©Leif
Laaksonen (E-mail:
Leif.Laaksonen@csc.fi), Center for Scientific Computing (CSC), Espoo, FINLAND
|A| B| C| D| E| F| G| H| I| J| K| L| M| N| O| P| Q| R| S| T| U| V| W| X| Y| Z| Å| Ä| Ö|
- Advanced Chemistry
Development, INC.
This Web Site is designed to give you up-to-date
information about ACD software products and to provide
immediate access to free software, on-line property
prediction engines, demonstration programs and more.
- AMBER
What is AMBER? Assisted Model Building with Energy
Refinement.
AMBER refers to two things: a molecular mechanical force
field for the simulation of biomolecules (which is in
general use in a variety of simulation programs); and a
package of molecular simulation programs which includes
source code and demos.
- Atom
World
Molecular Model Construction Kits and pictures of
bio-molecules made with space-filling atomic models, and
brief explanations of how the molecules work in Nature.
- Babel
BABEL is a program designed to interconvert a number of
file formats currently used in molecular modelling.
- The
Backbone-Dependent Rotamer Library Webpage
The Backbone-Dependent Rotamer Library Webpage includes
backbone-independent and backbone-dependent rotamer
libraries, a program for making sidechain conformation
predictions from input phi and psi values and for
evaluating the rotamers and chi angles of a preliminary
x-ray, NMR, or model structure in comparison to the
experimental distributions of rotamers and chi angles in
the Protein Databank. The site also presents in detail a
description of local steric interactions that influence
sidechain rotamer and chi angle choice and includes
graphical representations of the backbone-independent and
backbone-dependent rotamer libraries developed by
Dunbrack and Karplus annotated to show where local steric
interactions affect rotamer and chi angle populations.
- BioChemNet
Biology and chemistry educational resources online.
- Bio Online
A Web site for information and services related to
biotechnology on the Internet, combining resources of the
biotechnology companies, biotechnology centers, research
and academic institutions, industry suppliers, government
agencies, and non-profit special interest groups.
- Biosciences [*1*| *2*]
The World Wide Web Virtual Library: Biosciences
- BioTech
An interactive educational resource and biotechnology
reference tool.
- Web
based analysis tool for the BOSS/MCPRO program.
A web-based analysis tool for the BOSS/MCPRO
program, which has been develped in W. L. Jorgensen
group. The BOSS/MCPRO is a Monte Carlo simulation program
for organic molecules and proteins. This analysis tool
gives you plots of solvent-solvent and solvent-solute
radial distribution functions, solvent-solvent and
solvent-solute energy and energy pair distributions,
dihedral angle distributions, total energy, heat
capacity, volume, enthalpy, themal compressibility,
solute-solute and solvent-solute interaction energies,
intrasolute Coulombic and Lennard-Jones energies, etc.
Sample BOSS/MCPRO output files are available for
download.
- Brookahven Protein Data
Bank (PDB)
The Protein Data Bank (PDB) is an archival computer
database of three-dimensional structures of biological
macromolecules. The database contains atomic coordinates,
bibliographic citations, primary sequence and secondary
structure information, as well as crystallographic
structure factors and 2D-NMR experimental data.
Information is available on protein, DNA, RNA, virus and
carbohydrate structures. The database is updated
approximately every three weeks and a newsletter and CD
ROM are published quarterly. The data is normally
distributed using the PDB interchange format which has
become the standard for the field. The PDB is supported
by a combination of Federal Government Agency funds and
user fees. Support is provided by the U.S. National
Science Foundation, the U.S. Public Health Service,
National Institutes of Health, National Center for
Research Resources, National Institutes of General
Medical Sciences, and National Library of Medicine and
the U.S. Department of Energy under contract
DE-AC02-76Ch00016.
- CACTVS
The CACTVS system is a research project aiming to change
the ways of doing computational chemistry.
- Cambridge
Crystallographic Data Centre The Cambridge
Crystallographic Data Centre was established at the
University Chemical Laboratories in 1965 to undertake the
compilation of a computerized database containing
comprehensive data for organic and organometallic
compounds studied by X-ray and neutron diffraction.
- CambridgeSoft
Corporation
CambridgeSoft Corporation, formerly Cambridge Scientific
Computing, develops, markets and supports high quality
desktop applications for chemists and engineers. The
ChemOffice suite integrates our cornerstone product,
ChemDraw (chemical structure drawing), with Chem3D
(molecular modeling/analysis), and ChemFinder (chemical
information management). CS products enable chemists to
communicate in the 'language' of chemistry: chemical
structures and models.
