafael.najmanovich@ebi.ac.uk 2Richard.Morris@bbsrc.ac.uk
Title: Single-Family Analysis of Binding Site Structural Similarities
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Short abstract: We describe a method for the detection of pairwise local structural similarities between members of a given protein family using all non-hydrogen atoms in protein clefts allowing larger, over-predicted and apo-form binding sites to be analyzed. We uncover previously unknown similarities between members of the human cytosolic sulfotransferase family.
Full abstract
Number: 84
Authors: Zsuzsanna Dosztányi1, Márk Sándor2, István Simon
Institute of Enzymology, Budapest, Hungary, 1zsuzsa@enzim.hu 2sanmark@freemail.hu
Title: Prediction of Order and Disorder at the Domain Level
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Short abstract: During the target selection process of structural genomics projects it is important to be able to discern ordered globular domains from disordered regions. A method based on the IUPred algorithm is suggested to locate ordered and disodered domains from amino acid sequences and was tested on specific datasets.
Full abstract
Laptop Session Abstracts
Number: 11
Authors: Jorge H Fernandez1, Solange M Serrano2, Wilson Savino, Ana Tereza Vasconcelos
1LabInfo, Laboratório Nacional de Computação Cientifica/MCT, Petrópolis, R.J, Brazil, jorgehf@lncc.br 2Center of Applied Toxinology –Instituto Butantan, S.P., Brazil, serrano@butantan.gov.br
Title: Bothrostatin, a new RGD-type disintegrin from Bothrops jararaca venom: binding specificity in bothrostatin-αIIbβ3/αvβ3 integrin complexes.
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Short abstract: Disintegrins are among the most potent antagonists of several integrin receptors, blocking specific integrin-ligand interactions in important biological processes. We use molecular dynamics to study the integrin/ligand interaction specificity in αIIbβ3/αvβ3-disintegrin complexes. We found that C-terminal tail of disintegrin structure is crucial for integrin recognition and binding affinity.
Full abstract
Number: 12
Authors: Lie Li1, Meena Sakharkar2, Pandjassarame Kangueane3, Jacob Gan, Pandjassarame Kangueane
NTU, 1PG03074376@ntu.edu.sg 2mmeena@ntu.edu.sg 3mpandjassarame@ntu.edu.sg
Title: Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding of homodimers.
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Short abstract: The formation of homodimer complexes for interface stability, catalysis and regulation is intriguing. Here, we analyze 41 homodimer (25 `2S` and 16 `3S`) structures determined by X-ray crystallography to estimate structural differences between them. The findings are useful in the prediction of homodimer folding and binding mechanisms using structural data.
Full abstract
Number: 13
Authors: Francisco Torrens1, Gloria Castellano2
1Universitat de Valencia-Institut Universitari de Ciencia Molecular, Francisco.Torrens@uv.es 2Universidad Politecnica de Valencia-Universidad Catolica de Valencia, gcaste@trovador.zzn.com
Title: Binding of Water-Soluble, Globular Proteins to Anionic Model Membranes
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Short abstract: The electrostatics role in the adsorption of proteins to negatively-charged/neutral vesicles is studied. The interaction is monitored at low ionic strength for lysozyme/myoglobin/albumin as a function of pH. Adsorption is investigated via. fluorescence emission spectrum changes. Adsorption is found at pHs where the protein charge is at least 3 e.u.
Full abstract
Number: 14
Authors: Karsten M Borgwardt1, SVN Vishwanathan2, Nicol N. Schraudolph, Hans-Peter Kriegel
1Ludwig-Maximilians-University Munich, kb@dbs.ifi.lmu.de 2NICTA Australia, vishy@mail.rsise.anu.edu.au
Title: Fast Graph Kernels for Proteomics
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Short abstract: Graph kernels are the principled approach to mining graph structured data, e.g. protein molecular structure descriptions. However, known graph kernels are too slow for large-scale applications on molecular graphs. We present fast graph kernels that can be used for large-scale protein function prediction or protein structure comparison.
