No.	Representative Figure	Authors	Title
Invited Speaker Abstracts
Invited-1		Robert B. Russell	A Structural Perspective on Protein Interactions & Complexes
Invited-2		Ron Unger	Using Accumulated Dot Matrices to Detect RNA and Protein Structures
Invited-3		Gregorio Fernandez, Christine Kiel, Luis Serrano	In silico Prediction of Protein-Protein Interactions: How and When It Can Work
Invited-4		Gunnar von Heijne	Genome-wide Membrane Protein Topology Predictions
Invited-5		Florencio Pazos, Michael JE Sternberg	Automated Prediction of Protein Function from Structure
Invited-7		Martin Madera, Julian Gough, Sarah Kummerfeld, Cyrus Chothia 3	The Homology of Genome Sequences: Profile-Profile Sequence Matching and the SUPERFAMILY Database
Invited-8		Song Yang, Russell Doolittle, Philip E. Bourne	The Study of Evolution through Protein Domain Structure
Speaker Abstracts
5		Rune Linding, Robert B. Russell, Lars J. Jensen, Francesca Diella, Peer Bork, Toby J. Gibson	Intrinsic Protein Disorder - Function, Disease and Structural Proteomics.
9		Barry J. Grant, Leo S. Caves, Rob Cross	Stripping down the Kinesin Molecular Motor: a Combined Informatics and Simulation Approach
15		Eran Eyal, Marvin Edelman, Vladimir Sobolev	The Influence of Crystal Packing on Protein structure
18		Andreas Heger, Liisa Holm	Fast Fold Recognition by Consensus Alignment within Transitive Closure
22		Oxana V. Galzitskaya, Sergiy O. Garbuzynskiy, Bogdan S. Melnik, Michail Y. Lobanov, Alexei V. Finkelstein	Comparison of X-ray and NMR Protein Structures
24		Sanne Abeln, Charlotte M. Deane	Investigating Protein Structure Evolution by Fold Usage on Genomes
28		Antonio Del Sol, Paul A. O'Meara	Small-World Network Approach to Identify Key Residues in Protein-Protein Interaction.
31		Maxim Chapovalov, Roland L. Dunbrack	Using Statistical Analysis of Electron Density to Evaluate Protein Side-Chain Conformations and Rotamer Disorder
36		Maxim Totrov	Protein-Protein Docking Simulations with Local Backbone Flexibility
41		Johannes Soeding, Andrei N. Lupas	Homology Search By HMM-HMM Comparison Detects More Than Three Times As Many Remote Homologs as PSIBLAST or HMMER
43		Richard J. Morris, Abdullah Kahraman, Rafael Najmanovich, Fabian Glaser, Roman Laskowski, Janet M. Thornton	Protein Active Site Identification and Fast Shape Comparison
45		Arye Shemesh, Gil Amitai, Einat Sitbon, Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski	Structural Analysis of Residue Interaction Graphs
46		Gestel David, Ian Humphery-Smith	The Binding-Site Diversity of the Entire Non-denatured, Surface-exposed Human Proteome
47		Inge Jonassen, William R. Taylor	SPREK: A Method for Evaluating Structural Models using Structural Patterns
53		Jaspreet S. Sodhi, Kevin Bryson, Liam J. McGuffin, Jonathan J. Ward, Lornenz Wernisch, David T. Jones	Predicting the Location and Identity of Protein Functional Sites, Application to Genomic Fold Recognition
68		Marialuisa Pellegrini-Calace, William R. Taylor, David T. Jones	FILM2: a Novel Method for the Prediction of Transmembrane Helical Bundles in a Membrane-like Environment
72		Qiaojuan Jane Su, Orit Foord, Scott Klakamp, Holly Tao, Larry L. Green	Modeling and Simulation of Antibody-Antigen Interaction: An Integrated Approach
74		Joerg Hackermueller, Nicole-Claudia Meisner, Manfred Auer, Markus Jaritz	mRNA Openers – Computationally Designed Modulators of mRNA Secondary Structure which Manipulate Gene Expression
76		Yuval Inbar, Haim J. Wolfson, Ruth Nussinov	Prediction of Multi-Molecular Assemblies by Multiple Combinatorial Docking.
