MGMS'98 Talks and Posters

Sunday 6 December - evening keynote address

• Joachim Frank; The Ribosome: An Astounding Molecular Machine

Monday 7 December - morning session - Bootstrapping from Low Resolution Data/Bioinformatics

• Roger Burnett; Combining Information from X-ray Diffraction, Electron Microscopy, and Molecular Dynamics to Understand Virus Structure
• W. Wikoff. L. Liljas, R. Duda, R. Hendrix, J. Johnson; Crystal Structure of the Phage Hk97 Capsid Reveals a Structural Remodelling Mechanism Utilized During dsDNA Packaging
• W. Wriggers, R.A. Milligan, J.A. McCammon; Situs: A Pachage for the Docking of Protein Crystal Structures To Low-Resolution Maps From Electron Microscopy
• M.A. Canady, M. Tihova, T.N. Hanzlik, J.E. Johnson, M. Yeager; Electron Cryo-microscopy Combined with Molecular Modelling of an RNA Virus Assembly Intermediate Reveals a Change in the Geometry of the Particle
• J. Hirst; Functional Model Proteins and their Evolution
• T.A. Knoch, C. Munkel, J. Langowski; Three-Dimensional Organization of Chromosome Territories and the Human Interphase Cell Nucleus-Simulations Versus Experiments
• D. Goodsell; Escherichia Coli: From Atoms To Cells

Monday 7 December - afternoon session - General Methods and Collaborative Efforts

• Arthur Olson; Atoms-to-cells: Tools for Modelling and Visualizing Macromolecular Assemblies
• R.R. Gabdoulline, R.C. Wade, D. Walther; Using 2d Interface Maps To Navigate 3d Structures of Proteins
• R.E. Gillilan, R.H. Lilien, B.L. Atanacio, H.V. Shah; Tetramerization of Rxr: Dynamics of Molecular Assemblies at Atomic Resolution Using Rigid Hierarchical B-Splines
• J.A. Christopher, T.O. Baldwin; SPOCK: Real-time collaborative molecular modeling
• P. Bourne, P. Arzberger, G. Gilliand, P. Fagan, H. Berman, J. Westbrook: A New Macromolecuar Structure Database and its Impact on Molecular Modelling
• Kenneth Kelly: Clustering the Brookhaven Protein Databank Using Multiple-Sequence Structure-Based Alignment

Tuesday 8 December - morning session - Therapeutic Approaches

• Garland Marshall; Visualization of the Receptor-G-Protein Interface
• J.R. Blinn, D.C. Rohrer, G.M. Maggiora; Field-Based Similarity Forcing In Energy Minimization and Molecular Matching
• M.M. de las Alas, R.A.M. de Bruin, L. Ten Eyck, G. Los, S.B. Howell; Generating a Theoretical Model of the DNA Mismatch repair Protein hMSH2 using Prediction-based threading
• Z. Maslak, D.J. Steel, R.J. McDermott; A computer animation representing the molecular events of G Protein-coupled receptor activation
• Kal Ramnarayan; Accelerating Drug Discovery through Structural Bioinformatics Approach
• G.D. Purvis, T. Clark, J. Holland; Molecular Modeling In the Chemical Information Age
• C.R. Andrianjara, R. Wrigglesworth; An Application of Gasp To Reduce the Emesis Potential In the Pde4 Inhibitors

Wednesday 9 December - morning session - Multiphase Systems

• Jurg Rosenbusch; The Structure of Membrane Proteins: Fact and Fancy
• G. Zapata-Torres, G. Adams, D.J. Osguthorpe; Parameterising Simplified Potential Models for Membrane Protein Folding
• P. Herzyk, M. Afshar, L.S.D. Caves, R.E. Hubbard; Combined Biophysical and Biochemical Information Can Determine the Architecture of Transmembrane Domains of Helical, Integral Membrane Proteins
• Douglas Tobias; Atomistic Simulation of Lung Surfactants
• Y. Ueno & K. Asai; MOSBY: A Portable and Extendible Tool for Molecular Structure Browsing With Analysis
• B.P. Gaber; Space Time and Complexity in Biomembrane models

Wednesday 9 December - afternoon session - Crossing Time Scales

• Klaus Schulten; Manipulating Proteins by Steered Molecular Dynamics
• T.E. Cheatham, B.R. Brooks; Unbiased Forced Sampling of Complex Conformational Transitions
• X. Wu, S. Wang; Crossing the Time Scale of Protein Folding Through Self-Guided Molecular Dynamics Simulation
• H. Lu, K. Schulten; Steered Molecular Dynamics Study of Force-induced Domain Unfolding
• G.P. Tyrrell, L.S.D. Caves; Modeling Molecular Motor Mechanics: Structural Compliance In Myosin S1
• M.G. Wu, M.W. Deem; Optimized Monte Carlo Methods for Cyclic Peptides
• D.N. Chin, H.M. Chun; Efficiently Simulating Large Molecules Using Multibody Dynamics