Full abstract
Number: 16
Authors: Talapady N Bhat1, Anh D Thi Nguyen, Alexander Wlodawer, Mohamed Nasr
NIST, 1bhat@nist.gov
Title: Semantic Web and Chemical Ontology for Fragment-Based Drug Design and AIDS
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Short abstract: Effective use of available structural information is crucial for fragment based design or fragment mix and match approach to succeed in drug discovery. Web based methods and chemical ontology for annotation and presentation of structural data for this purpose with specific emphasis to AIDS and Semantic Web will be presented.
Full abstract
Number: 18
Authors: Alexander A Kantardjiev1, Boris P Atanasov2
Bulgarian Academy of Sciences, Institute of Organic Chemistry, 1alexkant@yahoo.com 2boris@orgchm.bas.bg
Title: Electrostatics in Protein Docking: pH-Dependent self-consistent orientation guide
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Short abstract: The protein electrostatic interactions are the only source for natural long-range interaction and are determinants of molecular recognition. Modern methodologies don’t treat properly pH-dependence and self-consistency of charge interactions. Our analysis of solved protein complexes proves self-consistence between charge systems. It is how Nature suggests docking methodology.
Full abstract
Number: 20
Authors: Sumeet Dua1, Praveen C Kidambi2
College of Engineering and Science, Louisiana Tech University, 1sdua@coes.latech.edu 2pck001@latech.edu
Title: Protein Structural Classification using Associative Discrimination of Orthonormal coefficients
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Short abstract: In this research, we present a novel automated computational framework for three dimensional (3D) structure-based classification of proteins using orthonormal transformation of the protein geometric shape descriptors, subsequently employing an association rule discovery-based supervised clustering approach to classify proteins.
Full abstract
Number: 21
Authors: Shula Shazman1, Yael Mandel-Gutfreund2
1Technion-Israel Institute of Technology, Faculty of Biology, shulas@tx.technion.ac.il 2yaelmg@tx.technion.ac.il
Title: A Machine Learning Approach for Predicting RNA-binding Proteins from their Three Dimensional Structure
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Short abstract: We apply a machine learning approach for predicting RNA-binding proteins from 3D structures. The method is based on characterizing unique properties of electrostatic patches on the protein surface. It does not rely on sequence or structural homology and could be applied to novel proteins with unique folds and/or binding motifs.
Full abstract
Number: 23
Authors: Oliver Sander1, Tobias Sing2, Francisco S. Domingues, Ingolf Sommer, Andrew Low, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer
1Max-Planck-Institute for Informatics, Saarbruecken, Germany, osander@mpi-sb.mpg.de 2tsing@mpi-sb.mpg.de
Title: Structural Descriptors Improve the Prediction of HIV Coreceptor Usage
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Short abstract: Reliable methods for inferring HIV coreceptor usage are required for monitoring during antiviral therapy. Our novel structural descriptor considerably improves the predictive performance of purely sequence-based methods and is a first step to gain insights into structural determinants of coreceptor usage.
Full abstract
Number: 25
Authors: Vishal Kapoor1, Sree Nivas gurram Reddy
HCL, 1vishal.kapoor@hcl.in
Title: In Silico Pathway of drug absorption, distribution and Metabolism(ADMET)
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Short abstract: Many of the drug candidates that fail in clinical trials are withdrawn because of unforeseen effects and unfavorable pharmacokinetic profiles. An ideal system would enable researchers to make a confident elimination decision based purely on the structure of a new compound and proposed in-silico parameters
Full abstract
Number: 27
Authors: Michal Milo1, Amiram Goldblum2
The Hebrew University of Jerusalem, 1mikmillo@md.huji.ac.il 2amiram@vms.huji.ac.il
Title: A Myristoyl Binding Site in Protein Kinases
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Full abstract
Number: 28
Authors: Claudia Bertonati1, Marco Punta2, Burkhard Rost, Barry Honig
Columbia University, 1cb2144@gmail.com 2mp2215@columbia.edu
Title: New Perspectives from Structural Genomics - a Case Study: 5 Recently-Solved North East Structural Genomics Targets Provide New Insights into the Structure and Function of the ASCH-PUA Fold.
