McCammon Group Meeting Archive

2004

Date Speaker Title
January 7 Yuhui Cheng
UCSD
Insight into Phosphoryl Transfer Mechanism of PKA with High Level ab initio QM/MM calculations and MD simulations
January 14 Richard Henchman
UCSD
Single Molecule Nanosimulation of the Alpha7 Nicotinic Receptor
January 21 Jessica Swanson
UCSD
Optimized radii for continuum solvent calculations; the importance of attentive parameters
January 28 Alex Perryman
UCSD
HIV Protease Drug Resistance
February 4 Dave Cerutti
UCSD
Rapid Approximations to Electrostatic Energy in Protein:Protein Association; Fitting Elephants with Unlimited, Unfounded Parameters
February 11 David Zhang
UCSD
Steered MD study of ligand unbinding in ha7-nAChR
February 18 - No Group Meeting
Biophysical Society Meeting
February 25 Jason Suen
UCSD
Adaptive finite element analysis in molecular electrostatics
March 3 Joanna Trylska
UCSD
1. Calcium binding to Cowpea Chlorotic Mottle Virus
2. Coarse-grained model of the ribosome: molecular dynamics simulations - preliminary tests
March 10 John Mongan
UCSD
Constant pH MD (reprise): Once more, with data
March 17 Julie Schames
UCSD
Further exploration into MMP Inhibitor Design
March 24 Richard Law
UCSD
A Model for Anesthetic Binding to Nicotinic AcetylCholine and GABA Receptors
March 31 - No Group Meeting
--ACS--
April 7 Sanjib Senapati
UCSD
Finite concentration effects on diffusion controlled reactions
April 14 - No Group Meeting
April 21 Cameron Mura
UCSD
Getting at the basis of indirect DNA readout by c-Rel and related proteins, Part I
April 28 Stewart Adcock
UCSD
I. A Quick Quick Introduction to the McWiki Wiki
II. Allineate: Rapid protein structure alignment
May 5 BenZhou Lu
UCSD
Structure and energetics of the C subunit of PKA during ADP release
May 12 - No Group Meeting
May 19 - No Group Meeting
May 26 Tongye Shen
UCSD
Conformation switch induced by multi-phosphorylation: a case study of NFAT regulatory domain
June 2 Justin Gullingsrud
UCSD
PKA; An open and closed case
June 9 BenZhou and Yuhui
UCSD
Joint meeting with Taylor Lab
PKA - From simulation to experiment and the path in between.
June 16 Donald Hamelberg
UCSD
Running all atom simulations as fast as real-time: Phosphorylation dependent cis/trans isomerization of proline and many more
June 23 Justin Gullingsrud
Richard Henchman
Jen Bui
Modified PB Chalk Talk
Converging Jarzynski...
Summary of the Biopolymer GRC
June 30 Jen Bui
UCSD
Cool Algorithms from the Snake Tamer's Lair
July 7 - No Group Meeting
July 14 Robert Konecny
UCSD
Viruses: don't open your email attachments!
July 21 Richard Henchman
UCSD
Bits and bobs of the nicotinic receptor
July 28 - No Group Meeting
July 31 LJCT Symposium La Jolla Computational Theory Symposium
9 am - 4 pm in NSB Auditorium
August 4 Dave Cerutti
UCSD
I. GRAPPLING with Free Energy Methodology in Flexible Protein Docking
II. A Cornucopia of Problems from the Immunoglobulin Superfamily Conference
August 11 - No Group Meeting
August 18 - No Group Meeting
Protein Society Meeting - SD,CA
August 25 David Zhang
UCSD
Rate constant calculations for tetrameric mAChE by solving the steady-state
Smoluchowski equation using finite element method
September 1 Kay Hamacher
UCSD
Evolution of Two-Component Signal Transduction: Darwinian Romps on Protein-Protein and Protein-Nucleic Acid Binding Energy Landscapes
September 8 Alex Perryman
UCSD
HIV Protease--Old Conclusions Receive New Support
September 15 John Mongan
UCSD
In Search of pH Driven Conformational Change:
Adjusting Hydrogen Bonding Strength in GB
September 22 Jie Liu
UCSD
Introduction to constructing yeast transcription networks
September 29 Joanna Trylska
UCSD
Assembly of the Small Ribosomal Subunit - An Implicit Solvent Approach
October 6 - No Group Meeting
October 13 Rich Law
UCSD
A gating mechanism proposed from a 15ns simulation of a complete human a7 nicotinic acetylcholine receptor model
October 20 Tushar Jain
UCSD
Configurational Bias-based Monte Carlo Methods
October 27 Bob White
UCSD
Pulling a Specificity Code up by the Bootstraps
November 3 Xiao-Lin Cheng
UCSD
Variant REM for Local Structure Refinement Simulations
November 8 Brooks,
Case,
& McCammon
Groups
Florence Tama (Brooks Lab): Mechanical properties of icosahedral viruses
Ross Walker (Case Lab): Refinements of the AMBER force field via the use of multi-dimensional parameter fitting
David Cerutti (McCammon Lab): Macromolecular Associations--Solvation, Motion, and Collossal Hubris
November 10 Joachim Dzubiella
UCSD
Water and Ion Permeation of Simple Hydrophobic Nanopores
November 17 Ben-Zhuo Lu
UCSD
An alternative PB solver: The Boundary Elementary Method
November 24 - No Group Meeting
December 1 Justin Gullingsrud
UCSD
Dynamic binding of PKA regulatory subunits
December 8 - No Group Meeting
December 15 Cameron Mura
UCSD
Investigation of the physical differences between some Rel proteins & some Sm-like stuff
December 22 - No Group Meeting
December 29 - No Group Meeting