Software Catalog

ASAD

url:

http://www.atm.ch.cam.ac.uk/acmsu/asad/index.html

abstract:

ASAD is a package that has been developed for integrating chemical schemes in atmospheric models.

targetenvironment:

contact:

mail to glenn@atm.ch.cam.ac.uk

CHARMM

url:

file:///MACHD/Desktop%20Folder/tmp/charmm.doc

abstract:

A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. Molecular dynamics package using Chemistry at Harvard Macromolecular Mechanics force field. Extensive scripting language for molecular mechanics, simulations, solvation, electrostatics, crystal packing, vibrational analysis, free energy perturbation (FEP) calculations, quantum mechanics/molecular mechanics calculations, stochastic dynamics, and graphing data.

targetenvironment:

Convex, IBM, Intel, Silicon Graphics, Sun, and VAX.

contact:

Dr. Martin Karplus, Department of Chemistry, Harvard University, mail to karplus@huchel.bitnet, brbrooks@helix.nih.gov,

Chem-X

url:

http://edisto.awod.com/netsci/Companies/CDL/products.html#further_inf

abstract:

Chem-X is a modular software system designed for use by specialists and more general users for new product research. Its application range is broad covering agrochemical, petrochemical and pharmaceutical organisations in both academic and industrial environments. Intuitive menus, toolbars and dialogs allow routine tasks to be simply performed by inexperienced users. This is achieved by careful selection of appropriate default options and automation of calculations.

targetenvironment:

contact:

Manufacturer: Chemical Design, Ltd. mail to CHEMDESIGN@applelink.apple.com

AMBER

url:

http://www.atm.ch.cam.ac.uk/

abstract:

AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules.

targetenvironment:

contact:

University of California, mail to pak@cgl.ucsf.edu

Chem3D Pro

url:

http://www.camsci.com/, ftp://ftp.camsci.com

abstract:

Structure building, manipulaition, MM2 energy minimization and molecular dynamics. Molfile conversion. Chem3D for stick, ball-and-stick, and space-filling display. 2D-to-3D conversion. ChemDraw for 2D chemical structure drawing. ChemDraw Pro for color 2D chemical structure drawing. Chem-Finder and ChemFinder Pro for managing libraries of 2D and 3D structures. ChemOffice and ChemOffice Profor integrated combinations of the other programs. Client-server link to Tripos's UNITY. Crossfire Client to Beilstein Handbook database. CS MOPAC for a graphical interface to MOPAC 93.

targetenvironment:

Macintosh, Pcs (Windows), Sun, Silicon Graphics, Digital workstations.

contact:

CambridgeSoft Corporation, mail to info@camsci.com, support@camsci.com,

ChemApp

url:

http://gttserv.lth.rwth-aachen.de/~sp/tt/chemapp/chemapp.htm

abstract:

ChemApp provides the powerful calculation capabilities of ChemSage [3] in the form of an easily programmable routine. It consists of an interface containing a library of subroutines that link to data-handling and phase equilibrium calculation modules.

targetenvironment:

contact:

Stephan Petersen, mail to sp@gtt.lth.rwth-aachen.de

ChemPlus

url:

http://www.hyper.com/Descrip/chemplus_features.html

abstract:

ChemPlus is a suite of extensions for HyperChem, bringing powerful new easy-to-use features to the premier desktop molecular modeling system. These include enhanced rendering features, conformational searching capability, RMS overlays for structural comparisons, 3D molecular orbital images, computation of molecular properties, new building tools for crystals and polysaccharides...and more.

targetenvironment:

contact:

Hypercube, Inc., mail to support@hyper.com

CLEW

url:

http://mercury.aichem.arizona.edu/clew.html

abstract:

CLEW is a program that uses machine learning techniques to propose potential pharmacophores. The program operates by examining a set of compounds that display varying degrees of biological activity toward a particular receptor. CLEW begins by examining the compounds and identifying features that may be relevant to biological activity. The program then utilizes inductive machine learning to develop at set of rules that define features present in the active compounds, but not present in the inactive compounds. CLEW uses these rules in conjunction with a set of conformations generated by WIZARD to produce a three dimensional model of a potential pharmacophore.

