| Afternoon Session |
Page |
| Protein Networks for Structural and Functional Protein Behavior by Robert Jernigan |
1 |
| Experimental and Computational Dynamics of Proteins in Crystals by George Phillips |
2 |
| Computational Analysis of the Assumptions Underlying Use of FRET as a Spectroscopic Rulerby Brent Krueger |
3 |
| An Automatic Method for Identifying Reaction Coordinates in Complex Systems by Ao Ma |
4 |
| Normal Mode Analysis of Domain Motions of S-Adenosylhomocysteine Hydrolase by Krzysztof Kuczera |
5 |
| Controlling Entropy: The Key to Protein Design by Garland Marshall |
6 |
| Computational Protocols for Functional Annotations of Proteins by Jarek Meller |
7 |
| A Framework for Globular Proteins by Jayanth Banavar |
8 |
| Recognizing Protein Folds by Cluster Distance Geometry by Gordon Crippen |
9 |
| Modeling Proteins in the Unfolded State by Karl Freed |
10 |
| Silico Folding of Small Proteins by Ulrich Hansmann |
11 |
| Structural Bioinformatics Prediction of Transcription Factors and Target Sites by Hui Lun |
12 |
| Interplay of Computation and Experiment in Studies of Microbial Pathogenesis: the Type II and Type III Secretion Mechanisms of Gram-negative Bacteria by William Wedemeyer |
13 |
| Morning Session |
Page |
| A Molecular Dynamics Study of Water Chain Formation in the Proton-Conducting K Channel of Cytochrome C Oxidase by Robert Cukier |
14 |
| Continuum Modelling of Biomolecular Electrostatics and Diffusion by Nathan Baker |
15 |
| Efficient Simulatio of Biomolecules with Implicit Solvent by Michael Feig |
16 |
| Properties of Polyunsaturated Lipids from MD Simulation by Scott Feller |
17 |
| The Iteratively Matched Interface (IMI) Fast Poisson Solver for the Prediction of Membrane Protein Structures by Guowei Wei |
18 |
| Toward Developing New Scoring Functions for Structure-Based Drug Design by Shaomeng Wang |
19 |
| Computer Simulation of the Pharmacophore Profiles for d-Opioid Receptor Selective Peptide Agonists by Paul Smith |
20 |
| A Hierarchical Model for Designing Protein Kinase Inhibitors by Chung Wong |
21 |
| Enrichment Enhancement in High Throughput Structure-based Virtual Screening through a Combination of FRED, ROCS, EON Scores and Naďve Bayesian Classification by Lakshmi Narasimhan |
22 |
| Catch Me If You Can: A New View of the Dynamical Mechanism of Protein-protein Recognition by Carlos Camacho |
23 |
| Protein Dynamics in the Catalysis by 6-Hydroxymethyl-7,8-dihydropterin Pyrophophokinase by Honggao Yan |
24 |
| Voxelized Protein Model for Fast Protein Docking and Function Prediction by Daisuke Kihara |
25 |
| Modeling Flexibility in Molecular Recognition by Maria Zavodszky |
26 |
| 1. |
Using Difference Refinement to Fit Myoglobin Coordinates from Time-resolved
X-ray Crystallographic Data by Aranda IV, Roman, Levin, Elena J. |
27 |
| 2. |
Using Low Complexity Regions for Target Selection in Structural Genomics by Bannen, Ryan M. |
28 |
| 3. |
Simulating Nucleic Acids: Comparison Between Explicit, Implicit
and Hybrid Solvation Models by Chocholoušová, Jana |
29 |
| 4. |
Folding Proteins by Constrained Minimization of a Statistical Potential
of Mean Force by Colubri, Andrés |
30 |
| 5. |
Effect of Sequence Length and Number of Taxa on Phylogeny
SimDB: The Simulation Database by Connelly, Brian |
31 |
| 6. |
A Model for Binding of Capping Protein to Barbed End of Actin by Ghosh, Shatadal |
32 |
| 7. |
Rapid Computational Prediction of the Substrates of cAMP-dependent
Protein Kinaseby Haenfler, Jill |
33 |
| 8. |
Molecular Dynamics Simulations of Phospholamban: Effects of Membrane,
Phosphorylation and Aggregation. by Houndonougbo, Yao |
34 |
| 9. |
