2009 Summer Workshop San Diego, California
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- Instructors
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- Charles L Brooks III, Department of Chemistry, University of Michigan
- Michael Feig, Department of Biochemistry and Molecular Biology, Michigan State University
- David A. Case, Biomaps Institute, Rutgers University
- Ross C. Walker, San Diego Supercomputer Center, University of California San Diego
- Jana Shen, Department of Chemistry, University of Oklahoma
- Jianhan Chen, Department of Biochemistry, Kansas State University
- Mentors
- Jennifer Knight, Department of Chemistry, University of Michigan
- Sishi Tang, Biomaps Institute, Rutgers University
- Workshop Reading
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Tutorials
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Useful Links
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Agenda
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Lectures: |
8:30 AM - 12:00 PM Humanities & Social Sciences (HSS) Building 1330 |
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Hands-on: |
2:00 PM - 5:00 PM Natural Sciences Building (NSB) 1205 |
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Schedule: |
Tuesday, Wednesday,
Thursday, Friday
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Tuesday, August 4
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- 8:30 AM - 9:45 AM - Welcome, historical overview and introduction to
molecular mechanics and modeling with CHARMM and the MMTSB Tool Set. (Brooks)
(download lecture)
- Welcome and overview of MMTSB and CTBP objectives
- Introduce CHARMM, AMBER and the MMTSB Tool Set with an historical perspective.
- A brief overview of methods in molecular modeling & nature of force field,
minimization and molecular dynamics, introduction to periodic boundary conditions.
- A brief introduction to the flow of CHARMM calculations.
- Comments on scope and range of problems that can be addressed with CHARMM.
- The nature of the CHARMM force field, molecular fragments and
parameterization strategies.
- 9:45 AM - 10:00 AM - Coffee Break
- 10:00 AM - 11:00 AM - The AMBER program suite for simulations of
molecular systems (Case) (download lecture)
- Introduce AMBER with an historical perspective.
- A brief introduction to the flow of AMBER calculations.
- Comments on the scope and range of problems that can be addressed with AMBER.
- The nature of the AMBER force field, molecular fragments and
parameterization strategies.
- 11:00 AM - 12:00 PM - Introduction to MMTSB scope and functionality. (Feig)
(download lecture)
- Overview of MMTSB scope, purpose and structure
- Description of tools their function and extensibility
- Introductory examples/illustrations
- 12:00 PM - 2:00 PM Lunch
- 2:00 PM - 5:00 PM - Elementary applications to peptides, proteins and nucleic acids
(Brooks, Case, Walker, Feig and mentors).
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Case/Walker
- Preparing DNA and RNA for
molecular dynamics (Tutorial).
- with AMBER DNA/RNA force fields
- using MMTSB Toolset
- Use of W3DNA (
http://w3dna.rutgers.edu/)
to build DNA starting structures.
7:00 PM - 10:00 PM Participant poster session with drinks and munchies.
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Wednesday, August 5
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- 8:30 AM - 9:30 AM - CHARMM analysis tools and facilities. (Chen)
(download lecture)
- Overview of CHARMM analysis facilities, trajectory analysis, NMR module.
- Illustrative examples of solvent analysis, hydrogen bonding, clustering w/
K-means cluster facility
- 9:30 AM - 9:45 AM CoffeeBreak
- 9:45 AM - 11:00 AM - Implicit solvent models in CHARMM and Amber. (Chen/Case)
- Chen: (download lectures)
- Overview of CHARMM empirical implicit solvent models (ASA,EFF,IMFF)
- Continuum solvent models in CHARMM (PB,GB)
- Overview of AMBER GB implicit solvent models
- 11:00 AM - 12:00 PM - Introduction to AMBER's Antechamber and
the General AMBER Force Field (Tang)
(download lecture)
- Overview of General AMBER Force Field. Antechamber, automated atom type and
parameter selection for ligands.
- Examples of combining GAFF with protein force fields (FF99SB).
- Problematic systems to be aware of.
- 12:00 PM - 2:00 PM Lunch
- 2:00 PM - 5:00 PM - Applications to membrane/protein systems, implicit solvent
simulations and trajectory analysis. Use of AMBER's Antechamber module. (Chen,
Feig, Case, Walker, Mentors)
Chen/Feig
- Basic analysis of MD trajectories with MMTSB Tool Set
(MMTSB Introduction)
- Advanced trajectory analysis with CHARMM
(CHARMM Trajectory analysis)
- Comparative analysis of protein structures (e.g., rmsd versus reference,
hydrogen bonding, secondary structure).
- Examples of analysis of solvent/solvation structure and dynamics.
- Clustering molecular trajectories based on backbone conformations
- Analysis of NMR properties, order parameters, T2, etc.
- Ensemble analysis and clustering with MMTSB Tool Set
(Ensemble analysis)
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Thursday, August 6
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- 8:30 AM - 9:30 AM - Replica-exchange molecular simulations with CHARMM and MMTSB (Chen)
(download lecture)
- Theoretical background of replica exchange MD
- Illustrative examples for membrane assembly, peptide folding and protein refinement
- Using umbrella sampling, WHAM analysis (w/Feig)
- 9:30 AM - 9:45 AM CoffeeBreak
- 9:45 AM - 10:45 AM - Constant pH molecular dynamics with CPHMD (Shen)
(download lecture)
- 10:45 AM - 11:45 PM - QM/MM Simulations in Amber (Walker)
(download lecture)
- 11:45 PM - 2:00 PM Lunch
- 2:00 PM - 5:00 PM - Replica exchange, constant pH and QM/MM
(Shen, Feig, Chen, Walker, Mentors)
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Friday, August 7
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- 8:30 AM - 9:30 AM - Using the MMTSB Tool Set with Modeller and CHARMM for
protein structure prediction (Feig)
(download lecture)
- Overview of structure prediction capabilities
- Applications from homology/loop modeling to de novo structure prediction
- 9:30 AM - 9:45 AM CoffeeBreak
- 9:45 AM - 10:45 AM - Developing and implementing multi-resolution models
with CHARMM. (Brooks)
(download lecture)
- Topological and flavored Go models for the investigation
of protein folding and unfolding.
- Multi-scale DNA models for DNA structure and thermodynamics
- 10:45 AM - 11:45 AM - Free energy simulations in Amber (Case)
(download lecture)
- 11:45 AM - 2:00 PM Lunch
- 2:00 PM - 5:00 PM - Structure prediction, multi-scale, multi-resolution modeling,
free energy (Brooks, Case, Feig)
Feig
- Template-based structure prediction
(Template predictions)
- Secondary structure prediction through psipred
- Sequence alignment through PSI-BLAST
- Homology modeling through the MMTSB Tool Set
- Loop modeling with Modeller and MMTSB Tool Set
(Loop modeling)
Brooks
- Using CHARMM and MMTSB to explore protein folding mechanism and thermodynamics
- Exploring single molecule protein pulling experiments with Go models
(Force protein unfolding)
- Workshop ends
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The workshop organizers wish to acknowledge the support
of the National Science Foundation Physics Frontiers Centers
program and the National Institutes of Health National Center for Research Resources program.
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