1. Implicit flexibility in protein docking: cross-docking and local refinement
   Marcin Król, Raphael A. G. Chaleil, Paul W. Fitzjohn and Paul A. Bates
7. A Holistic Approach to Docking
   Sanbo Qin and Huan-Xiang Zhou*Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA E-mail: zhou@sb.fsu.edu
8. 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, Beijing 100080, China. Email: fjiang@aphy.iphy.ac.cn
10. 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
11. Title: 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
12. Multi-Scale Scoring Scheme for Prediction of Protein Assemblies
    Gaurav Chopra, Julie Bernauer, Karine Bastard and Michael Levitt
13. Title: Inherent Limitations in Protein-Protein Docking Procedures
    Noga Kowalsman and Miriam Eisenstein
15. Prediction of protein-protein interaction using Evolutionary Trace method and molecular surface shape complementarities
    Eiji Kanamori¹ , Yoichi Murakami², Yuko Tsuchiya³, Daron Standley², Kengo Kinoshita³ and Haruki Nakamura(²)
    ¹Japan Biological Information Research Center ²Institute for Protein Research, Osaka University ³Institute of Medical Science, University of Tokyo
17. Protein-Protein Docking using Steered Molecular Dynamics Simulations in Water
    Sandeep Pal, Graham R. Smith Protein-Protein Interactions Group Biosystems Informatics Institute Marlborough House, Marlborough Crescent Newcastle upon Tyne NE1 4EE, United Kingdom
18. 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
19. Accounting efficiently for global and local flexibility during systematic protein-protein docking
    Andreas May and Martin Zacharias, Jacobs University Bremen, Campus Ring 6, D-28759 Bremen
21. Title: Funnel hunting in a rough terrain: Learning and discriminating energy funnels
    Nir London & Ora Schueler-Furman
25. 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
29. Dockground integrated system of databases for protein docking, 2nd release
    Ying Gao, Dominique Douguet, Andrey Tovchigrechko, Ilya Vakser
33. Docking without Docking: Prediction of interactions using known interfaces
    Stefan Gunther¹ and Patrick May ^{2,3
    1} Institute for Molecular Biology and Bioinformatics, Charité University Medicine Berlin, Arnimallee 22, D-14195 Berlin stefan.guenther@charite.de
    ² Computer Science Research, Zuse Institute Berlin, Takustr. 9, D-14195 Berlin
    ³ Algorithmic Bioinformatics, Institute for Computer Science, Free University, Takustr.7, D-14195 Berlin patrick.may@zib.de
34. 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, London SW7 2AZ, UK m.sternberg@imperial.ac.uk
42. 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, Baltimore MD
45. An FFT-Based Protein Docking Program with Pairwise Potentials
    Dima Kozakov, Ryan Brenke, Stephen R. Comeau, and Sandor Vajda, Boston University
51. Performance of the ClusPro Server in CAPRI Rounds 6-11
    Stephen R. Comeau, Jr.^1,2 and Sandor Vajda^{1,3
    1}Bioinformatics Program, Boston University, Boston, MA
    ²Dyax Corp. Biotherapeutics, Cambridge, MA
    ³Department of Biomedical Engineering, Boston University, Boston, MA
53. The Performance of ZDOCK and ZRANK in Rounds 6-11 of CAPRI
    Kevin Wiehe1, Brian Pierce1, Wei Wei Tong², Howook Hwang1, Julian Mintseris¹, Zhiping Weng^{1,2
    1}Bioinformatics Program, Boston University, ² Department of Biomedical Engineering, Boston University

Poster Presentations:

2. Prediction and scoring of docking poses with pyDock.
   Solène Grosdidier, Carles Pons, Albert Solernou, Juan Fernández-Recio Life Sciences Department, Barcelona Supercomputing Center, Spain.
