TABLE OF CONTENTS

TABLE OF CONTENTS

Page

Program

External Advisors

Advisory Committee Members

Talks - Saturday, April 30

Afternoon Session

Protein Networks for Structural and Functional Protein Behavior.............................................. 1

Robert Jernigan

Experimental and Computational Dynamics of Proteins in Crystals............................................ 2

George Phillips

Computational Analysis of the Assumptions Underlying Use of FRET as

a Spectroscopic Ruler................................................................................................................. 3

An Automatic Method for Identifying Reaction Coordinates in Complex Systems...................... 4

Normal Mode Anaysis of Domain Motions of S-adenosylhomocysteine Hydrolase................... 5

Krzysztof Kuczera

A Molecular Dynamics Study of Water Chain Formation in the Proton- Controlling Entropy:

The Key to Protein Design.......................................................................................................... 6

Garland Marshall

Computational Protocols for Functional Annotations of Proteins................................................ 7

A Framework for Globular Proteins........................................................................................... 8

Jayanth Banavar

Recognizing Protein Folds by Cluster Distance Geometry.......................................................... 9

Modeling Proteins in the Unfolded State................................................................................... 10

Silico Folding of Small Proteins............................................................................................... 11

Ulrich Hansmann

Structural Bioinformatics Prediction of Transcription Factors and Target Sites....................... 12

Interplay of Computation and Experiment in Studies of Microbial Pathogenesis: the

Type II and Type III Secretion Mechanisms of Gram-negative Bacteria............................. 13

William Wedemeyer

Conducting K Channel of Cytochrome C Oxidase..................................................................... 14

Continuum Modelling of Biomolecular Electrostatics and Diffusion........................................ 15

Efficient Simulation of Biomolecules with Implicit Solvent..................................................... 16

Properties of Polyunsaturated Lipids from MD Simulation....................................................... 17

The Iteratively Matched Interface (IMI) Fast Poisson Solver for the Prediction of

Membrane Protein Structures.............................................................................................. 18

Toward Developing New Scoring Functions for Structure-Based Drug Design....................... 19

Computer Simulation of the Pharmacophore Profiles for δ-Opioid Receptor Selective

Peptide Agonists................................................................................................................. 20

A Hierarchical Model for Designing Protein Kinase Inhibitors................................................ 21

Enrichment Enhancement in High Throughput Structure-based Virtual Screening through a

Combination of FRED, ROCS, EON Scores and Naïve Bayesian Classification............... 22

Lakshmi Narasimhan

Talks - Sunday, May 1

Morning Session

Catch Me If You Can: A New View of the Dynamical Mechanism of Protein-protein

Recognition......................................................................................................................... 23

Protein Dynamics in the Catalysis by 6-Hydroxymethyl-7,8-dihydropterin Pyrophophokinase. 24

Voxelized Protein Model for Fast Protein Docking and Function Prediction............................ 25

Modeling Flexibility in Molecular Recognition........................................................................ 26

Maria Zavodszky

Posters

1. Using Difference Refinement to Fit Myoglobin Coordinates from Time-resolved

X-ray Crystallographic Data ............................................................................................. 27

Aranda IV, Roman, Levin, Elena J.

2. Using Low Complexity Regions for Target Selection in Structural Genomics................... 28

Bannen, Ryan M.

3. Simulating Nucleic Acids: Comparison Between Explicit, Implicit

and Hybrid Solvation Models............................................................................................ 29

Chocholoušová, Jana

4. Folding Proteins by Constrained Minimization of a Statistical Potential

of Mean Force.................................................................................................................... 30

Colubri, Andrés

5. Effect of Sequence Length and Number of Taxa on Phylogeny

SimDB: The Simulation Database..................................................................................... 31

Connelly, Brian

6. A Model for Binding of Capping Protein to Barbed End of Actin...................................... 32

Ghosh, Shatadal

7. Rapid Computational Prediction of the Substrates of cAMP-dependent

Protein Kinase.................................................................................................................... 33

8. Molecular Dynamics Simulations of Phospholamban: Effects of Membrane,

Phosphorylation and Aggregation....................................................................................... 34

