McCammon Group Meeting Archive

2005

Date Speaker Title
January 5 Yuhui Cheng
UCSD
Synapse Modeling with Finite Element Method
January 12 Jennifer Bui
UCSD
Conformational Transitions of Flexible Protein upon Protein-Protein Binding Interactions
January 19 Lou Noodleman
UCSD
Quantum Chemical Studies of the Photocycle and Spectral Tuning in Photoactive Yellow Protein
January 26 - No Group Meeting
February 2 Donald Hamelberg
UCSD
Relating local energy landscape roughness and kinetic rates
February 9 Sanjib Senapati
UCSD
Acetylcholinesterase in a Unique Conformation
February 16 - No Group Meeting
February 23 John Mongan
UCSD
Generalized Born Beyond the van der Waals Surface: The Neck Correction
March 2 Jessica MJ Swanson
UCSD
Bridging Explicit and Implicit Solvation Models
March 9 David Cerutti
UCSD
GRAPPLE 2.0: Swiftius, Altius, Fortius
March 16 - No Group Meeting
March 23 Ivaylo Ivanov
UCSD
Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all atom molecular dynamics.
March 31 Dave Zhang
UCSD
Activation mechanism of nicotinic acetylcholine receptor revealed by ligand unbinding
April 6 Barry Grant
UCSD
Stripping Down the Kinesin Molecular Motor
April 13 Kay Hamacher
UCSD
Computation of amino-acid specific fluctuations - application to HIV1-Protease
April 20 Tushar Jain
UCSD
Principal Component Analysis: Searching for Conformational Population
April 27 - No Group Meeting
May 4 Alex Perryman
UCSD
Computer-Assisted Protein Structure Studies: Hunting Down the Hidden Secrets of HIV
May 11 Xiao-Lin Cheng
UCSD
Channel opening motion of alpha7 nAChR as suggested by normal mode analysis
May 18 Chia-En Chang
UCSD
1. HIV-1 protease internal motion and ligand encounter: Brownian dynamics in a coarse-grained model
2. The missing term in protein-ligand docking
May 25 Joachim Dzubiella
UCSD
Classical (dynamic) Density Functional Theory: any use for Biochemistry?
June 1 Jie Liu
UCSD
Discover dynamically the transcriptional regulatory network
June 8 Anushka Michailova and Kathy Lu
UCSD
3D model of synchronous calcium signals in ventricular myocyte
June 15 Ben-zhuo Lu
UCSD
Calculation of PB force on solvated molecule in boundary element method frame
June 22 Justin Gullingsrud
UCSD
All-atom and coarse-grained molecular dynamics studies of protein kinase A regulation
June 29 - No Group Meeting
July 6 - No Group Meeting
July 13 - No Group Meeting
July 20 Cameron Mura
UCSD
3D models of fibrillar Hfq and other Sm-like proteins
July 27 Donald Hamelberg
UCSD
Role of flexibility in the proteolytic machinery of HIV-1
August 3 William McLaughlin
UCSD
Transgressing the Scales: Predictions of Protein Interaction Partners with Help from MM/PBSA
August 10
I
Jingfang Huang
UNC Chapel Hill
A New Version of Fast Multipole Method for Screened Coulomb Interactions in Three Dimensions
August 10
II
Kevin Litchfield
UCSD
MD studies on the Barnase-Barstar System: Testing the Transferability and Convergence of Free Energy Estimates using MM-PBSA.
August 17 - No Group Meeting
August 24
I
Stuart E. Murdock
U Southampton
BioSimGrid, An Environent to Archive and Analyse Biosimulation Data
August 24
II
Steven Johnston
U Southampton
Data management in BioSimGrid
August 31 David Minh
UCSD
1. A Smattering of X-Ray Scattering
2. External Entropy Loss Upon Protein-Protein Binding
September 7 John Mongan
UCSD
The Wonderful World of Generalized Born
September 14 Xiyun Zhang
UCSD
Free Energies of TS Binding and the Origins of Enzyme Catalysis
September 20 Sanjib Senapati
UCSD
Why is the syn-isomer of TZ2PA6 the sole product in AChE environment?
September 27 David Cerutti
UCSD
Making Predictions within the MM-PBSA Framework
October 4 Alemayehu Abebe
UCSD
Dynamics of an Enzyme and a Peptide-DMPC Complex
October 11 Tongye Shen
UCSD
Elasticity of Biomolecules
October 18 - No group meeting
October 25 Yuhui Cheng
UCSD
Analysis of Synaptic Transmission in the Neuromuscular Junction
November 1 Jessica MJ Swanson
UCSD
Exploring Implicit Solvation Models
November 8 David Zhang
UCSD
Potenitals of mean force for ACh unbinding from alpha7 nAChR ligand-binding domain
November 15 Benzhuo Lu
UCSD
On the energy analysis of the dynamics of the catalytic subunit of PKA
November 22 Ivaylo Ivanov
UCSD
Dynamics of Proliferating Cell Nuclear Antigen
November 29 Barry Grant
UCSD
1. Comparative analysis of homologous protein structures
2. Phosphate release in Myosin: forcing the backdoor
December 6 - No Group Meeting
December 13 Tushar Jain
UCSD
Configurational-Bias Sampling for Predicting Side-chain Conformations in Proteins
December 20 - No group meeting
December 27 - No group meeting