Representative figure:
Short abstract: We analyze the structure of 5 different targets from the North East Structural Genomics consortium. All targets belong to the same fold (PUA domain-like) but share fairly low sequence similarity. Similarities and differences among the 5 targets provide new insights into their putative RNA-binding function.
Full abstract
Number: 31
Authors: Peter Røgen1, Per W Karlsson2
1Department of Mathematics, Technical University of Denmark, Peter.Roegen@mat.dtu.dk 2P.W.Karlsson@mat.dtu.dk
Title: Quantifying the Relative Positions of Proteins Secondary Structure Elements
Representative figure:
Short abstract: How parallel and anti-parallel are the helices of your favourite protein? - And which other proteins have a similar parallelity of their helices? To answer such questions, we introduce a notion of Local Self Parallelity of protein secondary structures, and use it for automatic classification of protein structures.
Full abstract
Number: 39
Authors: Jeff D Sander1, Peter C Zaback2, Drena L Dobbs3, Fengli Fu, Daniel F. Voytas
Iowa State University Bioinformatics and Computational Biology, 1jdsander@iastate.edu 2petez@iastate.edu 3ddobbs@iastate.edu
Title: Designing C2H2 Zinc Finger Proteins to Target Specific Genomic Sites
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Short abstract: Consisting of modular nucleic acid binding domains, C2H2 zinc finger proteins provide an excellent framework for engineering new sequence-specific DNA binding proteins. Using binding specificities determined by others, we have developed a program, ZiFit, to locate and rank candidate targets for zinc finger binding within a given DNA sequence.
Full abstract
Number: 40
Authors: Bala Krishnamoorthy1
1Washington State University, kbala@wsu.edu
Title: Characterization of Protein Structure using Geometry and Topology
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Short abstract: We define the neighborhood of a contiguous strand of amino acids in a protein as a series sub-complexes of the alpha complex of the protein at various growth levels. We characterize units of protein structure (motifs) by analyzing the geometry and topology of these neighborhood complexes.
Full abstract
Number: 41
Authors: Sergio A Alencar1, Julio C Lopes, Andrelly M. José
1Departamento de Quimica, Universidade Federal de Minas Gerais, sergiodealencar@bioinfo.dout.ufmg.br
Title: Chemoinformatics approach to Differential Drug Response of the Tyrosine Kinase Domain BCR-ABL to Imatinib in Chronic Myeloid Leukemia Patients
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Short abstract: Chemoinformatics approach to differential drug response of the tyrosine kinase domain BCR-ABL to imatinib in chronic myeloid leukemia (CML) patients in order to investigate the effects of three substitutions (Tyr315Ile, Phe317Leu and Phe359Val) at direct drug contact sites in CML patients that develop imatinib resistance.
Full abstract
Number: 42
Authors: Julio CD Lopes1
1Cheminformatics and Medicinal Chemistry Group - Departamento de Química – UFMG, jlopes@netuno.lcc.ufmg.br
Title: i-BioS: A System for Inverse Biological Virtual Screening Based on Inverse Docking Approach
Representative figure:
Short abstract: In the present work we develop a new system for inverse docking studies. Our system, called i-BioS (Inverse Biological virtual Screening), is based on Surflex docking program was used to reproduce some of the biological activities of violacein and found new ones, associated to its anti-oxidant character.
Full abstract
Number: 46
Authors: Garima Goel1, zaharul ahsan2, Srinivasa Reddy Gurram
HCL Technologies, 1garima.goel@hcl.in 2mahsan@hcl.in
Title: Development of an effective model for in-silico prediction of distribution parameters of ADMET for viable drug molecules.
Representative figure:
Short abstract: The model to define efficient distribution of the drug to its effecter site is based on SAR and Statistical approaches to calculate Vd, CD, BBB and plasma protein binding.
Full abstract
Number: 47
Authors: Prashanth k. Aitha1, Zaharul Ahsan2, Srinivasa Reddy Gurram
HCL Technologies, 1prashanth.aitha@hcl.in 2mahsan@hcl.in
Title: Toxicity Predication from Chemical Structure as a process of Lead optimization.
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Short abstract: A model to predict the toxicity of drug like molecules based on its structural similarity to existing drugs has been proposed using Structure activity relationship (SAR) and other Statistical approaches.