targetenvironment:

contact:

mail to pat@mercury.aichem.arizona.edu

Hingefind

url:

ftp://lisboa.ks.uiuc.edu/pub/wriggers/hingefind/hingefind.html

abstract:

A novel algorithm to investigate domain motions in proteins.

targetenvironment:

contact:

mail to

HyperChem

url:

http://www.hyper.com/, ftp://ftp.hyper.com/pub/demo

abstract:

Model building, manipulation. Stick, ball-and-stick, space-filling, and dot surface display. Semiempirical calculations by extended Huckel, CNDO, INDO/1, INDO/S, MINDO/3, MNDO, AM1, PM3, ZINDO/1, and ZINDO/S. UV, IR, electrostatic potential, and molecular orbital plots. 2D-to-3D conversion. Protein and DNA fragment libraries. MM+, BIO+ (implementations of MM2 and CHARMM, respectively), OPLS, and AMBER molecular mechanics and dynamics. Solvent box. ChemPlus for structure fitting, 3D rendering, crystal building, conformaitonal searching, sequence editing, and computing log P and other QSAR properties. HyperNMR for quantum mechanical computational prediction of chemical shifts and coupling constants.

targetenvironment:

PCs (DOS and Windows) and client to UNIX servers.

contact:

Hypercube, Inc., mail to info@hyper.com

HyperChem®

url:

http://synapse.bio.com/cgi-bin/bio1/product/2000812?se=hcdTc8jF&pg=397

abstract:

HyperChem® is an integrated and flexible molecular modeling product for chemists. It is a powerful package with capabilities for visualizing, analyzing, and simulating molecules, and for communicating information about molecular structures.

targetenvironment:

contact:

Hypercube, mail to sales@bio.com

HyperNMR

url:

http://www.hyper.com/Descrip/hypernmr_features.html

abstract:

This is an extension of ChemPlus. HyperNMR can load a molecular system using different file formats, including a Z-matrix format or the HIN format of HyperChem. Molecular systems can also be transferred directly into HyperNMR via Dynamic Data Exchange. from HyperChem. The molecular system can then be displayed using various rendering methods.

targetenvironment:

contact:

Hypercube, Inc., mail to support@hyper.com

MACCS-II & REACCS

url:

http://www.mdli.com/mbuhome.html

abstract:

MACCS-II, the Molecular ACCess System, is an interactive, graphical environment for the storage and retrieval of chemical information on mini/mainframe computers. MACCS-II allows scientists to use the language of chemical structures to retrieve, search, view, and print information related to chemical compounds. The MACCS-II standard configuration includes the Power Search Module, providing similarity searching and generic substructure (Rgroup) searching. REACCS, the REaction ACCess System, is an interactive graphical environment for the storage and retrieval of chemical reaction information on mini/mainframe computers. REACCS lets scientists search reaction databases using structure, text, and data queries to find information on chemical syntheses. Scientists can simultaneously search several databases covering different types of chemistry, including synthetic chemistry and heterocyclic chemistry among others. REACCS lets the user review a broad cross-section of novel significant reactions and allows access to years of collected reaction information in minutes.

targetenvironment:

contact:

MDL Information Systems, In., mail to techsupp@mdli.com

MacroModel

url:

http://www.columbia.edu/cu/chemistry/mmod/mmod.html

abstract:

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. Energy calculations use MM2*, MM3*, AMBER* or OPLSA* force fields, and an analytical GB/SA continuum treatment for solvation. Energetic processes are monitored interactively by MacroModel and can include multiple simultaneous tasks. Energetic calculations may be carried out on full structures or substructures prepared with the MacroModel substructure editor.

targetenvironment:

VAX, Convex, Alliant, Cray, and UNIX workstations.

contact:

University of California, mail to pak@cgl.ucsf.edu

AMBER

url:

http://www.atm.ch.cam.ac.uk/

abstract:

AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules.

targetenvironment:

contact:

AsahiKasei Joho Sys.Co., Ltd. Kenji Minami, mail to minami@ss.tokyo.asahi-kasei.co.jp

