Subject: Intro. to Computer-Aided Molec. Design Workshop

From: [email-masked] (Lisa A. Scott)
Date: Fri, 26 Apr 1996 12:28:51 -0400

Cornell Theory Center

Introduction to Computer-aided
Molecular Design Workshop

July 10-13, 1996
Cornell University, Ithaca, NY

This workshop provides a broad introduction to computer-aided molecular
design. We will describe how computational methods can be appropriately
applied to real-world problems in the pharmaceutical, biotechnology, and
chemical industries. A variety of methods will be discussed, ranging from
statistical methods based on experimental data to high-level ab initio
quantum chemical calculations. The methods to be introduced include
molecular dynamics, quantum chemistry, and dielectric-continuum solvent
models. Sections of the workshop will also introduce homology-based protein
modeling and general-purpose optimization methods used across a range of
computational chemistry methods.

The workshop will combine descriptions of methods with applications to
specific areas. Applications will include predictions of physical
properties of molecules (solubilities, conformations, pKas, diffusion
coefficients, etc.) and predictions of binding properties of drugs (binding
geometries and energetics). After each method is introduced, it will be
illustrated with a case study. The material in the lectures will be
reinforced through hands-on computer laboratory sessions, which will
include both introductory software tutorials and more extensive
"mini-research projects" using the computer resources at the Cornell Theory
Center.

WHO SHOULD ATTEND

*	Faculty, postdocs, and graduate students interested in developing
chemical modeling skills
*	Professionals in the pharmaceutical, biotechnology, or chemical
industries who are evaluating the usefulness of molecular modeling
*	Professionals moving into the area of modeling
*	Modelers who are expert in one field but who wish to broaden their expertise

COURSE OBJECTIVES

*	How computer modeling can be used to design molecules
*	How to choose the appropriate modeling method for specific problems
*	How to apply standard molecular modeling tools
*	How to assess the accuracy of predictions made by computer models

LECTURERS

Dr. Michael Colvin
Senior member of the technical staff at Sandia National Laboratories, in
Livermore, CA. Colvin's main research interest is the application of
quantum chemical methods to understand biochemical processes. The nature of
these research problems has involved him in more than a decade of research
on quantum chemical methods for massively parallel computers and the
development of methods for accurately simulating aqueous solvation.

Dr. Richard Judson
Senior member of the technical staff at Sandia National Laboratories, in
Livermore, CA. Judson has twelve years of experience in molecular modeling
using quantum mechanics, molecular dynamics, and statistical and
optimization methods. At Sandia he has headed a project in computational
drug design that produced new methods for drug-docking predictions, NMR
data analysis, and analysis of large databases of molecules. Other projects
have included modeling of electron impact on materials, design of laser
pulses for control of chemical motion, and the use of genetic algorithms
for protein structure prediction.

PROPOSED DAILY SCHEDULES

Wednesday

Overview of Molecular Modeling: Introduction to classical mechanics; force
fields; minimization; dynamics; conformation searching; docking; free
energy perturbation methods; case study: modeling thermolysin inhibitors
polarization; screening; embedded atom method for metals

Computer lab session: Introduction to building molecules; calculating
energies; conformations; visualization tools; dynamics and minimization

Thursday

Quantum Chemistry: Molecular Schršdinger equation, Born-Oppenheimer
approximation; Hartree-Fock; basis sets; analytical derivatives; electron
correlation; accuracy of thermodynamic and electronic properties; general
introduction to using QC programs; QC literature; QC resources on the
Internet; QC software; case study: chemical properties of environmental
carcinogens

Computer lab session: Introduction to ab initio quantum chemical software
and computational experiments on hydrogen peroxide, disilyne, and hydrogen
fluoride dimers

Friday

Modeling Solvation Effects: Importance of solvation effects; Born model;
self-consistent reaction fields; polarizable continuum models; case study:
protonation states of phosphoramide mustard anticancer drugs Protein
homology modeling: Need to predict structure from sequence; overview of
information available; meaning of homology, low vs. high; high homology
models; threading; multiple sequence alignment

Computer lab session: Mini-research project using computational chemistry
software

Saturday

Miscellaneous Modeling Topics: Commercially available modeling software;
optimization methods; parallel computers

Computer lab session: Mini-research project using computational chemistry
software

REGISTRATION FORM

Cornell Theory Center

Introduction to Computer-aided
Molecular Design Workshop

July 10-13, 1996
Cornell University, Ithaca, NY

Registration deadline: May 28, 1996

To apply, complete the registration form and return with payment.
Priority will be given to registrations received by May 28, 1996.
Payment may be sent separately for registrations that are submitted
electronically. However, the registration will not be acted upon until
the payment arrives. Refunds will be made to those applicants not
accepted to the workshop. Refunds cannot be made after applicant is
accepted. Return registration form to: Jeanne Butler, 427 Rhodes Hall,
Cornell Theory Center, Ithaca, NY 14853-3801, or [email-masked].

WORKSHOP REGISTRATION FEES

Academic/Government: $100
CPP Member: $250
Corporate: $400

Name: _________________________________________

Company/Institution: _________________________________________

Address: _________________________________________

Email address: _________________________________________

Telephone: _________________________________________

Academic discipline or Corporate Area of Interest:
_______________________________

Status (check all that apply):

__Corporate Participant
__Corporate Research Institute (CRI) Member
__Undergraduate Student
__Graduate Student
__Post-doctoral
__Faculty
__Smart Node Consultant
__Smart Node Advisor
__Smart Node Associate
__CTC Collaborator (explain):
__Other (explain):

Do you currently have an allocation at CTC?
__Yes
__No
__Pending

If you have an allocation, or an allocation pending, please indicate:
Principal Investigator: _________________________________________

If you have an allocation, please indicate:

Account number: _________________________________________
Your Userid: _________________________________________

Social Security #:_________________________________________
(for new supercomputer accounts)
(Submission of social security numbers is voluntary and will not
affect eligibility for access to the Center's facilities. However, they
are an integral part of the National Science Foundation's
information system and assist in managing the Supercomputer
Centers program. SSN solicited under NSF Act of 1950, as
amended.)

Indicate which of the following best describes you (optional):

__African American
__Caucasian
__Asian American
__Hispanic American
__Native American or Alaskan Native
__Other (please specify):

For technical information about this course, contact

Michael E. Colvin
Center for Computational Engineering
Sandia National Laboratories
Livermore, CA 94551
[email-masked]

Cyrus Umrigar
Computational Science & Engineering Research Group
Cornell Theory Center
Ithaca, NY 14853-3801
[email-masked]

Information also available at:
http://www.tc.cornell.edu/Events/comp.chem.html

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