W O R K S H O P

 

“Molecular-to-Cellular Modeling of Complex Biological Processes”

February 3, 2004

Mellon Institute Auditorium (2nd floor)

9 am - 4.30 pm
(pdf announcement)

 

The goal of this workshop is to jump-start the pre-Center’s goals by bringing together the experimental and computational communities, presenting the types of existing problems that could benefit from collaboration between the computational and experimental groups, discussing data, methods, and tools that different groups can provide, and so on. While we have identified three developmental projects in our proposal, the discussions will not be solely limited to these projects, and we invite all members of the community to join us in our discussions. Speakers would bring to the attention of the participants their current research problems/questions with emphasis on issues that may possibly benefit from cross-disciplinary interaction.

 

TIME

TOPIC, SPEAKER

   
9 – 9.15 am

Introduction
Dr. Ivet Bahar (CCBB, Pitt)
Dr. Joel Stiles (PSC/CMU)

   
9.15 - 10.15 am SESSION I
Nitric Oxide and Apoptosis
Dr. Yoram Vodovotz (Surgery, UPMC)
Dr. G. Bard Ermentrout (Math, Pitt)
9.15 – 9.25 am Dr. Yoram Vodovotz (Surgery, UPMC)
Nitric oxide and apoptosis
9.25 – 9.35 am Dr. G. Bard Ermentrout (Math, Pitt)
Modeling NO and apoptosis: theory and strategy
9.35 – 10.00 am  E. Zerrin Bagci (CCBB, Pitt)
Nitric oxide and apoptosis
10.00 – 10.15 am Discussion
10.15 – 11.15 am Session II
DNA Damage Recognition and Signaling
Dr. Richard Wood (UPCI and Pharmacology, Pitt)
Dr. Ivet Bahar (CCBB, PItt)
10.15 – 10.25 am Dr. Richard Wood (UPCI and Pharmacology, Pitt)

Function & mechanism of DDB: a protein from human cells that recognizes DNA damage

10.25 – 10.35 am Dr. John Rosenberg (Biol Sci, Pitt)
10.35 – 10.45 am Dr. Vesna Rapic-Otrin (MGB, Pitt)
From UV-DDB to Cullin-Containing Ubiquitin Ligase
10.45 – 10.55 am Discussion
10.55 – 11.15 am Dr. Baskaran Rajasekaran (MGB, Pitt)
11.15 am – 12.15 pm SESSION III
Signaling Ligands and Cascades
Dr. John Lazo (Pharmacology, Pitt)
Dr. Daniel Zuckerman
(CCBB, Pitt)
11.15 –  11.25 am Dr. John Lazo (Pharmacology, Pitt)
Modeling ligand interactions with signaling molecules
11.25 –  11.35 am Dr. Daniel Zuckerman (CCBB, Pitt)
Docking and binding computations: an overview
11.45 – 11.55 am Dr. Donald DeFranco (Pharmacology, Pitt)

Opposing roles of MAPK and Akt signaling pathways on 

neuronal cell survival: importance of temporal and spatial  parameters

11.55 am –  12.05 pm Dr. Dror Tobi (CCBB, Pitt)
CDC25A / NSC663284 docking model
12.05 pm – 12.15 pm Dr. Billy Day (Pharmaceutical Sciences, Pitt)
Proteomics as a tool in drug discovery
12.30 – 1.30 pm LUNCH (Mellon Institute Social Room)
1.30 – 2.30 pm SESSION IV
Integration Session (Multiscale Modeling)

Dr. Joel Stiles (PSC/CMU)
Dr. Jeffry Madura (Chem-Biochem, Duquesne)
1.30 - 1.45 pm Dr. Jeffrey Evanseck (Chem-Biochem, Duquesne) (Molecular)
1.45 - 2.00 pm Dr. Joel Stiles (PSC/CMU) (Subcellular)
Molecular-to-cellular modeling of complex biological processes
2.00 - 2.15 pm Dr. Shlomo Ta'asan (Math, CMU) (Cellular)
A framework for multiscale modeling  of biological systems
2.15 - 2.30 pm Panel Discussion
2.30 – 3.30 pm SESSION V
Other Projects

(membranes, signal transduction, hemoglobin)
Dr. Michael Cascio (MGB, Pitt)
Dr. Rob Coalson (Chem, Phys, Pitt)
2.30 – 2.40 pm Dr. Roni Rosenfeld (CS/LTI, CMU)

Inferring property selection pressure from positional residue  conservation

2.40 – 2.50 pm Dr. Michael Cascio (MGB, Pitt)
Nicotinicoid Ion Channel Structure
2.50 – 3.00 pm Dr. Rob Coalson (Chem, Phys, Pitt)
Modeling ion permeation through protein channels
3.00 – 3.10 pm Dr. Maria Kurnikova (Chem, CMU)
Hierarchica approaches to modeling of ion channels and receptors
3.20 – 3.20 pm Dr. Jeffry Madura (Chem-Biochem, Duquesne)
Bilayer simulations
3.20 – 3.30 pm Dr. Guillermo Romero (Pharmacology, Pitt)
Protein-lipid interactions
 
3.30 – 4.00 pm Breakout Session
4.00 – 4.30 pm Concluding Remarks

        

 

        

Questions/Comments regarding this workshop:
 

Dr. Michael Cascio, Chair, Pre-NPEBC Workshop Organizing Committee

Assistant Professor
Department. of Molecular Genetics & Biochemistry
School of Medicine, University of Pittsburgh
W1155 Biomedical Science Tower
Pittsburgh PA 1526

cascio@pitt.edu
office (412) 648-9488, fax (412) 624-1401, lab (412) 383-9563

 

Dr. Ivet Bahar

Center for Computational Biology & Bioinformatics

Departmentof Molecular Genetics & Biochemistry

School of Medicine, University of Pittsburgh

Biomedical Science Tower, Rm W1043

200 Lothrop Street, Pittsburgh, PA 15261

Voice: 412 648 3332, Fax: 412 648 3163

bahar@pitt.edu  |  www.ccbb.pitt.edu  www.health.pitt.edu/pcbc

 

Dr. Joel Stiles  

Associate Professor, Mellon College of Science & Pittsburgh Supercomputing Center

Carnegie Mellon University

Mellon Institute, Rm 220A

4400 Fifth Avenue, Pittsburgh, PA 15213

Voice: 412 268 4786, Fax: 412 268 8200

stiles@psc.edu  |  www.mcell.psc.edu

www.mcell.psc.edu/DReAMM  |  www.psc.edu/~stiles

 

Dr. Rajan Munshi, Pre-NPEBC Coordinator

Center for Computational Biology & Bioinformatics

University of Pittsburgh School of Medicine

W1044 Biomedical Science Center

200 Lothrop Street

Pittsburgh, PA 15261

rajan@pitt.edu  |  www.ccbb.pitt.edu  |  www.health.pitt.edu/pcbc

Tel: 412-648-7799, Fax: 412-648-3163