Free
Software - FREE Supplementary Software and other
goodies for use with ChemOffice.
- CAMEO
CAMEO (Computer Assisted Mechanistic Evaluation of
Organic reactions) is a modular expert system, a computer
program that predict the products of organic reactions
given starting materials, reagents, and conditions.
- CASCADE
(DOS/Win/OS2 VERSION)
CASCADE (Cascade Aids Semi-empiric Calculators Access
Displays Eventually)
Cascade V2 is a shell which converts semi-empirical data
(from programs like MOPAC, AMPAC and VAMP) into several
3d graphic formats. It thus enables the user to visualize
the resulting molecule geometry. The supported display
programs are: 3DV, Chemview, JMR, MOLWIN, MV, PC MODEL,
PLUTON, POVRAY, RASWIN.
You can also get the software from the CCL Archives: CASCADE
- Car-Parinello
MD program Car-Parinello MD code by Stumpf and
Scheffer from the Fritz - Haber - Institut der Max -
Planck - Gesellschaft, Berlin, Germany.
- ACCVIP
The Australian Computational Chemistry via the Internet
Project (ACCVIP). This has developed from the CAUT
Computational Chemistry Project.
- CCP4
The CCP4 Program Suite is an integrated set of programs
for protein crystallography developed in a close
collaboration between crystallographers under an
initiative by the UK Biotechnology and Biological
Sciences Research Council.
- CHARMM
CHARMM (Chemistry at HARvard Molecular Mechanics) is a
general and flexible software application for modelling
the structure and behaviour of molecular systems. A
variety of systems, from an individual organic molecule
to a large oligomeric protein in its solvent environment,
can be simulated.
- Chemical
Physics Preprint Database
This database is a joint effort by the Department of
Chemistry at Brown University and the Theoretical
Chemistry and Molecular Physics Group at the Los Alamos
National Laboratory. It is intended to provide a means
for rapid and efficient preprint distribution within the
international chemical physics community.
- Chemistry
The Word Wide Web Virtual Library: Chemistry.
- Chemistry
on Yahoo
Chemistry resources in the Internet at Yahoo. Good
starting point to various useful resources.
- Chemistry
Servers and Resources
Chemistry Servers and Resources (via Theoretical
Chemistry, University of Regensburg) by Herbert Homeier.
A good starting point with pointers to further
pointers...
- ChemSite
ChemSite is an interactive 3 dimensional molecular
visualization environment that allows you to model,
animate, render and export an unlimited variety of
molecular structures for precise visualization. Modelling
features include energy minimization and molecular
dynamics simulations with the AMBER force field for
biological molecules and an MM2 compatible force field
for organic molecules.
- Chemistry
on the Internet: The best of the Web 1995
A selection of high quality chemical information on the
Internet, presented as a poster at the ACS Symposium in
Chicago on August 21, 1995 as part of the "Chemistry
on the Infobahn" session. In compiling this
selection, we have focused on the work of key individuals
who we believe have shown a vision of the future in
creating innovative and original chemistry Internet
resources for us all. This selection reflects the
personal opinions of the three authors only, and does not
represent any form of official endorsement by anyone
else.
- Chemistry
Textbooks in Print
This archive, based at the University of Missouri-St.
Louis, contains a comprehensive list of chemistry
textbooks in print, in categories that correspond roughly
with typical university and graduate curricula.
- Chemistry Today
The Web's Daily Chemistry Jobs and News Source. Chemistry
Today is a daily service bringing you the latest
chemistry news, jobs, meetings and other information.
- ChemWeb.com Home Page
ChemWeb.com offers:
* A library of leading chemical periodicals, books and
databases
* A Shopping Mall with software, equipment, services and
publications
* A Job Exchange with hundreds of job offers and jobs
wanted, world wide
* Meeting Rooms, Discussion Groups, news and more
- ChemViz
stuff at NCSA
ChemViz is an NSF funded grant to use High Powered
Computing and Communications to help high school students
better visualize abstract concepts of Chemistry. Other
supporters are the Benjamin Cummings Company, Apple
Computer and NCSA. Our current module allows the student
(or teachers) to make images and animations of calculated
atomic and molecular orbitals. Although the project was
designed around the Macintosh, there is now a windows
version of the module.
