McCammon Group Meeting Archive

2008

Date Speaker Title
January 2 - No Group Meeting
January 9 Donald Hamelberg Sampling slow conformational switches in proteins beyond the microsecond timescale
January 16 Ilja Khavrutskii Ion permeation through the KcsA selectivity filter demystified. A transition path ensemble study.
January 23 - No Group Meeting
January 30 - No Group Meeting
February 6 - No Group Meeting
February 13 Sergio Wong Computational alanine scanning of the Colicin E9 Dnase/Im9 interface
February 13 Dipesh Risal Accelrys Discovery Studio & Pipeline Pilot
February 18 Maciek Dlugosz Association of aminoglycosidic antibiotics with the ribosomal A-site. Brownian dynamics simulation
February 27 Barry Grant Ras Nucleotide Dependent Dynamics: Tips and tricks for probing nucleotide dependent conformations
March 5 - Cancelled
March 12 Ivalyo Ivanov The interplay of AAA+ machines and sliding clamps at the DNA replication fork
March 19 Tony Ivatec Molecular dynamics simulations and membrane protein structure quality
March 26 Zeyun Yu Multiscale Modeling of Calcium Dynamics in Ventricular Myocytes: from Imaging to Simulation
April 2 Rob Swift Domain Gating in the mRNA Capping Enzyme
April 9 Mickey Kosloff Deciphering function and specificity in G-protein signaling
April 16 Alemayehu Gorfe Abebe Mechanisms of allostery and membrane attachment in Ras signaling: New insights from computations
April 23 Arneh Babakhani Computational Modeling of Membrane-Protein Systems
April 30 Sarah Williams Study of the dynamics and inhibition of M. tuber DXR - an enzyme of the non-melavonate pathway
May 7 Adam Van Wynsberghe Investigation of Thrombin-Thrombomodulin Binding Kinetics Using Brownian Dynamics Simulations
May 14 Gory Ghosh Current thoughts on the mechanism of IkappaB Kinase activation
May 21 - No Group Meeting
May 28 Riccardo Baron O2 diffusion into flavoproteins
June 4 - No Group Meeting
June 11 Sanjib Senapati Reverse Micellar Self Assembly and Ligand-Induced Protein Motions: Insights from Molecular Dynamics Simulations
June 18 Yongcheng Zhou Continuum modeling of electrostatic induced macromolecular deformation
June 25 Gary Huber Brownian Dynamics and Software Engineering: Tricks and Ideas
July 2 Ben Zhou Lu AFMPB: nanoscale electrostatics on PC
July 9 Yuhui Cheng The way toward exploring the self cleavage reaction mechanism in ribozymes: ab initio QM/MM approach
July 16 - No Group Meeting
July 23 - No Group Meeting
July 30 Meghan Cain Evolving Ligands: A quest for Neuraminidase Inhibitors
August 8 - No Group Meeting
August 13 - No Group Meeting
August 20 Mikolai Fajer Accelerating Free Energy Calculations with Replica Exchange Accelerated Molecular Dynamics
August 27 Jacob Durrant Identifying Secondary Targets of Recently Discovered TbREL1 Inhibitors
September 3 Ilja Khavrutskii Molecular mechanics of ion permeation and selectivity in the cell
September 10 Phineus Markwick Studying diverse dynamic processes of bio-molecular systems in the virtual laboratory
September 17 Gustavo Seabra Semi-empirical Methods Applied to Biological Molecules
September 24 Rommie Amaro Comparative Dynamics of Avian- and Human-Type Influenza Neuraminidases: A Generalized Born Molecular Dynamics Study
October 1 Cesar Oliveira I) Design of MMP2 inhibitors: Including Receptor Flexibility and Induced fit-Effects into Drug Design.
II) Coupling Accelerated MD Methods with Thermodynamic Integration Simulations.
October 8 - No Group Meeting
October 15 Morgan Lawrenz Probing the Binding Free Energy for N1 Neuraminidase Inhibitor Peramivir
October 22 Barry Grant Probing Allosteric mechanisms in Ras: A nucleotide dependent role for loop3
October 29 James Halpert Conformational Flexibility and Heterogeneity of Cytochromes P450
November 5 Jeff Wereszczynski The Mechanism and Free Energy of Human Topoisomerase I
November 10 Tony Ivatec Conformational Dynamics of HIV-1 Reverse Transcriptase
November 19 - No Group Meeting
November 26 Rob Swift Population shifts, stochastic gating and substrate specificity in the PBCV-1 mRNA capping enzyme
December 3 Arneh Babakhani A Virtual Screening Study of the Acetylcholine Binding Protein Using a Relaxed-Complex Approach
December 10 Ivaylo Ivanov Specific recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loading
December 17 - No Group Meeting
December 24 - No Group Meeting