McCammon Group Meeting Archive


Date Speaker Title
January 3 Cesar Oliveira Catalytic Activity of the Serine Protease of Human Cytomegalovirus: A Theoretical Study
January 10 Eduard Mateescu Nutrition-induced Growth Regulation of the Bacterial Cell Cycle
January 17 Chia-En Chang Brownian Dynamics Simulations in a Coarse-Grained Model: Gated Binding of Ligands to HIV-1 Protease
January 24 - No Group Meeting
January 31 - No Group Meeting
February 7 Kay Hamacher Assembly of the smaller ribosomal subunit - reduced model computations
February 14 Joachim Dzubiella Coupling of nonpolar and polar solvation in implicit solvent models
February 21 Jennifer Bui Protein Binding Mechanism: Fast Conformational Transitions of Neurotoxin Fasciculin-2 upon binding to Acetylcholinesterase
February 28 Jie Liu Construction of Transcription Modules
March 7 Justin Gullingsrud Allosteric activation of protein kinase A
March 14 Xiao-Lin Cheng Molecular Dynamics Study of Channel Gating in Nicotinic Acetylcholine Receptors
March 21 - No Group Meeting
March 28 Donald Hamelberg Long-time protein dynamics and critical role of explicit hydration
April 5 Rommie Amaro Initial Structural and Functional Investigations of an RNA Editing Ligase: Progress Towards a Novel Pharmacophore Model
April 12 John Mongan Comparison of electric field approximations for calculation of effective Born radii
April 19 - No Group Meeting
April 26 Yuhui Cheng TFK+/TFK0 Binding Mechanism Study in Wild-type and H447I mutated mAChE
May 3 - No Group Meeting
May 10 Jessica MJ Swanson Characterizing biomolecular recognition and solvation with end-point free energy calculations and implicit solvent models
May 17 David Cerutti Estimating the Water Density Around Biomolecules (Where the Plot Thickens)
May 24 Cameron Mura Investigation of the differences between c-Rel and v-Rel
May 30 Zoe Cournia (Heidelberg) Molecular Dynamics Simulations and Neutron Scattering Calculations of Cholesterol and Biologically-important Sterols in Biomembranes
May 31 - No Group Meeting
June 7 - No Group Meeting
June 14 Benzhuo Lu An order N algorithm for computation of electrostatic interactions in biomolecular system and its application to diffusion process.
June 21 Jesper Sorensen Molecular Dynamics Simulations of Transthyretin - Free energy calculations providing insight into the amyloid fibril formation
June 28 Tongye Shen Phosphorylation and folding
July 5 David Minh The Proper Use of Quasiharmonic Analysis
July 12 Alemayehu Abebe Structure and dynamics of membrane-bound H-Ras protein
July 19 Ivaylo Ivanov Origins of Selectivity and Barriers to Ion Translocation in the Nicotinic Acetylcholine and Glycine Receptors
July 26 Barry Grant 1. An introduction to bio3d: Utilities for the analysis of protein structure and sequence data;2. Investigating the inhibition of a mitotic kinesin: An Eg5 monastrol study
August 2 Tushar Jain Predicting binding free-energy changes on mutation: Is restrictive sampling the answer?
August 9 Cesar Oliveira On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations
August 16 Eduard Mateescu Control of Growth and Replication in Bacteria: Parameter-free Models for the Role of Amino Acid Availability
August 23 Arneh Babakhani Cell Membrane and Trans-Membrane Protein Phenomena: A Computational Approach
August 30 Chia-En Chang Configurational Entropy and Binding Pathways: Ligands and HIV-1 Protease Binding Studies
September 6 Justin Gullingsrud MD investigations of SRPK1
September 13 - No Group Meeting
September 20 - No Group Meeting
September 27 Yong Zhao (Scripps) FLIPDock: a New Program for Docking Flexible Ligands into Flexible Receptors
October 4 - No Group Meeting
October 11 Donald Hamelberg Biological implications of phosphorylation-induced conformational changes
October 18 Rommie Amaro A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase
October 25 Dana Reichmann (Weizmann) Protein-Protein Interaction: Architecture and Design of Binding Sites
November 1 David Cerutti What Lies Between Implicit and Explicit Solvent, or There's so Much Water in this Talk That I had to Keep it Short
November 8 Cameron Mura Molecular Dynamics of a kB DNA Element
November 15 Xiaolin Cheng The fast multipole method for electrostatic calculations
November 22 Zeyun Yu 3D Electron Microscopy Imaging: Applications to Structural Elucidations of Large Bio-molecular Complexes
November 29 Ilja Khavrutskii Enhanced Harmonic Fourier Beads Method
December 6 Riccardo Baron Preliminary overview: relaxed complex method / allosteric binding / DNase (Thermo)dynamics / diffusion of macromolecular oxygen in flavoprotein
December 13 Gary Huber Generic Programming For Molecular Simulations
December 20 - No Group Meeting
December 27 - No Group Meeting