Mini-Symposium on Computational Approaches on May 8th

Wednesday May 8th 2013, 9:00 AM to 5:00 PM
Gordon Center for Integrative Science, room W301/303
University of Chicago (directions)

Note: the Computational Modeling Core is also hosting a workshop specifically dedicated to membrane protein modeling at the University of Chicago on May 7th. Click here to learn more and register »

Force field and atomic models

9:00 Lei Huang: Advances in automatic force field optimization
9:15 Christopher Mayne: Force Field Toolkit (FFTK)
9:30 Sunhwan Jo: Recent developments in CHARMM-GUI and CHARMM-GUI Membrane Builder
9:45 Wei Han: Further development of a mixed all-atom/united-atom models for simulation of peptide folding, aggregation and proteins in membrane
10:00 George Khelashvili: Protein-membrane coupling and the calculation of the bending rigidity of multi-component lipid membranes
10:15 Brigitte Ziervogel: Simulation of membrane systems with asymmetrical conditions
10:30 Josh Vermaas: Developing novel in silico solvents with optimized properties mimicking membrane models
10:45 Break
11:00 Niklaus Johner: Membrane proteins in the cubic phase lipid environment – insights into in meso crystallization environments
11:15 Yifei Qi: Quantifying the Drive-Response Relationships between Residues in Protein Folding

Structural modeling with low-resolution data

11:30 Aashish Adhikari: LBT loop modeling protocols
11:45 Shahid Islam: Structural refinement using ESR/DEER histogram data
12:00 Fatemeh Khalili: Structural refinement using low-resolution LRET data
12:15 Lunch
1:30 Huan Rui: Probing Human Growth Hormone Receptor Structure Using Computational Simulations and NMR spectroscopy
1:45 Abhishek Singharoy: xMDFF – Molecular Dynamics Flexible Fitting of Low Resolution X-ray Structures
2:00 Hang Yu: Membrane Sculpting by F-BAR Domains by Molecular Dynamics Simulation

Transition pathways

2:15 Avisek Das: A simple method to determine conformational transition pathways based on a two-state anisotropic elastic network model
2:30 Mert Gur: Global Motions of Proteins Observed in Micro- to Milliseconds Simulations Concur with Anisotropic Network Model Predictions
2:45 Wen Ma: Study of conformational transitions of hexameric motors using the string method
3:00 Break
3:15 Mahmoud Moradi: Application of collective variables to describe large-scale conformational changes of membrane transporters
3:30 Zhe Wu: A New Hypothesis for the Mechanism of Synaptotagmin I in Synaptic Neurotransmitter Release
3:45 Po-Chao Wen: The impact of the lipid environment on gating of KcsA


4:00 Josh Carr: Introduction to computational analysis of 2D-IR spectroscopy


4:15 Roundtable discussion

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