Computer-Assisted Molecular Design Course

Teri Klein klein at cgl.ucsf.EDU
Tue Aug 1 17:38:29 EST 1995

			December 6-8, 1995
		   San Francisco, California

Presented by:
Department of Pharmaceutical Chemistry and UCSF Molecular Design Institute
University of California San Francisco

Course Coordinators:

Peter A. Kollman, PhD
Professor, UCSF Department of Pharmaceutical Chemistry 

Jeff Blaney, PhD
Senior Scientist, Chiron Corp.


        David Agard, PhD                Peter A. Kollman, PhD
        Jeff Blaney, PhD                ID Kuntz, PhD
        Fred E. Cohen, PhD              Paul Ortiz de Montellano, PhD
        Charles Craik, PhD              Tom Scanlan , PhD
        Ken Dill, PhD                   Ulrich Schmitz, PhD
        Tom E. Ferrin, PhD              Richard Shafer, PhD
        Robert Fletterick, PhD          David Spellmeyer, PhD
        Tom James, PhD                  Leslie Taylor


The goal of this course is to describe the state-of-the-art in
computer-assisted molecular design as applied to biological systems, with
focus on drug design, macromolecular design and structure function
relationships in proteins and nucleic acids.  The course faculty have a
wide varietyof expertise in both the computer based methodologies and in
the experimental approaches (X-ray crystallography, NMR spectroscopy and
protein engineering) that are complementary to the computer-based modeling.

This course should be of benefit not only to experts in some aspect of
computational (bio)chemistry, by giving them a broader perspective in this
area, but also to those with little exposure and experience in
computational research as applied to biological systems.  In the latter
case, this course should provide an exciting and stimulating introduction
to a growing research area, whose potential for meaningful impact on
experimental work is increasing dramatically.


A.  Protein Structure and Design

        1.  Protein Structure by X-Ray Diffraction
        2.  Protein Structure by NMR
        3.  The Fundamentals of Protein Stability
        4.  Protein 2o and 3o Structure Prediction
        5.  Molecular Mechanics and Molecular Dynamics
        6.  Predicting the Properties of Mutants with Simple Models
        7.  Protein Design from a Pragmatic Point of View
        8.  Catalytic Antibodies and Design

B.  Ligand Design

        1.  Predicting the Relative Conformational Free Energies in Solution
        2.  Lead Generation When the Receptor Structure is Known
        3.  Lead Refinement with Detailed MD Free Energy Calculations
        4.  Simple, Empirical Approaches to Ligand Design
        5.  Approaches to Ligand Design Without a Receptor Structure
        6.  Combinatorial Chemistry and Ligand Design

C.  Nucleic Acid Structure and Ligand Design

        1.  NMR of Nucleic Acids
        2.  Triplex, Quadriplex Stabilities and Structure
        3.  Theoretical Approaches to Sequence Dependent Stabilities
                and Ligand Design

D.  Technologies and Practicalities

        1.  What's new in hardware/software
        2.  How to design a computational experiment?
        3.  Use of Software Developed by Course Faculty

		(1)  AMBER
		(2)  DOCK
		(4)  MIDAS
		(5)  DGEOM 95

Registration Fees:

Early Registration (Before Sept. 1): $1250.00
Regular Registration (After Sept. 1): $1500.00
(Includes a dinner and reception for attendees)

Some scholarships will be available for those affiliated with non-profit
institutions.  Enrollment is limited, so register early.


Nancy MacKenzie
UCSF-Dept. of Pharmaceutical Chemistry
Tel, 415.476.1913  Fax 415.502.4690
email: nlmk at

WEB page

Department of Pharmaceutical Chemistry
University of Californa San Francisco
513 Parnassus Ave., Room S-926
San Francisco, CA 94143-0446
ATTN. Nancy MacKenzie

Make checks payable to: UC REGENTS

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