College of Liberal Arts & Sciences

2006 Seminars

2006 Fall Semester

Time: 3:00
Place: Conference Room at The Center for Bioinformatics (200 MRB)

9/5 Shiyong Liu (Vakser lab)
Protein-protein interface recognition and design
Note: time for only this seminar is 2:30

9/12 Jagtar Hunjan (Vakser lab)
Probing energy funnel in transient protein complexes

9/19 Sitao Wu (Zhang Lab)
Ab initio modeling of small proteins by iterative TASSER simulations

9/26 Ruvinsky/Vakser (Vakser lab)
Analysis of intermolecular energy landscape in protein-protein interactions

10/3 Thenmalar Ratinavelan (Im lab)
Towards de novo structure determination of biomacromolecules using
solely residual dipolar coupling

10/10 Zhengwei Zhu (Vakser lab)
GWIDD: A Genome-wide Docking Database

10/17 Luke Huan (EECS)
Graph-based pattern discovery in protein structures

10/24 No seminar

10/31 Andrey Tovchigrechko (Vakser lab)
Adapting intermolecular potentials to FFT correlation search

11/7 Stephan Lorenzen (Zhang Lab)
Refinement of docking decoys by Monte Carlo methods

11/14 Ying Gao (Vakser lab)
Database of Unbound structures from Protein-Protein
Co-crystal Structures

11/21 - no seminar

11/28 Jinhyuk Lee (Im lab)
Helix-helix restraint potentials

12/14 Wenjun Zheng (NHLBI, National Institutes of Health, Bethesda, MD)
Decrypting conformational dynamics in myosin motor with a coarse-grained elastic model
Time: 1:00
Location: Haworth Room 2031

2006 Spring Semester

January 26, Thu
4:00pm - 5:00pm, 6031 Haworth
Nilesh Banavali
Weill Medical College of Cornell Univesity, NY
Understanding Conformational Changes using Molecular Dynamics

February 2, Thu
3:30pm - 4:30pm, 1001 Malott
Margaret Shun Cheung
Institute for Physical Science and Technology, University of Maryland
Life in a Crowd: Macromolecular Crowding and Confinement Effects on Protein Interactions in Living Systems

February 6, Mon
3:30pm - 4:30pm, 1001 Malott
Jianhan Chen
Department of Molecular Biology, The Scripps Research Institute, CA
Folding Proteins from First-Principles

February 9, Thu
3:30pm - 4:30pm, 1001 Malott
Sandeep Patel
Department of Molecular Biology, The Scripps Research Institute, CA
Development and Applications of Polarizable Force Fields for Molecular Dynamics Simulations of Biological Molecules

February 15, Wed
3:30pm - 4:30pm, 1005 Malott
Gunasekaran Kannan
National Cancer Institute-NIH, MD
Conformational Flexibility and Function in Intrinsically Disordered and Ordered Proteins

February 20, Mon
3:30pm - 4:30pm, 6031 Haworth
Gennady Verkhivker
University of California at San Diego
Integrating bioinformatics, protein modeling and computational chemical genomics approaches in predicting protein kinases structure and binding with ligands and interacting proteins: Towards understanding the molecular basis of human disease and in silico drug discovery

April 28, Fri
3:00pm - 4:30pm, 1005 Haworth
Alex MacKerell
University of Maryland
Structure-function relationships of nucleic acids and protein-nucleic acid complexes studied via MD simulations

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