- Collaborative
Computational Projects (CCP)
The Collaborative Computational Projects (CCPs), assist
universities in developing, maintaining and distributing
computer programs and promoting the best computational
methods. Each focuses on a specific area of research and
are funded by the UK's EPSRC, PPARC and BBSRC Research
Councils. Many of them receive scientific support from
the Daresbury Laboratory.
- COLUMBUS
Quantum chemistry program package by Hans Lischka and Ron
Shepard.
- Chemistry Conference Listing
Links to conferences in: Theoretical/Computational
Chemistry (mainly), Theoretical Physics, and
Applied/Symbolic Mathematics.
- The CPC
International Program Library
Computer Physics Communications (CPC) is an international
interdisciplinary journal published by Elsevier Science B
V. It is aimed at the computing needs of the
computational physics and physical chemistry communities.
A unique feature of the CPC journal is its publication of
refereed computer programs in physics and physical
chemistry. The principal aim of the CPC Program Library
is the storage and dissemination of those computer
programs whose descriptions have been published in the
CPC journal.
- Dalton
The Dalton Quantum Chemistry Program represents a
powerful quantum chemistry program for the calculation of
molecular properties with SCF, MP2 or MCSCF wave
functions. The strengths of the program are mainly in the
areas of magnetic and (frequency-dependent) electric
properties, and for studies of molecular potential energy
surfaces, both for static and dynamical investigations.
- DeFT
DeFT is a linear combination of gaussian type orbitals
density functional program very similar to deMon or
Dgauss. It only has analytic first derivatives, so
geometry optimizations are efficient, but vibrational
analyses can become quite time consuming as this must be
done by finite differentiation of the analytic first
derivatives. Gradient-corrected functionals are included.
- DGauss basis sets
DGauss basis sets by the Oxford Molecular Group (http://www.oxmol.com/).
These contracted gaussian sets were optimized for DFT
calculations and include elements up to Xe. They also
include the auxilliary fitting uncontracted gaussian sets
for these programs which use them. The latest version of
the basis sets for DGauss version 4.0 is available from
Oxford Molecular ftp servers:
- EBI
The world-wide web (WWW) server of the European
Bioinformatics Institute (EBI).
- EGO
EGO - A Program for Parallel Molecular Dynamics EGO is a
program to perform molecular dynamics calculations on
parallel computers. Supported machines include the T3D of
CRAY, IBM's SP1, and inhomogeneous clusters of
workstations using PVM, as well as the powerXplorer
computers of Parsytec, Germany, under the PARIX operating
system.
- Elsevier Science
Information on Elsevier Science including descriptions of
Chemistry journals and books.
- FANTOM
The main purpose of the FANTOM program (Fast
Newton - Raphson Torsion Angle Minimizer) is the
calculation of conformations of linear and cyclic
polypeptides and proteins with low conformational
energies including distance and dihedral angle
constraints from nuclear magnetic resonance experiments
or for modeling purposes.
- GAMESS-USA
Home Page
The General Atomic and Molecular Electronic Structure
System (GAMESS) is a general ab initio quantum chemistry
package. This program is maintained by the members of the
Gordon research group at Iowa State University.
- GAMESS-UK
GAMESS-UK: A General Atomic and Molecular Electronic
Structure System
GAMESS--UK is a general purpose ab initio molecular
electronic structure program for performing SCF- and
MCSCF-gradient calculations, together with a variety of
techniques for post Hartree Fock calculations.
- GAMMA (General
Approach to Magnetic resonance Mathematical Analysis)
GAMMA is a computer package designed to facilitate
construction of programs that simulate magnetic resonance
phenomena. GAMMA is centrally located at the National
High Magnetic Field Laboratory (NHMFL) as part of the
Center for Interdisciplinary Magnetic Resonance (CIMAR).
- Gaussian
Basis Set Order Form
The Environmental Molecular Sciences Laboratory (EMSL)
Basis Set Order Form allows you to extract Gaussian basis
sets, and any related effective core potentials, from the
Molecular Science Research Center's Basis Set Library. A
user may request the basis set be formatted appropriately
for a wide variety of popular electronic structure
packages. In addition to the exponents and contraction
coefficient which define the basis set, the user can
obtain descriptive data which includes the overall
philosophy behind the basis, literature citations, the
angular momentum composition of the basis and many other
pieces of information.
- GRASP
GRASP: Graphical Representation and Analysis of
Structural Properties by Anthony Nicholls.
- GROMOS96
GROMOSTM is a general-purpose molecular
dynamics computer simulation package for the study of
biomolecular systems.