Full abstract
Number: 54
Authors: Francisco Melo1, Evandro Ferrada2
Catholic University of Chile, 1fmelo@bio.puc.cl 2evandro.ferrada@gmail.com
Title: Implicit Statistical Potentials for the Characterization and Prediction of Protein-ligand Binding Sites
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Short abstract: Here we will describe the first known method for protein-ligand binding site prediction that uses statistical potentials derived from experimental data and does not depend on explicit coordinates of a ligand nor transformations in three-dimensional space. The method is fast, robust and can be applied to any ligand.
Full abstract
Number: 60
Authors: Oxana V Galzitskaya1, Michail Yu Lobanov2, Sergiy O Garbuzynskiy
Institute of Protein Research, 1ogalzit@vega.portres.ru 2mlobanov@phys.portres.ru
Title: Prediction of Amyloidogenic and Unfolded Regions in Protein Chains
Short abstract: Identification of potentially amyloidogenic and unfolded regions in polypeptide chains is very important because such regions are essential for protein function.
Full abstract
Number: 61
Authors: youssef wazady1
1ESTC, wazady@yahoo.fr
Title: Conformational Analysis of N-Acetyl-N' Methylcyclopentyl Amide
Short abstract: the present study is interested in analysis of the structural behaviors of Acc5. The method used in this study is based on principles of the classical mechanics. It is applied with the PEPSEA program. The use of this residue in chemotactic peptides is discussed.
Full abstract
Number: 65
Authors: Mindaugas Margelevicius1, Ceslovas Venclovas2
Institute of Biotechnology, 1minmar@ibt.lt 2venclovas@ibt.lt
Title: A New Approach for Estimation of Statistical Significance in Sequence Profile-Profile Comparisons
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Short abstract: Sequence profile-profile comparison is one of the most sensitive techniques for distant homology detection. We propose a new approach to estimate statistical significance of the profile-profile alignments. The exhaustive testing showed that this approach combined with a newly developed comparison procedure compares favorably to a number of other existing methods.
Full abstract
Number: 68
Authors: Fabrice David1, Anne-Lise Veuthey2, Yum Lina Yip3
Swiss Institute of Bioinformatics - Swiss-Prot group, 1fabrice.david@isb-sib.ch 2anne-lise.veuthey@isb-sib.ch 3lina.yip@isb-sib.ch
Title: Incorporation of 3D Structure Information Into Swiss-Prot Annotation Workflow
Short abstract: In this work, we created an integrated platform to obtain consistent information on protein structures, and to semi-automatically generate UniProtKB/Swiss-Prot annotation from structural features (e.g. ligand binding sites). For this purpose, we set up a structure-sequence mapping. This mapping was already used to semi-automatically annotate disulfide bonds in UniProtKB/Swiss-Prot.
Full abstract
Number: 73
Authors: Henry van den Bedem1, Ankur Dhanik2, Jean-Claude Latombe, Ashley M. Deacon
1Joint Center for Structural Genomics / Stanford Synchrotron Rad. Lab., vdbedem@slac.stanford.edu 2Department of Computer Science, Stanford University, ankurd@stanford.edu
Title: Protein Dynamics from X-Ray Crystallography Data: Modeling Structural Heterogeneity with Inverse Kinematics
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Short abstract: We present a technique to model structural heterogeneity in protein main-chain fragments determined by X-ray crystallography. The technique also allows energetically plausible pathways between the conformations to be calculated, thus providing insight in the local dynamics of the main chain.
Full abstract
Number: 74
Authors: Xueping Quan1, Peter Doerner2, Dietlind L Gerloff3
University of Edinburgh, 1x.quan@sms.ed.ac.uk 2peter.doerner@ed.ac.uk 3d.gerloff@ed.ac.uk
Title: Partner Prediction for Transient Protein Interactions within sets of Paralogues: CDK-Cyclin homologue complexes in A.thaliana
Representative figure:
Short abstract: To predict which specific CDK homologue interacts with which cyclin homologue in Arabidopsis thaliana, a comparative modelling strategy was applied to model the 3-D structures of these proteins. All-by-all docking of the model structures using the program ZDOCK, combined with additional selection criteria, yielded 19 most likely interacting CDK-cyclin pairs.
