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Please, note the location for each seminar, as it may be different from one event to another.
We welcome prospective speakers. If you want to become a speaker at the Seminar, please, e-mail or call one of the organizing committee members from the Contact page.
-
2008 Spring Semester
5/20 Dr. Eugene Krissinel (Senior Technical Officer, European Bioinformatics Institute)
PISA, or a story about perceptions, expectations, naivety, macromolecular complexes and their complexity in bioinformatics and crystallography
Time: 11:00 am
Location: MRB 200 Conference Room
keb@ebi.ac.uk
5/6 Dr. Jie Liang (Department of Bioengineering, University of Illinois at Chicago)
Detecting geometric pattern and evolutionary signal from protein structure for understanding biological functions and predicting protein-protein interaction surfaces
Time: 11:00 am
Location: MRB 200 Conference Room
jliang@uic.edu
4/29 Dr. Alexander Tropsha (Professor and Chair, The Laboratory for Molecular Modeling, Division for Medicinal Chemistry & Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill)
Protein Comparison: From New Methods to Unexpected Discoveries
Time: 11:00 am
Location: MRB 200 Conference Room
alex_tropsha@unc.edu
4/22 Dr. Nick Grishin (Department of Biochemistry, University of Texas Southwestern Medical Center)
Protein Comparison: From New Methods to Unexpected Discoveries
Time: 11:00 am
Location: MRB 200 Conference Room
grishin@chop.swmed.edu
4/8 Dr. Michael Gilson (Center for Advanced Research in Biotechnology, University of Maryland)
Entropy, Affinity and the Design of Targeted Molecules
Time: 11:00 am
Location: MRB 200 Conference Room
gilson@umbi.umd.edu
3/13 Dr. Scott Christley (Department of Computer Science and Engineering, University of Notre Dame)
Vertebrate Limb Chondrogenesis and Invertebrate Comparative Genomics
Time: 2:00 - 3:15 pm
Location: Nichols Hall Apollo Room
schristl@nd.edu
3/11 Dr. Zhi Wei (Genomics and Comp. Bio. Graduate Group, Univ. of Penn. School of Medicine)
Markov Random Field Models for Network-Based Analysis of Genomic Data
Time: 2:00 - 3:15 pm
Location: Nichols Hall Apollo Room
zhiwei04@gmail.com
2/20 Dr. Phillip Bourne (University of California, San Diego)
What Does Evolution Tell Us About Drug Discovery?
Time: 1:30 pm
Location: MRB 200 Conference Room
bourne@ucsd.edu
2/5 Petras Kundrotas (University of Kansas)
Sequence-homology based approach in modeling of protein-protein interactions
Time: 11:00 am
Location: MRB 200 Conference Room
pkundro@ku.edu
1/31 Iddo Friedberg (University of California, San Diego)
New Challenges for Structural Bioinformatics: Towards a Better Understanding of Structure and Function Space
Time: 2:30 pm
Location: 2023 Haworth
idoerg@gmail.com
1/29 Dr. Jeffry D Madura (Duquesne University)
Simulations of LeuT and DAT Transporters
Time: 11:00 am
Location: MRB 200 Conference Room
madura@duq.edu
1/24 John Karanicolas (University of Washington)
Design of de novo protein-protein interfaces
Time: 2:30 pm
Location: 2023 Haworth
johnk4@u.washington.edu
1/17 Natarajan Kannan (University of California, San Diego)
Evolutionary Clues to Protein Kinase Regulatory Mechanisms
Time: 2:30 pm
Location: 2023 Haworth
2007 Fall Semester
12/11 Dr. Jooyong Lee (Korea Institute for Advanced Study)
High Accuracy Protein Structure Prediction by Global Optimization
Time: 11:00 am
Location: MRB 200 Conference Room
jlee@kias.re.kr
11/13 Dr. Nathan Baker (Washington University in St. Louis)
Assessing the performance of Poisson-Boltzmann continuum solvation models