- Hazardous
Chemical Database
This database will allow the user to retreive information
for any of ~2000 hazardous chemicals based on a keyword
search. Potential keywords include names, formula and
registry numbers (CAS, DOT, RTECS and EPA).
Primary resources for this database:
* 1996 North American Emergency Response Guidebook
NAERG96, 1996.
* Hazardous Chemicals Data. NFPA 49, PC-49-94, 1994.
* The Merck Index 11th edition, 1989.
- HBPLUS
HBPLUS is a hydrogen bond calculation program.
- History
of Chemical Engineering & Chemical Technology
The goal is to bring you a history of chemical
engineering that encompasses its conceptual origins in
Great Britain, subsequent struggle for survival in the
United States, and concludes with a cornucopia of
contributions made in this Century.
- History
of Science, Technology and Medicine
The WWWVL for the history of science, technology and
medicine was established on 6 September 1994 to keep
track of information facilities in the field of the
history of science, technology and medicine.
- Hückel
molecular orbital calculator
HMO performs Huckel theory calculations on planar
conjugated hydrocarbons. Undergraduate students find HMO
easy to learn and use. HMO accepts input interactively
with helpful suggestions. It traps and diagnoses common
student input errors. HMO calculates molecular orbital
coefficients and energies, pi-electron populations
(densities), bond orders, bond lengths, free valences and
self polarizabilities. Basic information on use of
reactivity indices is presented. HMO requires less than
120KB of free memory.
- ICON-EDiT
ICON-EDiT an Extended-Hueckel and Oscillator Strength
Calculation Package.
- Internet
Course on The Principles of Protein Structure
The main entry point into all aspects of the Internet
Course on The Principles of Protein Structure organised
by Birkbeck College in collaboration with the Virtual
School of Natural Sciences(VSNS) of the Globewide Network
Academy (GNA).
- JCPExpress
The JCPExpress is a free trial service for electronic
distribution of preprints of manuscripts between
acceptance and publication in the Journal of Chemical
Physics.
- Journal of
Biological Chemistry
Web version of the Journal of Biological Chemistry,
published by The American Society for Biochemistry and
Molecular Biology.
- Journal
of Molecular Modeling
Journal of Molecular Modeling, the first fully electronic
chemistry journal, was launched on 1 January 1995. The
new journal is an attempt to overcome the financial
problems associated with publishing full color
illustrations conventionally at a reasonable cost and to
avoid long publication delays.
- KLOTHO
Klotho: Biochemical Compounds Declarative Database
Klotho is part of our attempt to model biological
processes, beginning with biochemistry.
- MacroModel
The MacroModel molecular modeling software package allows
the user to construct and graphically manipulate both
simple and complex chemical structures, to apply
molecular mechanics and dynamics techniques to evaluate
the energies and geometries of molecules in vacuo or in
solution, and to display and examine graphically the
results of the modeling calculations.
- MDBNCH
Informations on MDBNCH, a molecular dynamics benchmark.
- MOIL (MOlecular
dynamics at ILlinois) (This is most likely outdated, I
can't find a working address!)
MOIL is a public domain molecular dynamics program that
is available via anonymous ftp. The code was developed by
Ron Elber, Adrian Roitberg, Carlos Simmerling Haiying Li,
Gennady Verkhivker and Robert Goldstein, Other
contributers that helped in testing, developing parameter
sets and writing documentation: Danuta Rojewska, Chyung
Choi and Alex Ulitsky.
- MOIL-View
(MOlecules at ILlinois)
MOIL-View (MOlecules at ILlinois) is a program for SGI
and IBM RS/6000 workstations designed to allow the user
to view and analyze molecular structures and dynamics.
The program ia available via anonymous ftp, with full
FORTRAN source code and documentation provided. Version
8.0 is a major upgrade from previously available
versions.
- MOLDEN
MOLDEN a visualization program of molecular and
electronic structure
G.Schaftenaar, CAOS/CAMM Center, the Netherlands
Molden is a package for displaying Molecular Density from
the Ab Initio packages GAMESS * and GAUSSIAN and the
Semi-Empirical packages Mopac/Ampac. (* referred to here
is the european version of GAMESS maintained M.F. Guest
et al, not to be confused with the american version
maintained by M.W. Schmidt et al).
- Moldy
Moldy is a general-purpose molecular dynamics simulation
program. It is sufficiently flexible that it ought to be
useful for a wide range of simulation calculations of
atomic, ionic and molecular systems.