Full abstract
Number: 75
Authors: Bruno Contreras-Moreira1, Julio Collado-Vides2
Centro de Ciencias Genómicas, UNAM, México, 1contrera@ccg.unam.mx 2collado@ccg.unam.mx
Title: Comparative footprinting of DNA-binding proteins
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Short abstract: We present the DNASITE software, designed for comparative footprinting
of DNA-binding proteins based solely on structural data. While we find limitations to the approach, it can also provide useful predictions of bindinf sites.
Full abstract
Number: 78
Authors: Nebojsa Jojic1, Manuel J. Reyes-Gomez2, David Heckerman, Carl Kadie, Ora Schueler-Furman
Microsoft Research, 1jojic@microsoft.com 2manuelrg@microsoft.com
Title: Learning MHC I - Peptide Binding
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Short abstract: Motivated by the ability of a simple threading approach to predict MHC I - peptide binding, we developed a new improved structure-based model, which we call adaptive double threading. The parameters of the threading model are learnable, and both MHC and peptide sequences can be threaded onto structures of other alleles.
Full abstract
Number: 79
Authors: Chavent Matthieu1, Claire Nourry2, Nadine Deliot, Jean P. Borg, Bernard Maigret
1Henri Poincaré University, UMR 7565, eDAM team, matthieu.chavent@edam.uhp-nancy.fr 2U119 INSERM and Institut Paoli-Calmettes, Laboratory of Molecular Pharmacology, nourry@marseille.inserm.fr
Title: Use of Docking Tools and Molecular Dynamic Simulations to Predict the Interaction Between the MH2 domain of SMAD3 and the PDZ Domain of ERBIN
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Short abstract: Erbin has been identified as a binding partner for Smad3, a major component of the transforming growth factor-beta signaling pathway. We present how the use of bioinformatics and molecular modelling tools such as molecular dynamics helped us to conceptualize the association between the Smad3 MH2 and Erbin PDZ domains.
Full abstract
Number: 80
Authors: Alexandre Beautrait1, Bernard Maigret2
eDAM group, UMR CNRS/UHP 7565, 1alexandre.beautrait@edam.uhp-nancy.fr 2bernard.maigret@edam.uhp-nancy.fr
Title: VSM-G: the Virtual Screening Manager Platform for Computational Grids. Use for the Identification of Putative Ligands of the Liver X Receptor.
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Short abstract: The VSM-G platform performs high throughput virtual screening based on ligand- and receptor-based algorithms running on computational grids. A central molecular funnel composed of successive filters allows the screening of large molecular libraries for compounds prioritization in experimental assays. Illustrations deal with the LXRß target protein involved in cholesterol regulation.
Full abstract
Number: 81
Authors: Michael Terribilini1, Jeffry Sander2, Byron Olson3, Jae-Hyung Lee, Robert Jernigan, Vasant Honavar, Drena Dobbs
Iowa State Univeristy, 1terrible@iastate.edu 2jdsander@iastate.edu 3byron.olson@gmail.com
Title: A Computational Method to Identify Amino Acid Residues Involved in Protein-RNA Interactions
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Short abstract: Protein-RNA interactions are vital for many biological processes. To the best of our knowledge, this is the first reported attempt to exploit both amino acid sequence and three-dimensional structure for prediction of RNA-binding residues in proteins.
Full abstract
Number: 85
Authors: Andrei L Lomize1, Mikhail A Lomize2, Irina D. Pogozheva
1College of Pharmacy, University of Michigan, Ann Arbor MI, 48109-1065, U.S.A., almz@umich.edu 2University of Michigan, Ann Arbor MI, 48109-1065, U.S.A., mlomize@umich.edu
Title: Spatial Orientations of Proteins in Membranes
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Short abstract: Spatial arrangements of 600 membrane-associated proteins in the lipid bilayer have been calculated and deposited in the OPM (Orientations of Proteins in Membranes) database http://opm.phar.umich.edu. The results were verified against available experimental data and compared for transmembrane proteins from different types of biological membranes.
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