Time: 11:00 am
Location: MRB 200 Conference Room
baker@ccb.wustl.edu
10/30 Dr. Qiang Cui (The University of Wisconsin-Madison)
Mechanochemical coupling in Molecular Motors: insights from molecular simulations at multiple scales
Time: 11:00 am
Location: MRB 200 Conference Room
cui@chem.wisc.edu
10/23 Dr. Arcady Mushegian (The University of Kansas School of Medicine, Stowers Institute for Medical Research)
Evolutionary history of bacteriophages with double-stranded DNA genomes
Time: 11:00 am
Location: MRB 200 Conference Room
arm@stowers-institute.org
10/09 Dr. Ram Samudrala (University of Washington)
Modeling Interactomes
Time: 2:00 pm
Location: MRB 200
ram@compbio.washington.edu
09/25 Dr. Krzysztof Kuczera (University of Kansas)
Domain motions in a tetrameric enzyme: modeling and experimental studies
Time: 2:00 pm
Location: MRB Conference Room
kkuczera@ku.edu
09/18 Dr. Jianwen Fang (University of Kansas)
Bioinformatics of Polyanion Binding Proteins
Time: 2:00 pm
Location: MRB Conference Room
jwfang@ku.edu
8/23 Dr. Marta Sales (Northwestern University)
Topology and Dynamics of Complex Biological Systems
Time: 11:00
Location: MRB 200
msales@northwestern.edu
8/7 Dr. Petras Kundrotas (Clemson University)
Predicting 3D structure of protein-protein complexes
Time: 11:00
Location: MRB 200
pkundro@clemson.edu
2007 Spring Semester
1/11 Leonor Saiz (Computational Biology Center at Memorial Sloan-Kettering Cancer Center, New York, NY)
Multilevel Modeling of Biological Processes: From Molecular Interactions at the Cell Membrane to the Dynamics of Gene Regulation Networks
Time: 2:00
Location: Haworth Room 2031
leonor@cbio.mskcc.org
1/17 Maricel Kann (NIH/NLM/NCBI)
Bioinformatics of protein domains: new computational approaches for the detection of protein domains and their interactions
Time: 2:00
Location: Haworth Room 2023
kann@ncbi.nlm.nih.gov
1/25 Min-yi Shen (Dept of Biopharmaceutical Sciences, UCSF)
High-Accuracy Modeling of Protein Structures
Time: 11:00
Location: MRB 100C
smy@salilab.org
2/13 Shailesh Date (Dept. of Genetics, University of Pennsylvania School of Medicine)
Computational modeling of interactomes: Tools, techniques and application to genomes of apicomplexan parasites
Time: 11:00
Location: 2001 Mallott
svdate@pcbi.upenn.edu
2/15 Huiying Li (UCLA-DOE Institute for Genomics and Proteomics)
From genome to gene expression: Understanding protein interactions and host-pathogen interactions
Time: 12:00
Location: 2001 Mallott
huiying@mbi.ucla.edu
2/22 Ester Lo (The University of Tulsa)
Influence of Meteorological Conditions on Early Spring Pollen in the Tulsa Atmosphere from 1987 to 2006
Time: 11:00
Location: MRB Conference Room
esther-lo@utulsa.edu
2/22 Craig Helstowski (The University of Connecticut)
Profiling Phylogenetic Informativeness in Angiosperms Amborella and Nymphaeales
Time: 11:45
Location: MRB Conference Room
craig.helstowski@uconn.edu
2/22 Dr. David Mobley (University of California San Francisco)
Challenges in predicting ligand binding free energies in a model binding site
Time: 3:00
Location: 2100 Mallott
dmobley@gmail.com
3/7 Dr. Jimin Pei (University of Texas Southwestern Medical Center)
Challenges in predicting ligand binding free energies in a model binding site
Time: 2:00
Location: 2100 Mallott
jpei@chop.swmed.edu
4/24 Toby Allen (University of California, Davis)
The energetics of arginine-lipid interactions with implications for ion channel gating
Time: 3:00
Location: MRB Conference Room
twallen@ucdavis.edu
5/01 Ioan Andricioaei (University of Michigan)