(Keith.Refson@earth.ox.ac.uk)
- Molecular
Dynamics News Letter
Molecular Dynamics News Letter: Home Page. MDN is edited
by Prof. Roger W. Anderson, Deptartment of Chemistry,
University of California, Santa Cruz, CA 95064, U.S.A.
(ANDERSON@CATS.UCSC.EDU) and Prof. Vincenzo Aquilanti,
Dipartimento di Chimica dell' Universitß, 06123 Perugia,
Italy (PGKIN@IPGUNIV.UNIPG.IT)
- Molecule
of the Month
Each month a new molecule will be added to the list on
this page. The links will take you to a page at one of
the Web sites at a University Chemistry Department or
commercial site in the UK, the US, or anywhere in the
world, where useful (and hopefully entertaining!),
information can be found about a particularly interesting
molecule.
- Molpro
MOLPRO is a complete system of ab initio programs for
molecular electronic structure calculations, written and
maintained by H.-J. Werner and P. J. Knowles, and
containing contributions from a number of other authors.
As distinct from other commonly used quantum chemistry
packages, the emphasis is on highly accurate computations
for small molecules, with extensive treatment of the
electron correlation problem through
multiconfiguration-reference CI wavefunctions.
- MolView
MolView is a molecular rendering program for the
Macintosh capable of reading most molecular data files
and can create output in a MolView file, PICT file, or
QuickTime movie format.
- MolEdit
MolEdit is an editor specially designed to prepare
input-files for quantum-chemical programs. The
molecule-viewer allows to rotate and to translate the
molecule. The structure can be displayed in five
different ways: Wire-frame, Ball-and-Stick, Dot-clouds,
Grid, Spheres.
- MOLSCAT
MOLSCAT is a code for quantum mechanical (coupled
channel) solution of the nonreactive molecular scattering
problem.
- Molecular Simulations Inc.
The Molecular Simulations Inc. (MSI) Home Page. MSI's
software combines the core atomistic simulation
technologies of molecular mechanics and quantum mechanics
with molecular visualization, modeling and instrument
simulation to provide solutions in science &
industry.
- MOLFDIR
Program Package
The MOLFDIR code is a quantum chemistry code that does
molecular Fock-Dirac many-electron calculations and
additional correlation calculations.
- MORASS
The MORASS Experience -
Multiple Overhauser Relaxation AnalysiS and Simulation
MORASS uses a full hybrid matrix eigenvalue/eigenvector
solution to the Bloch equations to derive
cross-relaxation rates and interproton distances. MORASS
analyzes 2D NMR NOESY data from oligonucleotides and
proteins to evaluate cross-relaxation rates from which
interproton distances are obtained. These are output in a
format suitable for use as distance constraints in
molecular dynamics calculations.
For more information please feel free to contact
"Bruce A. Luxon".
- MR Recources
MR Resources, your complete one-stop mangnetic resonance
supply house, proudly welcomes you to our office on the
Web. We are the first and only company dedicated to NMR
service.
- MSMS
MSMS allows to compute very efficiently triangulations of
Solvent Excluded Surfaces. This program is written using
the C programing language and can be used as a standalone
program or as an AVS (Advanced Visualisation System)
module. It has shown to be very reliable and produces
very regular triangulations.
- NAB
The NAB molecular manipulation language. Generation of
Models for "Unusual" DNA and RNA: A Computer
Language for Structural Exploration by Tom Macke and
David A. Case at the The Scripps Research Institute, La
Jolla.
- NAMD
The Theoretical Biophysics group at the University of
Illinois and the Beckman Institute would like to announce
the availability the program namd, a new package for high
performance parallel molecular dynamics simulations. This
software is being made available to the structural
biology research community free of charge, and includes
the source code for namd, documentation, and precompiled
binaries for various parallel platforms The
documentation, in postscript form, includes a programmers
guide and a users guide.
The software itself is available via anonymous ftp in the
directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/namd
Related information can be found in: VMD -
Visual Molecular Dynamics
- Nanothinc
Nanothinc is an Internet-based
publisher/developer/distributor webcasting interactive
and enhanced multimedia nanocontent.
- NAOMI
NAOMI is a computer program system for studying the
three-dimensional structure of proteins at the atomic
level.
- National
Institute of Standards and Technology (NIST)
- NIST WebBook
The NIST (National Institute of Standards and Technology)
WebBook provides access to the full array of data
compiled and distributed by NIST under the Standard
Reference Data Program. The current edition, the
Chemistry WebBook, contains: Thermodynamic data on an
extensive set of organic and small inorganic compounds -
enthalpy of formation, heat capacity and entropy for over
5000 compounds. A large set of ion-energetics data -
ionization potential and appearance potential for over
10000 compounds.