Houndonougbo, Yao

9. Predisposition of the Three-Dimensional Dark State Structure of Rhodopsin for

Functional Conformational Changes................................................................................... 35

10. The “other half” of the Folded State of Proteins................................................................. 36

11. Identifying Favourable Candidate Molecules Using Statistical Physics.............................. 37

12. Finding Alternate Binding Conformations in Proteins: A Molecular Dynamics and

Docking Study of p38 MAP Kinase.................................................................................... 38

Kesner, Tamara Frembgen

13. Protein Structure-Sequence Alignment with a Reliability Measure.................................... 39

Kihara, Daisuke

14. Mechanism of Control of Small Ligand Release in Nitrophorin and

Myoglobin.......................................................................................................................... 40

Kondrashov, Dmitry A.

15. Using Difference Refinement to Fit Myoglobin Coordinates from Time-resolved

X-ray Crystallographic Data.............................................................................................. 41

Levin, Elena and Aranda IV, Roman

16. A Molecular Dynamics Free Energy Study of the Large-scale Motion of Adenylate Kinase 42

17. Application of Rough Set Theory to the Analysis of Chemically-Induced Gene

Expression Patterns............................................................................................................ 43

Maggiora, Gerry

18. Atomically Detailed Simulations of Concentrated Protein Solutions:

Capturing the Effects of pH, Ionic Strength and Point Mutations........................................ 44

McGuffee, Sean R.

19. Binding of Dinitroanilines to a-Tubulin of Protozoan Parasites via Computational

Modeling............................................................................................................................ 45

20. Characterization of Internal and Global Dynamics of HIV-1 TAR RNA by

Molecular Dynamics and NMR.......................................................................................... 46

Musselman, Catherine

21. An Efficient Iterative Cost-Bounded Branch-and-Bound Search Algorithm for

Solving Discrete Optimization Problems in Computational Biology

Namilikonda, Sandeep K............................................................................................... 47

22. Effect of Domain-domain Interactions on Src Family Tyrosine Kinase

Activation........................................................................................................................... 48

Ozkirimli, Elif

23. Structural Insights into Mechanism of Actin based Cell Motility Via Computational

Modeling............................................................................................................................ 49

Rammohan, Aravind R.

24. Rapid Computational Identification of the Targets of Protein Kinase Inhibit...................... 50

Rockey, William M.

25. Human Topoisomerase I Relaxes Positive and Negative DNA Supercoils Differently....... 51

26. Molecular Dynamic Simulations of the Wild Type and Mutant (D25N) HIV Protease:

Insights into Enzyme Activity and Drug Resistance............................................................. 52

Seibold, Steve A.

27. A Multiscale Model for Actin Filaments............................................................................. 53

28. Structural Determinants of Brugia malayi Asparaginyl tRNA Synthetase Affinity and

Specificity for Inhibitors Discovered by Structure-Based Screening.................................. 54

Sukuru, Sai Chetan K.

29. Free Energy of G76 and the Mutants Rotation in Hepatitis Delta Virus

Ribozyme............................................................................................................................ 55

30. Replica Exchange Molecular Dynamics Simulations Coupled with the Heterogeneous

Dielectric Generalized Born Model: Helix Association.................................................... 56

Tanizaki, Seiichiro

31. Molecular Dynamics Simulations of Salt on Small Molecule Associations:

Effects on Electrostatic and Hydrophobic Interactions and Comparison with

Implicit Models................................................................................................................... 57

Thomas, Andrew S.

32. Repetitive Pulling Catalyzes Co-Translocational Unfolding of Barnase During Import

Through a Mitochondria Pore.............................................................................................. 58

33. New Developments in Empirical Scoring Function: X-Score Version 2005...................... 59

34. The PDBbind Database: A PDB-Wide Collection of Protein-Ligand Binding Affinities... 60

35. Functional Importance of Protein Dynamics in Enthalpy-Entropy

Compensation................................................................................................................ 61

36. SoftScore: A New Knowledge-Based Potential Scoring Function by Inclusion of the

Mobility of Protein Atoms................................................................................................... 62

37. A Molecular Dynamics Exploration of Dihydroneopterin Aldolase and the Exit Path

of its Product-bound Form................................................................................................... 63

Participant List........................................................................................................................ 64