No.	Representative Figure	Authors	Title
Invited Speaker Abstracts
72		Nick V Grishin	Dramatic Evolutionary Changes in Protein Structures
77		Christopher Dupont, Song Yang, Brian Palenik, Philip E. Bourne	Modern Proteomes Contain Imprints of Ancient Shifts in Environmental Chemistry
83		Wah Chiu, Matthew L Baker	Modeling Protein Components of Biological Nano-Machines in Subnanometer Resolution CryoEM Density Maps
86		Jeffery G Saven	Theoretical Methods for the Design and Engineering of Proteins
87		Janet M. Thornton, Gemma L. Holliday, Alex Gutteridge, James Torrance, Gail J. Bartlett, Daniel E. Almonacid, Noel M.O'Boyle, Peter Murray-Rust, John B. O. Mitchell	Using the Three Dimensional Structures of Enzymes to Understand Catalysis
Speaker Abstracts
8		Melissa R Landon, Spencer C Thiel, David R. Lancia Jr., Sandor Vajda	Identification of Druggabable “Hot Spots” in Ligand Binding Pockets by Computational Solvent Mapping of Proteins
10		Stefano Lise, David T Jones, Alice Walker-Taylor	Docking protein domains in contact space
15		Anna CV Johansson, Erik Lindahl	Simulation of Amino Acid Solvation Structure in Transmembrane Helices and Implications for Membrane Protein Folding
17		Diana K Ekman, Åsa K Björklund, Arne Elofsson	Evolutionary History of Multi-Domain Proteins
19		Michal J Gajda, Marta Kaczor, Janusz M Bujnicki, Anastasia Bakulina, Andrzej Kasperski, Alan M. Friedman, Chris Bailey-Kellogg	FILTREST3D: a Simple Method for Discrimination of Multiple Structural Models Against Spatial Restraints
26		Marcin Pawlowski, Janusz Bujnicki, Ryszard Matlak	Meta-MQAP: an SVM-based meta-server for the quality assessment of protein models
30		Antonio del Sol, Marcos J. Arauzo-Bravo, Dolors Amoros, Ruth Nussinov	Network Robustness and Modularity of Protein Structures in the Identification of Key Residues for the Allosteric Communications
34		Scooter Willis	Predicting co-evolving pairs in Pfam based on Mutual Information of mutation events measured along the phylogenetic tree
37		Avner Schlessinger, Marco Punta, Burkhard Rost	Identifying Natively Unstructured Proteins Using Residue Contact Predictions
43		Francisco Melo, Alejandro Panjkovich, Andrej Sali, Marc A. Marti-Renom,	Structure Specific Statistical Potentials for Protein Structure Prediction
44		Bingding Huang, Michael Schroeder	Integrate the Degree of Burial and Conservation of Surface Residues into Protein-protein Docking
45		Sandra Maguid, Gustavo Parisi, Sebastian Fernandez-Alberti, Julian Echave	Sequence-structure-flexibility relationship in protein evolution.
55		Iris Antes, Thomas Lengauer	DynaDock: Inhibitor based Refinement of Homology Modeled Protein Structures for Molecular Docking
59		Maria S Fornasari, Gustavo Parisi	Protein Structure Diversity and Sequence Divergence in Evolution
62		Ingo Ruczinski, Kevin W Plaxco, Tobin R. Sosnick	On the Precision of Experimentally Determined Protein Folding Rates and Φ Values
63		Elon Portugaly, Nathan Linial, Michal Linial	Assessment of Protein Domain Classifications: An Automatic Sequence-based Method and Methods Based on 3D Structures
66		Thomas Funkhouser, Roman Laskowski, Janet Thornton	Matching Volumetric Models of Protein Active Sites
69		Frank P DiMaio, Jude W Shavlik, George N. Phillips	A Probabilistic Approach to Protein Backbone Tracing in Electron Density Maps
76		Ilan Samish, Oksana Kerner, David Kaftan, Eran Goldberg, Avigdor Scherz	Datamining the Fourth Dimension from Crystal Structures: Structure-Function-Entropy Relationships in Membrane Proteins
82		Rafael J Najmanovich, Richard J Morris, Janet M. Thornton	Single-Family Analysis of Binding Site Structural Similarities
84		Zsuzsanna Dosztányi, Márk Sándor, István Simon	Prediction of Order and Disorder at the Domain Level
Laptop Session Abstracts
11		Jorge H Fernandez, Solange M Serrano, Wilson Savino, Ana Tereza Vasconcelos	Bothrostatin, a new RGD-type disintegrin from Bothrops jararaca venom: binding specificity in bothrostatin-αIIbβ3/αvβ3 integrin complexes.
12		Lie Li, Meena Sakharkar, Pandjassarame Kangueane, Jacob Gan, Pandjassarame Kangueane	Structural features differentiate the mechanisms between 2S (2 state) and 3S (3 state) folding of homodimers.