Predisposition of the Three-Dimensional Dark State Structure of Rhodopsin for Functional Conformational Changes by Isin, Basak |
35 |
| 10. |
The “other half” of the Folded State of Proteins by Jha, Abhishek |
36 |
| 11. |
Identifying Favourable Candidate Molecules Using Statistical Physics by Jones, Andrew |
37 |
| 12. |
Finding Alternate Binding Conformations in Proteins: A Molecular Dynamics and
Docking Study of p38 MAP Kinase by Kesner, Tamara Frembgen |
38 |
| 13. |
Protein Structure-Sequence Alignment with a Reliability Measure by Kihara, Daisuke |
39 |
| 14. |
Mechanism of Control of Small Ligand Release in Nitrophorin and Myoglobin by Kondrashov, Dmitry A. |
40 |
| 15. |
Using Difference Refinement to Fit Myoglobin Coordinates from Time-resolved
X-ray Crystallographic Databy Levin, Elena and Aranda IV, Roman |
41 |
| 16. |
A Molecular Dynamics Free Energy Study of the Large-scale Motion of Adenylate Kinase by Lou, Hongfeng |
42 |
| 17. |
Application of Rough Set Theory to the Analysis of Chemically-Induced Gene Expression Patterns by Maggiora, Gerry |
43 |
| 18. |
Atomically Detailed Simulations of Concentrated Protein Solutions:
Capturing the Effects of pH, Ionic Strength and Point Mutations by McGuffee, Sean R. |
44 |
| 19. |
Binding of Dinitroanilines to a-Tubulin of Protozoan Parasites via Computational
Modeling by Mitra, Arpita |
45 |
| 20. |
Characterization of Internal and Global Dynamics of HIV-1 TAR RNA by
Molecular Dynamics and NMR by Musselman, Catherine |
46 |
| 21. |
An Efficient Iterative Cost-Bounded Branch-and-Bound Search Algorithm for
Solving Discrete Optimization Problems in Computational Biology by Namilikonda, Sandeep K |
47 |
| 22. |
Effect of Domain-domain Interactions on Src Family Tyrosine Kinase
Activation by Ozkirimli, Elif |
48 |
| 23. |
Structural Insights into Mechanism of Actin based Cell Motility Via Computational
Modeling by Rammohan, Aravind R. |
49 |
| 24. |
Rapid Computational Identification of the Targets of Protein Kinase Inhibit by Rockey, William M. |
50 |
| 25. |
Human Topoisomerase I Relaxes Positive and Negative DNA Supercoils Differently by Sari, Levent |
51 |
| 26. |
Molecular Dynamic Simulations of the Wild Type and Mutant (D25N) HIV Protease:
Insights into Enzyme Activity and Drug Resistance by Seibold, Steve A. |
52 |
| 27. |
A Multiscale Model for Actin Filaments by Sept, David |
53 |
| 28. |
Structural Determinants of Brugia malayi Asparaginyl tRNA Synthetase Affinity and
Specificity for Inhibitors Discovered by Structure-Based Screening by Sukuru, Sai Chetan K. |
54 |
| 29. |
Free Energy of G76 and the Mutants Rotation in Hepatitis Delta Virus
Ribozyme by Sun, Juan |
55 |
| 30. |
Replica Exchange Molecular Dynamics Simulations Coupled with the Heterogeneous
Dielectric Generalized Born Model: Helix Association by Tanizaki, Seiichiro |
56 |
| 31. |
Molecular Dynamics Simulations of Salt on Small Molecule Associations:
Effects on Electrostatic and Hydrophobic Interactions and Comparison with
Implicit Models by Thomas, Andrew S. |
57 |
| 32. |
Repetitive Pulling Catalyzes Co-Translocational Unfolding of Barnase During Import
Through a Mitochondria Pore by Tian, Pu |
58 |
| 33. |
New Developments in Empirical Scoring Function: X-Score Version 2005 by Wang, Renxiao |
59 |
| 34. |
The PDBbind Database: A PDB-Wide Collection of Protein-Ligand Binding Affinities by Wang, Renxiao |
60 |
| 35. |
Functional Importance of Protein Dynamics in Enthalpy-Entropy
Compensation by Ward, Joshua |
61 |
| 36. |
SoftScore: A New Knowledge-Based Potential Scoring Function by Inclusion of the
Mobility of Protein Atoms by Yang, Chao-Yie |
62 |
| 37. |
A Molecular Dynamics Exploration of Dihydroneopterin Aldolase and the Exit Path
of its Product-bound Form by Yao, Lishan |
63 |