MDScope

url:

http://www.ks.uiuc.edu/Research/mdscope/

abstract:

MDScope is an integrated set of computational tools which functions as an interactive visual computing environment for the simulation and study of biopolymers. The project implements standard visualization and simulation methods and offers a foundation for testing new algorithms and capabilities. Three major software components. (The programs can be used together or independently.):

(1). VMD (Visual Molecular Dynamics) is program for interactive display and animation of molecules; It runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library is available. Full source code and binaries for SGI's running IRIX 5.X are included in the distribution. (Note: I did not check the possibility to compile under Linux, however since the source code is available, it could be compiled. See WWW page for details.), http://www.ks.uiuc.edu/Research/vmd/.

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Contact: vmd@ks.uiuc.edu

(2). NAMD (Not (just) Another Molecular Dynamics program) is a MD program designed for the simulation of large biomolecular systems on distributed memory machines. It is written in C++ in a modular fashion so that new algorithms may be readily tested. (Note: this should be fully Linux compatible, as suggested by authors of NAMD.) http://www.ks.uiuc.edu/Research/namd/ Contact: namd@ks.uiuc.edu.

(3). MDComm is a set of communications routines and programs which exchanges simulation data and interactive forces between NAMD and VMD. It is built on the RAPP software package (developed by Rick Kufrin at NCSA), which simplifies the process of building and maintaining interactive client/server applications. (Note: The latest MDComm library is still under development and the source code and pre-built binaries will be released once it is completed.) http://www.ks.uiuc.edu/Research/mdcomm/

targetenvironment:

contact:

, mail to

MOIL

url:

ftp://128.248.186.70

abstract:

Molecular dynamics and minimization of proteins; locally enhanced sampling and free energy calculations along reaction paths by perturbation or thermodynamic integration. Hewlett-Packard, IBM, Silicon Graphics, and Stardent workstations.

targetenvironment:

contact:

Dr. Ron Elber, Department of Physical Chemistry and the Israel Center for Structural Biology, The Hebrew University, mail to ron@ala.fh.huji.ac.il, ron@pap.chem.uic.edu

Moldy

url:

ftp://earth.ox.ac.uk/pub/

abstract:

Molecular dynamics of solvated mineral surfaces.

targetenvironment:

UNIX and VAX.

contact:

Dr. Keith Refson, Department of Earth Sciences, mail to Oxford University, keith@earch.ox.ac.uk

NAMD

url:

http://www.ks.uiuc.edu/Research/namd/

abstract:

NAMD is a parallel, object-oriented molecular dynamics program designed for high performance molecular dynamics simulations of large biomolecular systems. NAMD is made available via anonymous ftp free of charge by the Theoretical Biophysics Group of the Beckman Institute at the University of Illinois at Urbana-Champaign. It is part of the MDScope system which links NAMD with the molecular graphics program VMD to allow researchers to view and interact with a running molecular dynamics simulation.

targetenvironment:

contact:

, mail to

Nemesis

url:

http://www. oxmol.co.uk/

abstract:

Structure building, manipulation. Stick, ball-and-stick, space-filling, and dot surface display. Energy calculations with the COSMIC force field. Partial charges from Charge-2. PC-PROT+ (sequence analysis), PC-TAMMO+ (protein-lipid modeling), and MASCA (statistics).

targetenvironment:

Macintosh and Pcs (Windows).

contact:

Oxford Molecular Inc., mail to syazdi@presto.ig.com or Oxford Molecular Ltd., mail to omlemail@vax.ox.ac.uk (U.K.)