3. Modeling 3D structures of homo protein-protein complexes by structural homology and correlated mutations analysis
   P. Kundrotas and E. Alexov, Computational Biophysics and Bioinformatics,Department of Physics, Clemson University, SC 29634
4. Utilizing profile-to-profile alignment to predict 3D structures of protein-protein complexes
   Petras Kundrotas and Emil Alexov, Computational Biophysics and Bioinformatics Department of Physics, Clemson University,Clemson, SC 29634
5. Solvated docking: introducing water into the modelling of biomolecular interactions
   Alexandre M.J.J., Bonvin, Faculty of Science, Utrecht University, Padualaan 8,3584 CH Utrecht, The Netherlands E-Mail: a.m.j.j.bonvin@chem.uu.nl
6. Protein-protein docking studies of alpha-lytic protease with 2 inhibitors using ZDOCKpro
   Tina Yeh and Dana Haley-Vicente* Accelrys Inc., 10188 Telesis Ct., San Diego, CA 92121 E-Mail: dhv@accelrys.com
9. Docking prediction and structure selections by the EMPIRE scoring function in CAPRI Round 10 and 11*
   Shide Liang, Chi Zhang, Song Liu and Yaoqi Zhou Indiana University School of Informatics, IUPUI, and Center for Computational Biology and Bioinformatics, Indiana University School of medicine, 719 Indiana Ave. Suite 319, Indianapolis, IN 46202, USA.
14. On the Value of Biological Information in Docking Simulations
    Miriam Eisenstein, Noga Kowalsman and Avraham Ben-Shimon
16. QSAR/QSPR Models for Identification and Evaluation of Native Protein-Protein Interfaces
    ALEXANDER HEIFETZ AND GRAHAM R. SMITH, Protein-Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne, NE1 4EE, United Kingdom
20. The multi-copy approach of flexible docking: application to domain movements
    Adrien Saladin, Karine Bastard, Martin Zacharias, Chantal Prévost
    Laboratoire de Biochimie Théorique, CNRS UPR 9080, IBPC, 13 rue Pierre et Marie Curie, F-75005 Paris - Adrien.Saladin@ibpc.fr
22. RosettaDock in CAPRI 6-11: Success with computational mutagenesis and pitfalls with flexible backbones
    Aroop Sircar1, Arvind Sivasubramanian1, Sidhartha Chaudhury2, Monica Berrondo1, and Jeffrey J. Gray1,2 1Chemical and Biomolecular Engineering, 2Program in Molecular and Computational Biophysics, Johns Hopkins University, Baltimore, MD, USA
23. Flexible docking using multi-copy/mean field approaches
    Karine Bastard, Adrien Saladin and Chantal Prévost
24. Protein-protein docking using homology models
    Karine Bastard, Adrien Saladin, Julie Bernauer and Chantal Prévost
26. The Targets of CAPRI Rounds 6-12
    Joël Janin Yeast Structural Genomics, IBBMC, Université Paris-Sud, Orsay, France joel.janin@u-psud.fr
27. A scoring study and a new search scheme for protein-protein docking
    Cun-Xin Wang, Shan Chang, Xin-Qi Gong, Chun-Hua Li, Wei-Zu Chen
    College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
28. A new searching scheme in protein-protein docking prediction
    Cun-Xin Wang, Xin-Qi Gong, Shan Chang, Qing-Hua Zhang,
    Chun-Hua Li, Ming-Hui Wang, Wei-Zu Chen College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100022, China
30. Modeling Dimerizations of Transmembrane Proteins using Brownian Dynamics Simulations
    Meng Cui, Mihaly Mezei, Roman Osman Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU, Box 1218, New York, NY 10029, USA; E-mail: meng.cui@mssm.edu
31. Abstract title: Binding-Folding coupling: why folding instability has only a small effect on binding affinity
    Marta Bueno & Carlos J Camacho
32. ROTAFIT: Monte Carlo refinement of docking decoys using a smoothed potential
    Stephan Lorenzen, Yang Zhang
35. 3DGARDEN - A new docking protocol applied to targets 27 and 28 in CAPRI
    Victor Lesk and Michael J E SternbergCentre for Bioinformatics, Division of Molecular Bioscience, Imperial College London, London SW7 2AZ, UK, m.sternberg@imperial.ac.uk
36. Protein-Protein Docking: Experience in CAPRI using a Combination of Rigid-Body, Semi-Flexible and Fully Flexible Techniques
    Alexander Heifetz, Sandeep Pal and Graham R. Smith Protein-Protein Interactions Group Biosystems Informatics Institute Marlborough House, Marlborough Crescent Newcastle upon Tyne NE1 4EE, United Kingdom
37. Development of Methods for the Modelling, Docking and Affinity Assessment of Antibody-Antigen Complexes Alexander Heifetz, Sandeep Pal, Shane S. Sturrock, Philip H. McNeil and Graham R. Smith