13		Francisco Torrens, Gloria Castellano	Binding of Water-Soluble, Globular Proteins to Anionic Model Membranes
14		Karsten M Borgwardt, SVN Vishwanathan, Nicol N. Schraudolph, Hans-Peter Kriegel	Fast Graph Kernels for Proteomics
16		Talapady N Bhat, Anh D Thi Nguyen, Alexander Wlodawer, Mohamed Nasr	Semantic Web and Chemical Ontology for Fragment-Based Drug Design and AIDS
18		Alexander A Kantardjiev, Boris P Atanasov	Electrostatics in Protein Docking: pH-Dependent self-consistent orientation guide
20		Sumeet Dua, Praveen C Kidambi	Protein Structural Classification using Associative Discrimination of Orthonormal coefficients
21		Shula Shazman, Yael Mandel-Gutfreund	A Machine Learning Approach for Predicting RNA-binding Proteins from their Three Dimensional Structure
23		Oliver Sander, Tobias Sing, Francisco S. Domingues, Ingolf Sommer, Andrew Low, Peter K. Cheung, P. Richard Harrigan, Thomas Lengauer	Structural Descriptors Improve the Prediction of HIV Coreceptor Usage
25		Vishal Kapoor, Sree Nivas gurram Reddy	In Silico Pathway of drug absorption, distribution and Metabolism(ADMET)
27		Michal Milo, Amiram Goldblum	A Myristoyl Binding Site in Protein Kinases
28		Claudia Bertonati, Marco Punta, Burkhard Rost, Barry Honig	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.
31		Peter Røgen, Per W Karlsson	Quantifying the Relative Positions of Proteins Secondary Structure Elements
39		Jeff D Sander, Peter C Zaback, Drena L Dobbs, Fengli Fu, Daniel F. Voytas	Designing C2H2 Zinc Finger Proteins to Target Specific Genomic Sites
40		Bala Krishnamoorthy	Characterization of Protein Structure using Geometry and Topology
41		Sergio A Alencar, Julio C Lopes, Andrelly M. José	Chemoinformatics approach to Differential Drug Response of the Tyrosine Kinase Domain BCR-ABL to Imatinib in Chronic Myeloid Leukemia Patients
42		Julio CD Lopes	i-BioS: A System for Inverse Biological Virtual Screening Based on Inverse Docking Approach
46		Garima Goel, zaharul ahsan, Srinivasa Reddy Gurram	Development of an effective model for in-silico prediction of distribution parameters of ADMET for viable drug molecules.
47		Prashanth k. Aitha, Zaharul Ahsan, Srinivasa Reddy Gurram	Toxicity Predication from Chemical Structure as a process of Lead optimization.
54		Francisco Melo, Evandro Ferrada	Implicit Statistical Potentials for the Characterization and Prediction of Protein-ligand Binding Sites
60		Oxana V Galzitskaya, Michail Yu Lobanov, Sergiy O Garbuzynskiy	Prediction of Amyloidogenic and Unfolded Regions in Protein Chains
61		youssef wazady	Conformational Analysis of N-Acetyl-N' Methylcyclopentyl Amide
65		Mindaugas Margelevicius, Ceslovas Venclovas	A New Approach for Estimation of Statistical Significance in Sequence Profile-Profile Comparisons
68		Fabrice David, Anne-Lise Veuthey, Yum Lina Yip	Incorporation of 3D Structure Information Into Swiss-Prot Annotation Workflow
73		Henry van den Bedem, Ankur Dhanik, Jean-Claude Latombe, Ashley M. Deacon	Protein Dynamics from X-Ray Crystallography Data: Modeling Structural Heterogeneity with Inverse Kinematics
74		Xueping Quan, Peter Doerner, Dietlind L Gerloff	Partner Prediction for Transient Protein Interactions within sets of Paralogues: CDK-Cyclin homologue complexes in A.thaliana
75		Bruno Contreras-Moreira, Julio Collado-Vides	Comparative footprinting of DNA-binding proteins
78		Nebojsa Jojic, Manuel J. Reyes-Gomez, David Heckerman, Carl Kadie, Ora Schueler-Furman	Learning MHC I - Peptide Binding
79		Chavent Matthieu, Claire Nourry, Nadine Deliot, Jean P. Borg, Bernard Maigret	Use of Docking Tools and Molecular Dynamic Simulations to Predict the Interaction Between the MH2 domain of SMAD3 and the PDZ Domain of ERBIN
80		Alexandre Beautrait, Bernard Maigret	VSM-G: the Virtual Screening Manager Platform for Computational Grids. Use for the Identification of Putative Ligands of the Liver X Receptor.
81		Michael Terribilini, Jeffry Sander, Byron Olson, Jae-Hyung Lee, Robert Jernigan, Vasant Honavar, Drena Dobbs	A Computational Method to Identify Amino Acid Residues Involved in Protein-RNA Interactions
85		Andrei L Lomize, Mikhail A Lomize, Irina D. Pogozheva	Spatial Orientations of Proteins in Membranes