On the Force Dependence of Biomolecular Conformational Kinetics
Time: 11:00
Location: MRB Conference Room
andricio@umich.edu
2006 Fall Semester
Time: 3:00
Place: Conference Room at 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
liushiyong@gmail.com
9/12 Jagtar Hunjan (Vakser lab)
Probing energy funnel in transient protein complexes
jagtar@ku.edu
9/19 Sitao Wu (Zhang Lab)
Ab initio modeling of small proteins by iterative TASSER simulations
stwu@ku.edu
9/26 Ruvinsky/Vakser (Vakser lab)
Analysis of intermolecular energy landscape in protein-protein interactions
ruvinsky@ku.edu
10/3 Thenmalar Ratinavelan (Im lab)
Towards de novo structure determination of biomacromolecules using
solely residual dipolar coupling
thenmcr@ku.edu
10/10 Zhengwei Zhu (Vakser lab)
GWIDD: A Genome-wide Docking Database
zzhu@ku.edu
10/17 Luke Huan (EECS)
Graph-based pattern discovery in protein structures
jhuan@eecs.ku.edu
10/24 No seminar
10/31 Andrey Tovchigrechko (Vakser lab)
Adapting intermolecular potentials to FFT correlation search
andrey@ku.edu
11/7 Stephan Lorenzen (Zhang Lab)
Refinement of docking decoys by Monte Carlo methods
stephlo@ku.edu
11/14 Ying Gao (Vakser lab)
Database of Unbound structures from Protein-Protein
Co-crystal Structures
ygao1@ku.edu
11/21 - no seminar
11/28 Jinhyuk Lee (Im lab)
Helix-helix restraint potentials
jinhyuk@ku.edu
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
2005 Fall Semester
- August 31, Wed
11:00am - 12:00am, Pine Room, Kansas Union
James Lu
Lawrence Berkeley National Lab, Berkeley, CA
When Visual Simulation meets Computational Biology - September 21, Wed
10:00am - 11:00am, Pine Room, Kansas Union
Ping Yang
Michigan Technological University
Intramolecular Hydrogen Bonding Network in myo-inositol phosphates and Surface Passivation of Quantum Dots - November 11, Fri
3:30pm - 4:30pm, Alcove F, Level 3 of the Kansas Union
Matthew Miller
University of Missouri, Kansas City
Quantum Mechanical Methods for Prediction of Thermodynamic Properties and QSAR Modeling - November 23, Wed
9:00am - 10:00am, International Room, Kansas Union
Alexander Rubinstein
Eppley Institute for Research in Cancer and Allied Diseases and Department of Pharmaceutical Science, College of Pharmacy, University of Nebraska Medical Center, Omaha
Non-local electrostatic effects at the protein-solvent interface within macroscopic continuum model - December 2, Fri
10:00am - 11:00am, Regionalist Room, Kansas Union
Dennis Law
San Diego Supercomputer Center, CA
Combining Experimental Information and Computational Methods to Produce Testable Models for Protein Complexes - December 22, Thu
11:00am - 12:0pm, International Room, Kansas Union
Anatoly Ruvinsky
Center for Bioinformatics, The University of Kansas
A novel statistical-thermodynamic method for computation of the protein-ligand association entropy: the profound consequences for docking accuracy
2005 Spring Semester
- May 4, Wed
1:30pm - 2:30pm, Apollo Room, Nichols Hall
Daniel Fischer
University of Buffalo
Unraveling the puzzle of genomic ORFans - May 23, Mon
4:00pm - 5:00pm, rm 1005, Haworth Hall
Hui Lu
University of Illinois Chicago
Structural Bioinformatics Prediction of Protein-DNA interactions - June 21, Tue
10:00am - 11:00am, rm 2046, Haworth Hall
Vitaly Khutorsky
Larial Proteomics Inc., Toronto
Structure Activity Relationships (SAR) of Membrane Bound Compounds and Complexes - June 22, Wed
10:00am - 11:00am, rm 2046, Haworth Hall
Ying Gao
Purdue University, Indiana
Protein-protein interfaces and drug design
- January 26, Thu
