There are a variety of recommended sources of information on this web site, including:

• The MolViz Application Guide
• Scream Saver Newsletters from the MolViz Facility
• Links to other Molecular Modeling WWW sites
• On-line Discover Manuals (ONLY Accessible from SGI workstations in the Department of Chemistry that are connected to the MolViz Server). The Theory and Methodology Section is also available in hardcopy form in the Discover Part 1 version 95.0 Manual available in A701. Manuals in A701 must not leave this room without permission from the MolViz Facility Staff.

There are also a variety of recommended sources of information available in the Chemistry Library. If you check out one of these textbooks, please return the text in a timely manner so that others can benefit from the text. If you want to read a textbook that is on this list, but is not available in the library, contact me.

JOURNALS

Methods of Molecular Modeling

Journal of Computer-Aided Molecular Design
Journal of Molecular Graphics and Modeling
Perspectives in Drug Discovery & Design

 

Theory of Molecular Modeling

Journal of Computational Chemistry
Theoretical Chemistry Accounts

 

Applications of Molecular Modeling

Biochemistry
Biopolymers
Macromolecules
Nature Structure & Biology
Nucleic Acids Research
Proteins: Structure Function & Genetics
Protein Science

TEXTBOOKS

Molecular Modeling: Basic Principles and Applications

Authors: Holtje & Folkers
Year: 1997
Location in Chemistry Library: QP517.M3 H64
An excellent, very readable text describing classical force fields, minimization, and dynamics, electrostatic potentials and other molecular properties, sequence alignments, docking, and ligand design. This text has two very good case studies---one for small molecules and one for large molecules.

 

Computational Approaches to Biochemical Reactivity

Editors: Naray-Szabo & Warshel
Year: 1997
Location in Chemistry Library: QP517.M3 C635
This vol. 19 of the "Understanding Chemical Reactivity" series contains several excellent chapters:

• Molecular Mechanics and Dynamic Simulation of Enzymes, by Slate, Dejaegere, & Karplus, pp. 153-198.
• Electrostatic Interactions in Proteins, by Sharp, pp. 199-236.
• Protein-Ligand Interactions, by Lybrand, pp. 363-374.

Problem Solving in Computational Molecular Science

Editors: Wilson & Diercksen
Year: 1997
Location in Chemistry Library: QC173.3.P75
From the "Molecules in Different Environments" series. The Chapter Molecular Simulation - A Primer by Muller-Plathe, pp. 389-412, is a very good description of classical molecular simulation methods and hybrid quantum mechanics-molecular mechanics schemes. The remainder of the text is not recommended for this course.

 

Molecular Modeling of Inorganic Compounds

Authors: Comba & Hambley
Year: 1995
Location in Chemistry Library: QD480.C66
A general description of classical force fields, minimization, and dynamics followed by a critique of the strengths and limitations of classical modeling as applied to:

• structure of inorganic molecules
• stereoselectivities
• metal ion selectivity
• spectroscopy
• electron transfer
• electronic effects
• bioinorganic chemistry
• organometallics
• and compounds with s, p, and f block elements.

Understanding Molecular Simulation from Algorithms to Applications

Authors: Frenkel & Smit
Year: 1996
Location in Chemistry Library: QD 461.F86
A sophisticated, detailed, yet very comprehensible description of Monte Carlo and Molecular Dynamics Methodologies in vacuum and condensed phases.

 

Molecular Modeling on the PC

Authors: Schlect
Year: 1998
Location in Chemistry Library: QD480.S36
An excellent manual for PC-MODEL for the PC. Our version of PC-MODEL on the SGI workstations has a different graphical user interface, but the functionality of the PC version and SGI version are extremely similar. This text also has a good comparison of force fields, and applications and exercises for small molecules.

More Sophisticated/More Specific Molecular Modeling Methodologies:

Guidebook on Molecular Modeling in Drug Design

Editor: N.C. Choen
Year: 1996
Location in Chemistry Library: RS420.G85
An excellent, very readable text covering docking and ligand design. Consider this REQUIRED reading if your Individual Modeling Project will focus on docking or ligand design.

 

Advanced Computer-Assisted Techniques in Drug Design

Author: van de Waterbeemd
Year: 1995
Part of the "Methods and Principles in Medicinal Chemistry" series, this text is not available on campus. Contact me if you want access to this text. This text focuses on ligand design and QSAR techniqies.

 

Exploring QSAR Fundamentals and Applications in Chemistry and Biology

Authors: Hansch & Leo
Year: 1995
Location in Chemistry Library: QP517.S85 S97
A thorough description of QSAR techniques and application examples.

 

Genetic Algorithms in Molecular Modeling

Editors: Devillers
Year: 1996
Location in Chemistry Library: QA402.5.6455
A compilation of computing methods for analysis of phylogenetic and genetic sequence data for the interpretation of biological phenomena. This text focuses on bioinformatics, and many sections are not recommended for this course. However, Individual Modeling Projects can include this type of bioinformatics information depending on your interests.

 

Distance Geometry and Molecular Conformation

Authors: Crippen & Havel
Year: 1988
Location in Chemistry Library: QD481.C76
THE text for distance geometry calculations

 

The Art of Molecular Dynamics Simulation

Author: Rapaport
Year: 1995
Location in Chemistry Library: QC173.3.R36
Even though this text focuses on atomic fluids, this text is a very practical description of how to write and run molecular dynamics programs. The material in this text regarding programming is not recommended for this course. However, the material regarding molecular dynamics methodologies is recommended.

 

Computer Simulation in Liquids

Authors: Allen & Tildesley
Year: 1987
Location in Swain Hall Library: QC145.2.A43
A manual for people who want to to use computers to simulate the behavior of atomic and molecular liquids. The "bible" of molecular simulation. The material in this text regarding programming is not recommended for this course. However, the material regarding molecular dynamics methodologies is recommended.