Thursday 10 December - morning session - Design and Manipulation of Large Scale Systems

• M. Reza Ghadiri; Peptide Assemblies: from Nanotubes to Replicators
• M. Dougherty, W. Chui; Animation of Large Macromolecular Assemblies
• Russell Taylor; The nanoManipulator: Towards the Ideal Interface for Scanned-Probe Microscopes
• K. Eric Drexler; Simulating the Ultimate Technology

Poster Presentations

• J.D. Adcock, T.J. Minehardt, R.E. Wyatt; Visualization of the dynamics of energy flow in benzene
• E.G. Bartykov, S.M. Nikolaev, Y.A. Barnakov, B.B. Mitypov; The use of Se-cluster lattice doped into the chabazite as an antioxidant in the processes of catecholamine-induced myocardial necrosis.
• K. Butenof, J.L. Nauss, D.N. Chin, D. Haney; A Comparison of Ligand Unbinding From Native and Mutant HIV-1 Proteases Using Applied Force Simulations: Atomic Molecular Dynamics and Mbo(N)D Methods
• P. Contans, J.D. Hirst; Nonparametric Analysis and Design Of Heteropolymer Libraries
• J. Godden, F. Stahura, J. Bajorath; Protein-Ligand Docking Strategies and Scoring Functions
• P.H. Hasler, I. Novak-Hofer, P.A. Schubiger; Homology Modeling of the Ce7 Antibody Binding On Neuroblastoma Cancer Cells
• T. Herz, P. Gedeck, T. Clark; Nature's Diode: The energies and Natures of Negative ion states in alpha-helices
• A.D. Kovacs, B. Derecskei, Z.A. Schelly; Atomic Level Molecular Modelling of the Nonionic Surfactant Triton X-100: The OPE9 Component In Vacuum and Water
• P. Labute; Binary QSAR: A New Method for the Determination of Quantitative Structure-Activity Relationships
• F. Molnar, L.S. Norris, K. Schulten; Binding Mechanism of Arachidonic Acid In Prostaglandin H Synthase-1 Steered and Targeted Molecular Dynamics Simulations
• P. Natarajan, M. Tihova, A. Schneemann, M. Yeager, J.E. Johnson; Molecular Modeling of An Ellipsoidal Particle Formed In Vitro Due To Deletion of a Part of the Molecular Switch in a Spherical Insect Virus
• N. Nikbon, S.S. Mansori, H. Komeilizaheh, M. Mahmoudian; Study of the energy of Binding of D-THC Analogs to human Cannabinoid Receptor using Autodock Program
• T.H. Nyronen, A.M. Hoffren, T. Salminen, L. Laaksonen, M.S. Johnson; Receptor-Ligand complex models of Human Adrenergic receptor a2A-.
• L. Pasternack, D-H. Huang, W-Q, Wu, K.M. Koeller, O. Seitz, C-H. Wong; Sequence-Dependent Structural Features of An O-Linked Sialyl-Lewis-X Glycopeptide
• C. Qu, J. Speir, G. Wang, T. Baker, J. Johnson; Modeling of the native and swollen forms of cowpea chlorotic mottle virus based on cryo-electron microscopy data.
• M.S. Rao, I. Ghosh; Modeling and Binding of Moenomycin and Its Fragments To the Active Site of Transglycosylase Enzyme Model
• V.S. Reddy, R. Morton, C. Brooks, J. Johnson; Energetics of Protein-Protein Interactions and Assembly of Icosahedral Viruses
• T.A. Soares, D.S. Goodsell, A.J. Olson; Docking of 4-Oxalocrotonate tautomerase substrates: Implications for the catalytic Mechanism
• T. Tanaka, N. Miwa, S. Kawamura, H. Sohma, K. Nitta, N. Matsushima; Molecular Modeling of FROG P26OLF from S100B(beta beta)
• C.N. Yoon, S. Kim, M.W. Chi; Group Interaction Energy Descriptions In Qsar Study of Angiotensin-Converting Enzyme (Ace) Inhibitory Peptides
• Y. Zhou, M.E. Johnson; Specific H-Bond formation by 5-aminoindole provides S1 specificity for thrombin and factor Xa