77		Matthew L. Baker, Wah Chiu	Analysis of Intermediate Resolution Structures
Laptop Session Abstracts
1		Anne Marie Quinn, Luke Fisher, Dana Haley-Vicente	From Gene to Function: In Silico Warfare on the West Nile Virus
2		Efrat Ben-Zeev, Miriam Eisenstein	Weighted Geometric Docking with MolFit: Incorporating External Information in the Rotation-Translation Scan
3		James Bradford, David Westhead	Prediction of Protein-Protein Binding Sites using Support Vector Machines
4		Kim Henrick, Tom Oldfield, 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	MSD Relational Database, Search and Visualisation of Queries and Results
6		Sarel J. Fleishman, Vinzenz M. Unger, Mark Yeager, Nir Ben-Tal	A Model Structure of the Gap-Junction Transmembrane Domain Specifying C-alpha Positions
7		Thomas Lütteke, Claus W. von der Lieth	Towards Deciphering the Structural Features of Glycosylation Sites: Analysis of Carbohydrate-Related Data contained in the Protein Data Bank
8		Wolfgang F. Bluhm on behalf of the PDB team	PDB-in-a-Box
10		Howard J. Feldman, Christopher WV Hogue, Kevin Snyder	MMDBBIND - Macromolecular Interactions with Atomic Level Detail
11		Philip C. Biggin, Yalini Arinaminpathy, Mark SP Sansom	Conformational Dynamics of Glutamate Receptors: Simulation Studies.
12		Nicola D. Gold, Richard M. Jackson	A Searchable Database for Comparing Protein-Ligand Binding Sites for the Discovery of Structure-Function Relationships
13		Andreas Bohne-Lang, Claus W. von der Lieth	Glyprot: a Web-tool for in-silico Glycosylation of Proteins
14		Vladimir Potapov, Vladimir Sobolev, Marvin Edelman, Alexander Kister, Israel Gelfand	Interface Cores in Sandwich-like Proteins
16		Eran Eyal, Vladimir Sobolev, Rafael Najmanovich, Brendan J. McConkey, Marvin Edelman	Modeling Side Chain Conformations using Contact Surfaces and solvent Accessible Surface
17		Gail J. Bartlett, James W. Torrance, Craig T. Porter, Jonathan A. Barker, Alex Gutteridge, Malcolm W. MacArthur, Janet M. Thornton	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
19		Andreas Prlic, Thomas A. Down, Tim JP. Hubbard	Protein DAS, Distributed Annotation System for Proteins
20		Ingolf E. Sommer, Joerg Rahnenfuehrer, Francisco S. Domingues, Ulrik de Lichtenberg, Thomas Lengauer	Predicting Protein Structure Classes from Function Predictions
21		Jean-Luc Pellequer, Shu-wen W. Chen, Gilles Imbert, Olivier Pible, Isabelle Vergely	Selecting Non-Redundant Protein Structures from the Protein Data Bank
23		Samantha L. Kaye, Mark SP Sansom, Philip C. Biggin	Simulation and Modelling studies of the NMDA Receptor
25		Silke Trissl, Kristian Rother, Ulf Leser	COLUMBA - A Database of Annotated Protein Structures
26		Merridee A. Wouters, Ken K. Lau, Philip J. Hogg	Cross-Strand Disulphides in Cell Entry Proteins: Redox Switches in Protein Nanomachines
27		Alessandro Pandini, Giancarlo Mauri, Laura Bonati	BioPySDS: an Object-Oriented Interface to Manage Protein Dynamics in an Evolutionary Framework
29		Chen Yanover, Ori Shachar, Yair Weiss	Inference in Graphical Models for Side-chain Prediction
30		Fabrizio Ferre', Gabriele Ausiello, Andreas Zanzoni, Manuela Helmer-Citterich	Large Scale Surface Comparison for the Identification of Functional Similarities in Unrelated Proteins