- NCBI Genbank
National Center for Biotechnology Information. The NCBI
is responsible for building, maintaining, and
distributing GenBank, the NIH genetic sequence database
that collects all known DNA sequences from scientists
worldwide.
- NetLib
Netlib is a collection of mathematical software, papers,
and databases. The Netlib repository contains freely
available software, documents, and databases of interest
to the numerical, scientific computing, and other
communities.
- Network Science
This service provides articles and information about
products, people, positions and topics of interest in the
chemical, pharmaceutical and biotechnology industries.
- 13C-NMR-Module
for Windows
13C-NMR-Module for Windows by: H.Hoenig; Copyright (C)
May 1995
Description:
The module essentially consists of two main parts:
- 13C-NMR-shift prediction of acyclics(C1-C6, all
isomers; C8, alkenes, alkines) and rings (C3-C8
isocyclics; aromatics like benzene, naphthalene,
anthracene and quinoline; and decalines).
- Data input, storage and retrieval for 13C-NMR
data from own spectra or literature values. Built
in formula checks, retrieval of name segments or
empirical formulas, spectral display (including
comparison of two spectra) and printout.
Presently roughly 700 spectra are contained in
the beta-version.
- O
Molecular graphics program for the process of building a
model from initial electron density maps for solving
x-ray structures.
- ORTEP-III
ORTEP-III, Oak Ridge Thermal Ellipsoid Plot Program for
Crystal Structure Illustrations.
- Oxford Molecular
Oxford Molecular was established in 1989 to facilitate
the commercialisation and rapid transfer of new
computational chemistry software developed in the world's
finest academic research laboratories for use in
industry.
- PDB++ and PDB libraries
PDB++ is available by ftp from cgl.ucsf.edu as
/pub/libpdb++.shar; there is also a C version with the
name /pub/libpdb.shar. All it does is handle line-by-line
I/O of PDB files, so it saves you the trouble of having
to deal with Fortran-formatted files from C or C++.
- PERCH
(PEak reseaRCH) - an integrated
NMR-software package for research, analytics and
education. The spectral analysis and simulation up to 10
spins is based on the program MLDC (Modified LAOCOON with
Dipolar Couplings)" - PERCH Project,
Univ. of Kuopio, FINLAND. The
U.S. source of information is here
- PMD -
Scalable Parallel Molecular Dynamics
PMD is a scalable, parallel program for the efficient
simulation of the molecular dynamics of biological
macromolecules. PMD utilizes the Greengard/Rokhlin Fast
Multipole Algorithm to allow the simulation of very large
biological macromolecular systems without sacrificing the
important long-range Coulomb interactions. PMD is
suitable for high powered parallel supercomputers as well
as for single workstations and desktop PCs.
- Q-CHEM Home Page
Q-Chem is a quantum leap into the future of chemistry,
providing HF, DFT, and Hybrid HF-DFT methods in quantum
chemistry.
- QCPE
Home Page
You can also try the QCPE ftp to get
information about the Quantum Chemistry Program Exchange
(QCPE) program library and catalogues.
- The QSAR
Server
The Quantitaitve Structure-Activity Relationship Server
at UNC Chapel Hill.
- RAMVIB
RAMVIB is a set of FORTRAN programs to ease pains of
interpreting resonance Raman spectra of metalloproteins
and metalloporphyrins. It uses normal mode analysis
approach to model vibrations of molecules.
- RasMol
RasMol molecular graphics visualization tool for UNIX,
VMS, Macintosh and Microsoft Windows (OS/2 and Windows
NT).
- RE_VIEW
Re_View is essentially a molecular viewer, animator,
analyzer, and MOPAC reaction path and MOPAC vibrational
analysis converter. The program runs under Windows 3, and
although the program definitely benefits from 8 Mbytes
(or even more memory) the minimum recommended memory is 4
Mbytes.
- REVIEWS IN
COMPUTATIONAL CHEMISTRY
Besides the table of contents for every volume and
general information about the books, this home page gives
inclusive pagination for each chapter in the published
volumes, so these data are readily available to
individuals who wish to cite a chapter. Contents of the
volumes in press are provided too.
The Question and Answers offer a useful, sometimes
lighthearted, look at the book series. The Author and
Subject Index pages are provided as a free online
citation index of published volumes.
