Computational Chemistry Software

Computational Chemistry Software Companies

Accelrys

Chemaxon

ChemSilico - ADMET property prediction software

ClassPharmer suite of programs from SimulationsPlus can be used to analyse HTS or virtual screening data.

Equbits - predictive modeling tool designed for HTS and ADME chemists

MarvinSpace - 3D molecule visualization tool for Windows, Linux, Mac OS X, and Solaris.

Milano Chemometrics and QSAR Research Group

MOE from Chemical Computing Group

Molecular Conceptor - Medicinal Chemistry & Drug Design Courseware - 25% discount to ACS members

Molecular model building kits

Molinspiration - interactive calculation of molecular properties

Chemical Drawing programs (review)

SONNIA (formerly KMAP) - neural networks to analyze data from high-throughput screening

SARNavigator and SYBYL from Tripos

General Computational Chemistry Software Resources

Cheminformatics.org - programs and datasets

Chemistry Mailing Lists

Computational Chemistry in the Classroom - using computers as learning aids

Computational Chemistry List - email discussion list

Computational Science and Engineering Online – Web-based Grid enabled environment for molecular modeling and simulations

CoSyM - Continuous symmetry measures, provides tools for calculating continuous symmetry measures online for any molecule given in pdb format, using Jmol for three-dimensional visualization.

EMSL Gaussian Basis Set Order Form

GLARE (Global Library Assessment of Reagents) - optimizes list of commercially available reagents (used for combinatorial library design)

JChemPaint - editor for 2D molecular structures

JMol - visualisation and analysis tool for 3D molecular structures

Peter Kollman memorial journals and symposia

LeadId - HTS Data Analysis and Lead Identification

logP and logS calculator from VCCLAB Virtual Computational Chemistry Laboratory

Open Babel - cross-platform program and library designed to interconvert between many file formats used in molecular modeling, computational chemistry, and related areas

ORCA - general purpose electronic structure program

Oxford University Press - 30% discount to COMP members

Persistence, Bioaccumulative, and Toxic (PBT) Profiler

Protein Library - C++ toolkit for a wide range of protein structure and sequence calculations

QSAR Project - a GUI that enables people to build quantitative structure activity (or property) relationship models

Quantum Chemistry Program Exchange (QCPE)

Sherrill Research Group - notes on quantum chemistry, configuration interaction, and more

Similarity Searching - http://cheminformatics.org/simsearch/ online from Andreas Kieron Patrick Bender

VEGA - analyze, display and manage the 3D structures of molecules

Vigyaan - electronic workbench for computational biology and computational chemistry.

Web Accessible Tools and Datasets from the National Cancer Instittute

XML - Standard XML Dictionaries for Chemistry

Structure Databases & Datasets

Binding Database - database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds

Cambridge Structure Database

Centre for Molecular and Biomolecular Informatics

Computational Chemistry Comparison and Benchmark DataBase

Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network - standard format, structure-annotated chemical toxicity data files for open public access

Inorganic Crystal Structure Database

National Cancer Institute Database Browser

PGM Database - physical, mechanical and chemical data for the platinum group metals (platinum, palladium, rhodium, iridium, osmium and ruthenium) and their alloys.

Protein structures

QSAR and Modelling Society Data Sets

QSAR World - web-based portal for the Quantitative Structure Activity Relationship modeling community. Includes 48 searchable datasets.

The QSAR World data sets

ZINC - free database of commercially-available compounds for virtual screening

Publishing Computational Chemistry

Guidelines for Authors in the Journal of Medicinal Chemistry (see especially sections i and p) and the Journal of the American Chemical Society (see especially "Computations" section) both discuss criteria for successful publications in this area. More detailed information can be found in J. Med. Chem. 31, 2230-2234 (1988) "Guidelines for Publications in Molecular Modeling Related to Medicinal Chemistry" and Acc. Chem. Res. 27, 179-181 (1994) "Ethical Guidelines to Publication of Chemical Research". Places to publish include:

Chemical Physics (info for authors)

Chemical Physics Letters (info for authors)

Computer Physics Communications and program library

International Journal of Quantum Chemistry

Journal of the American Chemical Society

Journal of Chemical Information and Modeling

Journal of Chemical Physics (info for authors)

Jounal of Chemical Theory and Computation

Journal of Computational Chemistry

Journal of Computational Physics

Journal of Computer-Aided Molecular Design

Journal of Medicinal Chemistry

Journal of Molecular Graphics and Modelling

Journal of Molecular Modeling

Journal of Physical Chemistry (info for authors)

Journal of Theoretical and Computational Chemistry

Molecular Physics

Organic & Biomolecular Chemistry

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Presenting Computational Chemistry

When presenting research results, at an ACS national meeting or any forums, a few tips from veteran presenters may come in handy.

