Computational Chemistry Resources

• Alex Tropsha's QSAR Server
• Binding Database - database of measured binding affinities for biomolecules, genetically or chemically modified biomolecules, and synthetic compounds
• c2sar
• Chemaxon
• Chemical Drawing programs (review)
• Chemical Markup Language - XML for chemists
• Cheminformatics.org - programs and datasets
• Chemistry Mailing Lists
• ChemSilico - ADMET property prediction software
• ChemTK Lite - A free cheminformatics toolkit for Windows
• ClassPharmer suite of programs from BioReason for analysing HTS or virtual screening data.
• Computational Chemistry in the Classroom - using computers as learning aids
• Computational Chemistry Comparison and Benchmark DataBase
• 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.
• Distributed Structure-Searchable Toxicity (DSSTox) Public Database Network - standard format, structure-annotated chemical toxicity data files for open public access
• Drug Design and Molecular Modeling resources
• EMSL Gaussian Basis Set Order Form
• Equbits - predictive modeling tool designed for HTS and ADME chemists
• 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
• MarvinSpace - 3D molecule visualization tool for Windows, Linux, Mac OS X, and Solaris.
• Milano Chemometrics and QSAR Research Group
• Modeller - homology or comparative modeling of protein three-dimensional structures
• MOE from CCG
• Molecular Conceptor - Medicinal Chemistry & Drug Design Courseware - 25% discount to ACS members
• Molecular model building kits
• Molinspiration - interactive calculation of molecular properties
• National Cancer Institute Database Browser
• 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
• PGM Database - physical, mechanical and chemical data for the platinum group metals (platinum, palladium, rhodium, iridium, osmium and ruthenium) and their alloys.
• Pharma Algorithms and the Algorithm Builder package, including QSAR
• Protein Library - C++ toolkit for a wide range of protein structure and sequence calculations
• QSAR and Modelling Society Data Sets
• QSAR World - web-based portal for the Quantitative Structure Activity Relationship modeling community. Includes 48 searchable datasets.
• http://www.qsarworld.com/qsar-datasets-search.php
• QSAR Project - a GUI that enables people to build quantitative structure activity (or property) relationship models
• Quantum Chemistry Program Exchange (QCPE)
• RECON - rapid reconstruction of molecular charge densities and charge density-based electronic properties of molecules
• SARNavigator and SYBYL from Tripos
• Sherrill Research Group - notes on quantum chemistry, configuration interaction, and more
• Similarity Searching - http://cheminformatics.org/simsearch/ online from Andreas Kieron Patrick Bender
• SONNIA (formerly KMAP) - neural networks to analyze data from high-throughput screening
• Structure Databases
  • Cambridge Structure Database
  • Centre for Molecular and Biomolecular Informatics
  • Protein structures
  • Inorganic Crystal Structure Database
    
• 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
• 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' CEN Chemjobs

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
• University of Missouri at St Louis - Center for Molecular Electronics
• University of North Carolina at Chapel Hill - Molecular Modeling Laboratory
• 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 QSAR and Modelling Society
  • Archives of society's email listserve
• National ACS Meetings - Future and Past national meeting information
• Gordon Research Conferences
  • Combinatorial Chemistry
  • Computational Chemistry - including info on the 2004 conference
  • Computer Aided Drug Design (formerly called Quantitative Structure-Activity Relationships)
• Theoretical Chemistry Conferences by date.
• 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

Any additions or corrections to this list should be send to lisa@balbes.com.