This home page is also used to post supplementary
material, color graphics, errata, and other items the
authors ask to be posted. Those chapters for which there
are additional items available are signified by having a
hypertext link where they are listed in the tables of
content.
We like to hear from our readers. We seek to improve our
efforts, so suggestions are appreciated. Feel free to use
the e-mail address given at the end of this document.
- DATABASE
'RTAM'
DATABASE "Relativistic Theory of Atoms and
Molecules" (RTAM), (C) Pekka Pyykko
This database contains the bibliography part of the two
books "Relativistic Theory of Atoms and Molecules
I-II" (Springer, Berlin, 1986 and 1993), (LNCh 41
and 60) as well as additional references, mainly from
1993-1996. The contents of the references are analyzed in
the books.
- SCARECROW
Molecular graphics visualization tool and MD trajectory
analysis program.
- Schrödinger Inc.
Schrödinger is a software company committed to the
development of highly refined and efficient software to
solve electronic structure problems. During the past
several years, Schrödinger has developed a new approach
to solving ab initio electronic structure equations which
involves the use of pseudospectral methods. These new
algorithms are now available in the program PS-GVB.
- Sequence
Retrieval System (SRS) links together all the most
important set of biological databases. The user interface
is based solely on WWW. Great system!
- SoftShell Online
SoftShell Online has discussions and information on: Web
publishing of chemical papers, the free ChemWeb GIF
structure editor, and other chemistry software, such as
ChemWindow and ChemIntosh.
- Software
at 'cuhhca.hhmi.columbia.edu'
- CIF Directory of Crystallographic
Information File (CIF) programs and data
- CW Directory of Crystallographic Workbench
programs, data and doc.
- MADSYS MAD System of programs from Wayne
Hendrickson and modified by Bill Weiss.
- MMQL Macromolecular Query Language -
System to ask intelligent questions of the PDB
data See Shindyalov et al. Protein Engineering
Nov. 1994.
- PDB Directory of tools and libraries to
use on PDB data.
- WPDB The PDB through Microsoft Windows -
PC based software to query and display structures
stored in compressed form.
-
- Software at
'rani.chem.yale.edu'
drwxr-xr-x 2 root sys 512 Nov 16 1993 MindTool
drwxr-xr-x 2 root sys 512 Feb 3 1992 eht
-rw-r--r-- 1 root sys 22541 Jul 2 1993 freeread.tar.Z
drwxr-xr-x 3 root sys 512 Jan 5 13:22 psi88
-rw-r--r-- 1 root sys 210091 Aug 25 1992 xcalc.tar.Z
- Software at
'sdchemi2.ucsd.edu'
- Alberta/Caltech Version 3.0 of Frodo/TOM, a
molecular modelling program for crystallographic
map-fitting on SGI IRIS workstations.
- The UCSD Molecular Modeling System, by Steve
Dempsey.
- SPARTAN
Spartan is a computational chemistry software package, by
Wavefunction Inc., that is designed to be an easy to use,
yet extensive modelling package that is ideal for the
bench and theoretical chemist alike.
- Steric
A Program to Calculate the Steric Size of Molecules about
a Point in terms of their Cone Angles and Solid Angles,
as well as their total Volumes and Projected Areas.
- SwaN-MR
(NMR data processing)
SwaN-MR is a program for the Macintosh (requires FPU) and
Power Macintosh, and it processes and analyzes NMR
spectra. It is also very useful in annotating, printing
and presenting spectra. Spectra coming from Varian
Gemini, Bruker AC and Bruker AMX have been routinely
processed. Some VXR, Unity and TecMag files can be
converted. SwaN-MR was conceived to deal with
4-dimensional data-sets.
- THEOCHEM
The THEOCHEM HomePage on the Elsevier WWWW-server.
The HomePage is updated regularly and gives a wealth of
information, o.a.
- Editorial Information containing background information
on the
recent changes which are aimed at increasing the quality
of the journal
- Full addresses of Editors (incl. email addresses) and
Editorial Board Members
- Instructions to authors
- List of forthcoming and published special issues
- Information on Elsevier Books and journals in the area
- Links to other sites of interest to computational
chemists
- Information on electronic initiatives related to
THEOCHEM
* THEOCHEM-Alert: a free email service for automatically
obtaining
the Table of Contents of Fortcmoming issues.
- Tinker
The TINKER molecular modeling software is a complete
package for molecular mechanics and dynamics of
molecules, especially polypeptides. The distribution
version of TINKER, with full source code, is made
available free of charge to anyone who wants it.
