Program Information
Preliminary Program 3rd CAPRI Evaluation Meeting April 20-21, 2007 Toronto, Canada
| Friday, April 20, 2007 | |
| 8:00 am - 9:00 am | Continental Breakfast and Registration |
| 9:00 am - 9:15 am | Welcome and introduction TBA |
| 9:15 am - 10:30 am |
Current status of docking procedures: general overview by the CAPRI assessors
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| 10:30 am-10:45 am | Coffee break |
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Recent results and new methodology for the prediction of protein complexes: Reports by individual CAPRI participants (Part I) |
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| 10:45 am - 11:10 am | The Performance of ZDOCK and ZRANK in Rounds 6-11 of CAPRI Kevin Wiehe, Brian Pierce, Wei Wei Tong, Howook Hwang, Julian Mintseris Zhiping Weng,, Bioinformatics Program, Boston University |
| 11:10 am - 11:35 am | Prediction-driven and data-driven docking with HADDOCK2.0: performance on the docking benchmark and CAPRI targets. Sjoerd J. de Vries and Alexandre M.J.J. Bonvin, Utrecht University |
| 11:35 am - 12:00 pm |
An FFT-Based Protein Docking Program with Pairwise Potentials Dima Kozakov, Ryan Brenke, Stephen R. Comeau, and Sandor Vajda, Boston University |
| 12:00 am - 12:25 pm |
A Holistic Approach to Docking Sanbo Qin and Huan-Xiang Zhou, Institute of Molecular Biophysics and School of Computational Science, Florida State University |
| 12:25 am - 12:50 pm |
Inherent Limitations in Protein-Protein Docking Procedures Noga Kowalsman and Miriam Eisenstein, Department of Biological Chemistry, Weizmann Institute of Science |
| 12:50 pm - 2:00 pm | Lunch |
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Recent results and new methodology for the prediction of protein complexes: Reports by individual CAPRI participants ( Part II) |
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| 2:00pm - 2:25 pm |
Implicit flexibility in protein docking: cross-docking and local refinement Marcin Król, Raphael A. G. Chaleil, Paul W. Fitzjohn and Paul A. Bates, Cancer Research, UK |
| 2:25 pm - 2:50 pm |
Incorporating backbone flexibility into protein-protein docking with RosettaDock. Chu Wang, Ora Schueler-Furman, Ingemar Andre, Nir London, Sarel Fleishman, Phil Bradley, Bin Qian and David Baker, Washington University, |
| 2:50 pm - 3:15 pm |
Fully automated flexible docking with explicit consideration of hinge motion in one of the proteins Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson Tel Aviv University, Tel Aviv, Israel |
| 3:15 pm - 3:45 pm | Coffee break |
| 3:45 pm - 4:10 pm |
Accounting efficiently for global and local flexibility during systematic protein-protein docking Andreas May and Martin Zacharias, Jacobs University Bremen, Germany |
| 4:10 pm - 4:35 pm |
Performance of the ClusPro Server in CAPRI Rounds 6-11 Stephen R. Comeau, Jr. and Sandor Vajda,1Bioinformatics Program, Boston University, Dyax Corp. Biotherapeutics, Department of Biomedical Engineering, Boston University |
| 4:35 pm - 5:00 pm |
Why not to bury acidic groups in protein interfaces: Solvated Asp cavities and missing targets in CAPRI Carlos J. Camacho, Department of Computational Biology, University of Pittsburgh |
| 5:00 pm - 5:45 pm | Invited Lecture: Recent Progress in CASP 2006 John Moult |
| 5:45 pm - 6:30 pm | Round Table discussion: integrating docking procedures with structural genomics and proteomics efforts; use of the CAPRI experiment as a permanent community-wide platform for the prediction of protein-protein interactions and for testing new force fields and scoring functions |
| 6:30 pm - 7:45 pm | Poster Session |
| 7:45 pm - 9:30 pm | Conference Reception dinner / Poster and exhibition session |
| Saturday, April 21, 2007 | |
| 8:00 am - 9:00 am | Continental Breakfast |
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Recent results and new methodology for the prediction of protein complexes: Reports by CAPRI participants and others |
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| 9:00 am - 9:25 am |
Towards ensemble docking in RosettaDock: Local docking of idealized, energy minimized structures with multiple backbone conformations Sidhartha Chaudhury and Jeffrey J. Gray, Program in Molecular and Computational Biophysics, Department of Chemical and Biomolecular Engineering, Johns Hopkins University |
| 9:25 am - 9:50 am |
SOFTDOCK Application to protein-protein interaction benchmark and CAPRI evaluation Nan Li, Zhonghua Sun, and Fan Jiang, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences |
| 9:50 am - 10:15 am |
Title: Funnel hunting in a rough terrain: Learning and discriminating energy funnels Nir London & Ora Schueler-Furman, The Hebrew University, Jerusalem |
| 10:15 am - 10:40 am |
Multi-Scale Scoring Scheme for Prediction of Protein Assemblies Gaurav Chopra, Julie Bernauer, Karine Bastard and Michael Levitt, Computational Structural Biology, Stanford University |
| 10:40 am - 10:55 am | Coffee Break |
| Highlighting alternative approaches | |
| 10:55 am - 11:20 am |
Protein-Protein Docking using Steered Molecular Dynamics Simulations in Water Sandeep Pal, Graham R. Smith Protein-Protein Interactions Group Biosystems Informatics Institute Marlborough House |
| 11:20 am - 11:45 am |
A General Approach for Developing System Specific Functions to Score Protein Ligand Using Support Vector Inductive Logic Programming. Ata Amini, Paul Shrimpton and Michael J E Sternberg Centre for Bioinformatics, Division of Molecular Bioscience, Imperial College London |
| 11:45 am - 12:10 am |
Prediction of protein-protein interaction using Evolutionary Trace method and molecular surface shape complementarities Eiji Kanamori , Yoichi Murakami, Yuko Tsuchiya,, Daron Standley, Kengo Kinoshita and Haruki Nakamura,Japan Biological Information Research Center Institute for Protein Research, Osaka University Institute of Medical Science, University of Tokyo |
| 12:10 am - 12:35 pm |
Docking without Docking: Prediction of interactions using known interfaces Stefan Gunther and Patrick May, Institute for Molecular Biology and Bioinformatics, Charité University Medicine Berlin |
| 12:35 pm - 1:00 pm |
Dockground integrated system of databases for protein docking, 2nd release Ying Gao, Dominique Douguet, Andrey Tovchigrechko, Ilya Vakser, Center for Bioinformatics, The University of Kansas |
| 1:00 pm - 2:00 pm | Lunch |
| Invited Lectures | |
| 2:00 pm - 2:45 pm |
Dr. Ivet Bahar, Director, Center for Computational Biology and Bioinformatics, University of Pittsburgh School of Medicine. Title: Structural changes induced upon substrate binding: Insights from elastic network models |
| 2:45 pm - 3:30 pm |
Dr. Yang Zhang, Scientist, Center for Bioinformatics and Department of Molecular Biosciences, University of Kansas. Title: New approaches to protein structure prediction |
| 3:30 pm - 4:15 pm |
Dr. Cheryl Arrowsmith, Senior Scientist, Division of Cancer Genomics and Proteonics, Ontario Cancer Institute (OCI)The Structural Genomics Consortium: Structural Coverage of Human Title: Gene Families and Protein-Protein Interactions among Families. |
| 4:15 pm - 5:00 pm | Closing Remarks |