• A 20 minute time slot means a 15 minute talk
  
  
• 7-10 slides are appropriate for a 20 minute time slot
  
  
• Watch the use of color (some colors on black are difficult to read)
  
  
• Practice with the laptop ahead of time, especially if you are using a borrowed machine
  
  
• Be sure to have a back-up with you - hard copy, overheads, a keychain USB drive
  
  
• Arrive at your session room early and introduce yourself to the session chair
  
  
• Practice hooking up your laptop before the session
  
  
• Speak up so people can hear you
  
  
• Keep an eye on the session chair, who will signal when your time is about to end
  
  
• Acknowledgements should be short
  
  
• Don't switch between the LCD projector and the overhead projector more than once
  
  

For more tips, start with the following web sites:

How not to give a presentation - http://bmj.bmjjournals.com/cgi/content/full/321/7276/1570

Presentation Helper - http://www.presentationhelper.co.uk/

Employment and Education

Current postings of job openings in computational chemistry are available through the CCL Job Board, and more general chemisty job postings are available through ACS.

Graduate Programs in Computational Chemistry

University of California at San Francisco - Molecular Design Institute

University of Georgia - Computational Center for Molecular Structure and Design

University of Ilinois at Chicago - Computational Chemistry Facilities

The University of Minnesota computational chemistry program.

University of Missouri at St Louis - Center for Molecular Electronics

University of North Carolina at Chapel Hill

University of Pittsburgh - Center for Molecular and Materials Simulation and Department of Computational Biology

University of Texas at Austin

Continuing Education

ACS Short Course: Computational Chemistry and Computer-Assisted Drug Design: Practical Approaches

Societies and Meetings

Possible sources of funding for travel to meetings inlude NIH and the ACS-PRF

The Cheminformatics and QSAR Society

National ACS Meetings lists national meeting information for past and future programs.

Gordon Research Conferences

3rd Workshop on Computational Chemistry and Its Applications, part of ICCS 2008 : "Advancing Science through Computation, 23-25 June 2008, Krakow, Poland. Deadline for submission of papers is 22 Dec 2007.

Modeling and Design of Molecular Materials 2008, Piechowice, POLAND, 23-28 June 2008.

Sixth Congress of the International Society for Theoretical Chemical Physics (ISTCP-VI) , July 19-24, 2008 ,University of British Columbia (UBC) at Vancouver, BC, Canada.

Online conference on Computational and Theoretical Chemistry Applications in Chemical Education, part of CONFCHEM Conferences on Chemistry, during the summer of 2008. Abstracts (maximum one A4 page) to Ponnadurai Ramasami by the end of September 2007.

COMP in the News

Drugs by Design in Chemical and Engineering News November 28th, 2005 issue.

Turbocharging Computers, Chemical and Engineering News, September 27, 2004, Volume 82, Number 39, pp. 35-40.

Enzyme by Design, Chemical and Engineering News, July 12, 2004, Volume 82, Number 28, p. 24.

Calculating Carbohydrates., Chemical and Engineering News, April 26, 2004, Volume 82, No 17, pages 36-39.

Dealing with Data Overload, Chemical and Engineering News, March 22, 2004, Volume 82, Number 12, pages 19-24.

Better than Fourier? Vibrational spectra of molecules can now be calculated more quickly and accurately, Chemical and Engineering News, February 9, 2004, Volume 82, Number 6, pp. 30-31

Any additions or corrections to this list should be send to Web Support for the Site.

Home         Contact Us         Content of the site is Copyright © 2003-2008         Site Map

The views and opinions expressed in this page are strictly those of the Division of Computers in Chemistry. The contents of this page have not been reviewed or approved by the American Chemical Society. The Division assumes all responsibility and liability for the content of its pages. Please address all comments and other feedback to the COMP Division.