- Tripos Home Page
Tripos is a supplier of scientific software and services
to facilitate the discovery of new therapeutic and
bioactive compounds in the pharmaceutical,
biotechnological, chemical, and agrochemical industries.
- UniChem
The UniChem environment is a complete, easy-to-use
molecular modeling package that provides a single,
graphical interface to a variety of powerful quantum
mechanics programs. Researchers may easily apply advanced
theoretical methods to complex molecular systems such as
pharmaceuticals, proteins, agrochemicals, catalysts, and
materials
- UNIMOL
This directory contains Fortran code, sample input and
sample output for the UNIMOL package. Theory for use of
the programs is described in the text "Theory of
Unimolecular and Recombination Reactions" by R G
Gilbert and S C Smith, Blackwell Scientific Publications,
Oxford (UK) and Cambridge (Mass.), 1990. The manual is in
the doc/ directory.
- Virtual
Chemistry Viewer
Virtual Chemistry INC. has developed a PC molecular
graphics viewer (VCHEM) that has been designed to produce
high quality visualizations and hardcopy stills. The
viewer is based on the OpenGL 3D graphics standard and
has been developed for Windows 95 and NT PCs.
- VMD -
Visual Molecular Dynamics
The Theoretical Biophysics group at the University of
Illinois and the Beckman Institute would like to announce
the availability of version 1.0 of the program VMD, a new
package for the graphical display and visualization of
biomolecular systems. This software is being made
available to the structural biology research community
free of charge, and includes the source code for VMD,
documentation, and a precompiled binary for Silicon
Graphics workstations running version 5 or later of the
IRIX operating system. The documentation, in postscript
form, includes an installation guide, a users guide, and
a programmers guide for interested researchers. VMD also
provides on-line help through the use of an external HTML
viewer such as Mosaic or Netscape.
The software itself is available via anonymous ftp in the
directory: ftp://ftp.ks.uiuc.edu/pub/mdscope/vmd
Related information can be found in: NAMD
- WebLab
Viewer
The WebLab Viewer is a high-performance graphical
molecular viewer. The viewer supports a number of popular
CAMD file formats: Cerius2, Insight II, Catalyst,
Brookhaven PDB, Cambridge Crystallographic, MDL MOL, and
Sybyl MOL2 files. The WebLab Viewer supports several
different graphics rendering schemes as well. Basic CPK,
Line, Ball and Stick, and Stick styles are available for
all molecules. For advanced protein and DNA
visualization, the WebLab Viewer provides: C Alpha Trace,
Ribbon, Ladder, and Schematic (Richardson) displays. In
addition, molecules with Unit Cell information can have
advanced Symmetric and Periodic display options. It is
supported on the WindowsNT, Windows95, Windows 3.1, Power
Macintosh and Macintosh platforms.
- WebMol
Java PDB Viewer
WebMol was designed to display and analyse
structural information contained in theBrookhaven Protein
Data Bank (PDB).
- The
WWW Chemical Structures Database
The WWW chemical structures database contains more than
2250 automatically collected chemical structures from the
Internet, complete with information about the refering
HTML pages. This database is searchable with the usual
chemical search operations - full-structure and
substructure search, formula search, name search, and
more.
- WHAT IF
WHAT IF is a versatile protein structure analysis program
that can be used for mutant prediction, structure
verification, molecular graphics, etc.
- The World Wide Chemnet
The World Wide Chemnet is the first to bring buyers of
chemicals (including petrochemicals, oils, solvents,
gasses, specialty products, and even raw materials)
together with manufacturers, distributors, and packagers
via the Internet and the World Wide Web.
- WWW
Links for Chemists
Pages provide a selection of links to chemistry resources
worldwide as well as links to the staff, research,
undergraduate courses and postgraduate opportunities
pages at other UK University Chemistry Departments.
- XMol
Molecular structure viewer using X-Window system. XMol FAQ
- X-PLOR
Axel Brunger's Research Group and the X-PLOR Home Page
- Xtal
View
XtalView is a complete package for solving a
macromolecular crystal structure by isomorphous
replacement, including building the molecular model.
- YAeHMOP
Home Page
This page exists to provide easy access to Yet Another
extended Hückel Molecular Orbital Package (YAeHMOP). A
package of programs for performing extended Hückel
calculations and visualizing the results.
Copyright Leif Laaksonen/CSC 1995,1997
Please feel free to throw me with a mail if you have any opinions
or suggestions about this list (E-mail:
Leif.Laaksonen@csc.fi ).
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