    Protein-Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
38. GRAMM-X: Adapting to evolutionary pressure in CAPRI ecosystem
    Andrey Tovchigrechko, Anatoly Ruvinsky, Zhengwei Zhu, Ying Gao, Ilya Vakser
39. SKE-DOCK server and human teams based upon a combined method of shape complementarity and free energy estimation.
    Genki Terashi_$B"w_(B, Mayuko Takeda-Shitaka_$B"w_(B, Kazuhiko Kanou,Mitsuo Iwadate, Daisuke Takaya, Hideaki Umeyama*, School of Pharmacy, Kitasato University, Tokyo, Japan
40. Combining Voronoi-based coarse-grained statistics and atomic refinement: towards efficient multi-scale knowledge-based scoring functions
    Julie Bernauer, Joël Janin, Michael Levitt
41. Geometric packing potential function for model selection in protein structure and protein-protein binding predictions
    Xiang Li, Zheng Ouyang and Jie Liang, Department of Bioengineering, University of Illinois at Chicago
43. Molecular docking identifies a chemical function specifically binding to the S1 pocket of SARS-CoV Mpro
    Chunying Niu¹, Jiang Yin¹, Jianmin Zhang², John C. Vederas², Michael N. G. James^{1,3
    1} Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
    ²Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
    ³Alberta Synchrotron Institute, University of Alberta, Edmonton, AB, T6G 2E1
44. DESITE: a complete database of destabilising sites in proteins of known structure; indicating the location of potential binding sites.
    Marc F. Lensink, Benoît H. Dessailly, Shoshana J. Wodak
46. Refinement of rigid-body protein docking predictions using semi-definite underestimation
    Yang Shen, Pirooz Vakili, Ioannis Ch. Paschalidis, and Sandor Vajda, Boston University
47. Mapping the reaction pathway for protein association via domain swapping
    Anatoly Malevanets and Shoshana J. Wodak, Hospital for Sick Children, 555 University Ave. Toronto Ontario M5G 1X8, Canada
48. CAPRI Rounds 6-12: overview of prediction results
    Shoshana J. Wodak,², Marc Lensink ^2,4, Raúl Méndez ^{2,3
    1}Structural Biology Program, Hospital for Sick Children, 555 University Av. Toronto, Ontario M5G 1X8 Canada;
    ²Service de Conformation de Macromolécules Biologiques, et Bioinformatique, Centre de Biologie Structurale et Bioinformatique, CP 263, BC6, Université Libre de Bruxelles, Blvd du Triomphe, 1050 Bruxelles, BELGIUM,
    ³Grup Biomatemàtic de Recerca. Institut de Neurociències. Unitat de Bioestadística. Facultat de Medicina. Universitat Autonòma de Barcelona. 08193 Bellaterra, SPAIN.
49. The CAPRI Scorer experiment: what have we learned?
    Marc Lensink ^2,4 and Shoshana J. Wodak,^{1
    1}Structural Biology Program, Hospital for Sick Children, 555 University Av. Toronto, Ontario M5G 1X8 Canada;
    ²Service de Conformation de Macromolécules Biologiques, et Bioinformatique, Centre de Biologie Structurale et Bioinformatique, CP 263, BC6, Université Libre de Bruxelles, Blvd du Triomphe, 1050 Bruxelles, BELGIUM,
50. Using an ensemble approach in the refinement of an NMR derived structure accurately reproduces the internal dynamics without application of additional restraints.
    Mehdi Bagheri Hamaneh, Yufeng Tong, Sabine Bouguet-Bonnet and Matthias Buck
    Department of Physiology and Biophysics, Department of Neuroscience, & Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Ave., Cleveland, Ohio 44106, USA
52. A meta-docking approach for the in silico prediction of protein-protein complexes.
    Juan A. Padrón-Garcia1,^5*5, Tirso Pons^2,5*5, Danny J. Martínez³5, Leonardo Mokarzel-Falcón^1,4 and Luis A. Montero-Cabrera1
    ¹Laboratorio de Química Computacional y Teórica, Facultad de Química, Universidad de La Habana, Cuba.² Graduate program in Biochemistry, Facultad de Biología, Universidad de La Habana, Cuba.³ Centro de Estudio de Proteínas (CEP), Facultad de Biología, Universidad de La Habana, Cuba. ⁴ Departamento de Microbiología y Virología, Facultad de Biología, Universidad de La Habana, Cuba.