32		Ruchir R. Shah, Luke Huan, Deepak Bandyopadhyay, Wei Wang, Alexander Tropsha	Structure Based Identification of Protein Family Signatures for Function Annotation
33		Ilan Samish, Eran Goldberg, Oksana Kerner, Avigdor Scherz	Centrality of Weak Interhelical H-bonds in Membrane Protein Functional Assembly and Conformational Gating
34		Dmitry S. Kanibolotsky, Konstantin A. Odynets, Alexander I. Kornelyuk	Homology Modeling and Molecular Dynamics Simulation Study of Cytokine-like C-terminal Module of Mammalian Tyrosyl-tRNA Synthetase
35		Elmar Krieger, Tom Darden, Sander B. Nabuurs, Alexei V. Finkelstein, Gert Vriend	Making Optimal Use of Empirical energy Functions: Force Field Parameterization in crystal Space
37		Antonis Koussounadis, David W Ritchie, Antonis Koussounadis, Chris J. Secombes	Modelling b-Trefoil Proteins Using an Object-Oriented Database
38		Juan Fernandez-Recio, Tom L. Blundell	Computer Simulations of Protein-Protein Interactions: Rigid-Body Docking and Flexible-Link Refinement Applied to Multi-Domain Signalling Complexes
39		Hugh P. Shanahan, Sue Jones, Carles Ferrer, Janet M. Thornton	Detecting DNA-binding Proteins using Structural Motifs and Electrostatics
40		Robert M. MacCallum	Self-Organized Maps of Sequence Profiles for Protein Structure Prediction
42		Craig J. Lucas, Andrew Bulpitt	Automatic Identification of Key Patterns Within Multiple Protein Structures
44		Damien Devos, Svetlana Dokudovskaya, Marc A. Marti-Renom, Rosemary Williams, Brian T. Chait, Andrej Sali, Michael P. Rout	Evidence for A Common Evolutionary Origin of Nuclear Pore Complexes and Coated Vesicles
48		Cristina Benros, Alexandre G. de Brevern, Serge Hazout	Predicting Local Structural Candidates from Sequence by the "Hybrid Protein Model" Approach
49		Abraham Nahmany, Francesco Strino, Jimmy Rosen, Graham JL. Kemp, Per-Georg Nyholm	Prediction of Oligosaccharide Conformations using Genetic Algorithms and Molecular Mechanics MM3
50		Björn Wallner, Arne Elofsson	Benchmark of Different Homology Modelling Programs
51		Patrick May, Thomas Steinke, Michael Meyer	THESEUS: A Parallel Threading Core
52		Ermanna Rovida, Pasqualina D'Ursi, Paola Fossa, Luciano Milanesi	Modelling the Interaction of Human Estrogen Receptor alpha with Organic Polychlorinated Compounds
54		Julian Mintseris, Zhiping Weng	Optimized Protein Representations from Information Theory
55		Nalin C. Goonesekere, Byungkook Lee	Frequency of Gaps Observed in a Structurally Aligned Protein Pair Database Suggests a SIMPLE GAP PENALTY FUNCTION
56		Victoria F. Dominguez Del Angel, Luis Mochan, Bernard Caudron, Charles Roth	PP2A(alpha) Interactions Domains, a Model of 3D Pattern Representation
57		Qingjuan Gu, William W. Reenstra, John J. Rux	MMD: A Macro-Molecular Docking Program for Locating Domain-Domain Interactions
58		Gianni De Fabritiis, Rafael Delgado-Buscalioni, P. V. Coveney	A Minimisation Method for the efficient Insertion of Solvent Water Molecules
59		Jim Procter, Andrew Torda	Protein sequence-structure Alignments for Prediction, Classification, and Visualization
60		Alexandra Shulman-Peleg, Shira Mintz, Ruth Nussinov, Haim J. Wolfson	Protein Functional Sites Recognition and Classification
61		Dina Schneidman, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson	FlexDock: An Algorithm for Flexible Hinge-Bent Docking.
62		Meytal Landau, Sarel J. Fleishman, Nir Ben-Tal	Down-Regulation of the Catalytic Activity of the EGF Receptor via Direct Contact between the Kinase and C-Terminal Domains
63		Håkan Viklund, Arne Elofsson	Profile-profile HMMs for Structure Predictions
64		Thomas P. Walsh, Geoffrey J. Barton	A PERL Library for Generating Hierarchical, Tree-based Browser Interfaces for SCOP Database Searches.
65		Jan Reichert, Kristina Mehliss, Juergen Suehnel	The IMB Jena Image Library of Biological Macromolecules - Recent Developments
66		Liam J. McGuffin, Stefano A. Street, David T. Jones, Soren-Aksel Sorensen	The Genomic Threading Database
67		Hannes Ponstingl, Janet M. Thornton	Structure and Sequence Characteristics of Oligomeric Proteins
69		Vichetra Sam, Chin-Hsien (Emily) Tai, Peter J. Munson, Jean Garnier, Jean-François Gibrat, Byungkook Lee	Comparison of Protein Structural Comparison Methods, VAST and SHEBA, with the SCOP Classification, using Statistical Methods
70		Apostol Gramada, Philip E. Bourne	A Multipole-Based Method for Comparison of Protein Structures
71		Goran Neshich, Roberto Higa, Adauto Mancini, Paula Kuzer, Michel Yamagishi, Renato Fileto	Selecting a Set of the Protein Structure Descriptors Uniquely Defining the Active Site Residues
73		Javier De Las Rivas, Carlos Prieto, Alberto De Luis	Exploring Protein Interaction Networks and Functional Relationships at a Genomic Scale with a Agile Browser
75		Rafael Najmanovich, Richard J. Morris, Roman Laskowski, Janet M. Thornton	Shape Description of Protein Clefts
79		Silvia N. Crivelli, James Lu, James Lu, Oliver Kreylos, Nelson Max, and Wes Bethel	ProteinShop: a Tool for Interactive Protein Manipulation
80		Jessica Fong, Amy Keating, Mona Singh	Large Scale, High-Confidence Predictions of bZIP Protein-Protein Interactions
81		Jessica C. Shapiro, Douglas L. Brutlag	Automatic Structural Motif Discovery using FOLDMINER
82		Deepak Bandyopadhyay, Luke Huan, Wei Wang, Jack Snoeyink, Jan Prins, Alexander Tropsha	Graph Representations and Algorithms for Protein Family Classification and Functional Annotation
83		Agnes Tan	Automated Contruction of WD40 proteins
84		Alvin Ng	Homology Model and Substrate Recognition of Yeast Prk1p Kinase
85		Michael L. Sierk, William R. Pearson	Benchmarking Protein Structure Alignment Statistics Against the CATH Database
86		Christina Kiel, Luis Serrano, Alfred Wittinghofer, Sabine Wohlgemuth	Recognizing and Defining true Ras Association (RA) Domains based on Protein Sequence and Structure
87		Kay Gottschalk, Hani Neuvirth, Gideon Schreiber	Docking Protein Complexes from their Predicted Binding Site
88		Juliette Martin, Jean-François Gibrat, François Rodolphe	Hidden Markov Model for Protein Secondary Structure
89		C. Jayaprabha, N. Santhi, J. Kamesh, P. Chitra, N. Bharathi, S. Krishnaveni, S. Valarmathi, S. Sujatha and S. Seethalakshmi	In Silico Transfer of Neurotransmitter Transporter Motif Between Structurally Analogous Protein (Catechol-O-methyltransferase)
90		Giacomo De Mori, Raul Mendez, Didier Croes, Shoshana J. Wodak	Analysis of Conformational Changes on Protein - Protein Complexes.
91		YY Cai, BF Lu, ZW Fan, and KT Lim	3D Structure Image Generator using Virtual Reality Technology for Protein Immersive Visualization
92		Dinesh C. Soares, Paul N. Barlow, Dietlind L. Gerloff	The CCP-Module Model Database - Automated Large-Scale Protein Structure Modelling of Individual Human Complement Control Protein (CCP)-Modules
93		Joaquim Mendes, Luis Serrano	Incorporating an Accurate Solvation Model into Computational Protein Design