PMD --- Scalable Parallel Molecular Dynamics Simulation

url:

http://tincan.bioc.columbia.edu/Lab/pmd/

abstract:

This is an extension of ChemPlus. PMD is a scalable, parallel program for the efficient simulation of the 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.

targetenvironment:

contact:

mail to windemut@cumbnd.bioc.columbia.edu

AMBER

url:

http://www-prophet.bbn.com, ftp://www-prophet.bbn.com (192.1.100.150), gopher://www-prophet.bbn.com

abstract:

Molecular building, molecular mechanics, simulations, and graphics. Statistical and mathematical modeling and display. Sequence analysis. Structural and sequence database retrievel.

targetenvironment:

contact:

BBN System and Technologies Corporation, mail to prophet-info@bbn.com

QUANTA/CHARMm

url:

ftp://avs.ncsc.org

abstract:

Structure building, manipulation, energy minimization, molecular dynamics, Boltzmann jump Monte Carlo conformational searching, and proteing homology building. QUANTA molecular graphics system is integrated with the CHARMm molecular dynamics software using force fields derived from the Chemistry at Harvard Macromolecular Mechanics force fields and the Merck Modeling Force Field. Cluster CHARMm and FARMm CHARMm for simulations in clustered computing environments. X-PLOR for X-ray and NMR structure refinement and simulated annealing. Crystal Workbench combining Quanta and X-PLOR. NMR Workbench with NMR.Pipe and NMR.Compass for multidimensional spectral processing and assigning peaks to proteins. QUANTA/NMR for protein construction. QUANTA/Bones for fitting electron density maps, X-FIT for model fitting, QUANTA/StAR for X-ray model building. QSPR-Polymer for property estimation. Enzymix for enzymatic reaction energies. Polaris for modeling and solvation free energies. UHBD for Brownian dynamics. BIOGRAF for modeling of drugs, proteins, carbohydrates, lipids, and DNA/RNA. Polygraf for modeling and structure-property analysis. Cerius suite of programs for modeling of polymeric, small molecular, and inorganic material. Drug Discovery Workbench (DDW) for spreadsheet QSAR with modules C.Alignment, C.Analysis, C.Conformers, C.Genetic Alsorithms, C.MSA, C.QSAR+, C.Receptor, and C.Visualizer. MCSS for identifying ligand binding sites; GROUPBUILD and HOOK for de novo ligand design. MODELER to build proteins by homology. Quantum Mechanics Workbench with modules C.MOPAC, C.Garssian, and C.CASTEP for plane wave pseudopotential calculations of solids and surfaces. C.SDK for software developer's kit.

targetenvironment:

contact:

Molecular Simulations Inc., mail to support@msicam.com.uk

Re_View

url:

http://http1.brunel.ac.uk:8080/depts/chem/ch241s/re_view/re_view.htm

abstract:

Re-View is a 4D-chemical viewer/analyser which is capable of 3D-molecular display, animation (4D-display), geometrical analysis. Re_View runs under Windows 3, and requires a the minimum of 4 Mbytes of memory.

targetenvironment:

contact:

, mail to

SCULPT

url:

http://www.intsim.com/index.html

abstract:

The SCULPT interface and the paradigm embody a radically different approach to computer-based molecular modeling in that it lets a user manipulate a structure in a direct and intuitive manner. SCULPT has made improvements over other modeling systems in that it couples the user's manipulations of a structure to a novel minimization algorithm that is orders-of-magnitude faster than conventional methods.

targetenvironment:

contact:

Interactive Simulations, Inc., mail to intsim-sales@intsim.com

SPARTAN

url:

http://www.atm.ch.cam.ac.uk/

abstract:

Model building, molecular mechnics (SYBYL, MM2, MM3), and ab initio (Hartree-Fock, Moller-Plesset, direct HF) and semiempirical (MNDO, AM1, PM3) molecular orbital calculations with and without solvent effects. Graphical front-end and postprocessor of the output. Electron density and electrostatic plots.

targetenvironment:

Interface to Gaussian 92. Convex, Digital, Hewlett-Packard, IBM, and Silicon Graphics versions.

contact:

Wavefunction, Inc., mail to sales@wavefun.com, support@wavefun.com

SYBYL

url:

http://www.nih.gov/molecular_modeling/mmhome.html ftp://extreme.chem.rpi.edu

abstract:

An integrated molecular modeling package with capabilities for molecular mechanics, conformational searching, minimization, semiempirical and ab initio molecular orbital calculations, molecular graphics, active analog approach, and molecular dynamics.

targetenvironment:

contact:

Tripos, Inc., mail to support@tripos.com

VMD

url:

http://www.ks.uiuc.edu/Research/vmd/

abstract:

VMD is a molecular visualization and analysis program designed to be easy to use and modify. It runs on Silicon Graphics workstations and may be compiled for HP-UX workstations if the NPGL library is available. Full source code and binaries for SGI's running IRIX 5.X are included in the distribution. VMD is made available via anonymous ftp free of charge by the Theoretical Biophysics Group, located in the Beckman Institute of the University of Illinois at Urbana-Champaign.

targetenvironment:

contact:

, mail to

WHATIF

url:

http://swift.embl-heidelberg.de/whatif/, ftp://swift.emb-heidelberg.de/pub/whatif/writeup

abstract:

Protein modeling package with molecular graphics, homology building, database searches, and options for NMR- and X-ray-related work. Interfaces to GROMOS, GRID, RIBBONS, and DSSP.

targetenvironment:

contact:

Dr. Gert Vriend, European Molecular Biology Laboratory, mail to vriend@embl-heidelberg.de

Quantum chemistry calculations

CACAO

url:

ftp://cacao.issecc.fi.cnr.it (149.139.10.2)

abstract:

targetenvironment:

contact:

Dr. Davide M. Proserpio, Istituto di Chimica Strutturistica Inorganica dell', Universita di Milano, mail to stinch@imisiam.mi.cnr.it, mealli@cacao.issecc.fi.cnr.it

CADPAC

url:

http://www.cray.com/PUBLIC/DAS/files/CHEMISTRY/CADPAC.txt

abstract:

Cambridge Analytical Derivatives Package. General purpose ab initio calculations. Cray and other versions. Spectro for analyzing anharmonic force fields and calculating positions and intensities of lines, including Fermi resonance effects.

targetenvironment:

contact:

Lynxvale WCIU Programs, mail to cadpac@theory.chemistry.cambridge.ac.uk

keyword:

comments:

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COLUMBUS Program System

url:

ftp://ftp.tcg.anl.gov (146.137.200.2)

abstract:

Modular FORTRAN programs for performing general ab initio, multireference single and double excitation configuration interaction (CI), averaged coupled-pair functional, and linearized coupled-cluster method calculations.

targetenvironment:

contact:

Department of Chemistry, Ohio State University, mail to shavitt@mps.ohio-state.edu, pitzer@neon.mps.ohio-state.edu, shepard@tcg.anl.gov, lischka@itc.univie.ac.at

keyword:

comments:

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CORMA

url:

http://picasso.ucsf.edu/corma.html

abstract:

corma (COmplete Relaxation Matrix Analysis) is a FORTRAN program for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2DNOE experiment.

targetenvironment:

contact:

Thomas James, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, fax: 415.476.8780, mail to james@picasso.uscf.edu

keyword:

comments:

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GAMESS

url:

http://www.msg.ameslab.gov/GAMESS/GAMESS.html

abstract:

GAMESS is a program for ab initio quantum chemistry. Briefly, GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these. Analytic gradients are available for these SCF functions, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies. A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, and together with effective core potentials, all elements up to Radon may be included in molecules. Several graphics programs are available for viewing of the final results. Many of the computational functions can be performed using direct techniques, or in parallel on appropriate hardware.

targetenvironment:

GAMESS runs on nearly all computer systems, workstations or mainframes, scalar or parallel. We have IBM RS/6000 and DEC AXP workstations, and a 8 node IBM SP2 in Ames, and these are the only machines we can guarantee will work correctly. However, versions for many other computer systems exist, including DEC VAX/VMS, IBM mainframes (MVS or VM), Cray, Intel Paragon, Thinking Machines CM-5, and HP, Sun, or SGI workstations, although not all of these will have been tested recently.

contact:

Mike Schmidt, mail to mike@si.fi.ameslab.gov

keyword:

comments:

gamess-users@Glue.umd.edu mailing list. The GAMESS Users List is a Majordomo based list. http://mineral.umd.edu/gamess-users/archive/

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KGNMOL

url:

ftp://malena.crs4.it (156.148.7.12)

abstract:

Ab initio calculations. ATOMSCF, ALCHEMY-II (direct CI and MCSCF), ATOMCI, BNDPKG2 (bands in solids), BROWIAN, GDFB, GDFMOL/GDFMD, HONDO-8, HYCOIN (Hylleraas-CI), MELD (CI), MOLCAS-1, PHOTO (excited states), PLH-91 (band structure of polymers), QMDCP (Kohn-Sham orbitals), REATOM, SIRIUS (complete and restricted active space MCSCF calculations), VEH-91 (Valance Effective Hamiltonian method). KGNGRAF for interactive computer graphics. Molecular dynamics by KGNMCYL, KGNMD, and KGNNCC. PRONET for predicition of backbone conformations of proteins with a neural network procedure.

targetenvironment:

contact:

Dr. Enrico Clementi, Centro di Ricerca, Sviluppo e Studi Superiori in Sardegna,, mail to enrico@crs4.it

keyword:

comments:

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MOLCAS

url:

http://garm.teokem.lu.se/MOLCAS/index.html

abstract:

MOLCAS is a general computer software for electron structure calculations, which emphasizes the use of high quality basis set, the importance of an adequate treatment of electron correlation, and general applicability to closed and open shell systems, to ground and excited states with a balanced treatment. Even if contains programs for single reference calculations, such as MP2, SDCI, Coupled Pair Functional (CPF) or full fourth order MBPT, the main emphasis is on the multiconfigurational approach to the electron correlation problem. The software includes codes for multiconfigurational SCF calculations, using both Complete and Restricted Active Space (CAS or RAS) type wave functions. These wave functions can be used as reference in subsequent Multi-Reference (MR) CI, or Average Coupled Pair Functional (ACPF) calculations.

targetenvironment:

contact:

mail to molcas@garm.teokem.lu.se

keyword:

comments:

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MOLPRO

url:

http://www.tc.bham.ac.uk/molpro/

abstract:

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 the multiconfiguration-reference CI, coupled cluster and associated methods.

targetenvironment:

contact:

Peter Knowles, mail to molpro-support@tc.bham.ac.uk

keyword:

comments:

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MOPAC 93 and MOZYME

url:

http://iti2.net/jstewart/, ftp://qcpe6.chem.indiana.edu(129.79.74.206)

abstract:

MOPAC 93 and MOZYME are Semiempirical Computational Chemistry Programs developed by Fujitsu, and J.J.P. Stewart. MOPAC can be used for the study of the electronic structure and energetics of ground-state and excited-state atoms, molecules, ions, and solids, using the semiempirical methods MINDO/3, MNDO, AM1, and PM3. MOZYME is designed for the study of macromolecules, including proteins, DNA fragments, polymers, and solids. In this Web-Site refers to material within the current page, involves going to a different page.

targetenvironment:

contact:

QCPE, mail to qcpe@ucs.indiana.edu

keyword:

comments:

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MOPLOT2

url:

ftp://infomeister.osc.edu (128.146.36.5)/pub/chemistry/software/SOURCES/FORTRAN/moplot2

abstract:

Orbital and desity plots from linear combinations of Slater or Garssian type orbitals.

targetenvironment:

contact:

Dr. Dennis L. Lichtenberger, Department of Chemistry, University of Arizona, mail to dlichten@ccit.arizona.edu

keyword:

comments:

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Naccess

url:

http://www.biochem.ucl.ac.uk/~roman/naccess/naccess.html

abstract:

Naccess is a stand alone program that calculates the accessible area of a molecule from a PDB file. The program uses the Lee & Richards (1971, J. Mol. Biol., 55, 379-400) method, whereby a probe of given radius is rolled around the surface of the molecule, and the path traced out by its centre is the accessible surface. Typically, the probe has the same radius as water (1.4 Angstroms) and hence the surface described is often referred to as the solvent accessible surface.

targetenvironment:

contact:

mail to sjh@sjh.bi.umist.ac.uk

keyword:

comments:

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OpenMol & gOpenMol

url:

http:// www.mpa-garching.mpg.de/~opmolsrv/OpenMol.shtml

abstract:

OpenMol is an integrated program for electronic structure and property calculations of molecules. User guidance, the evaluation and interpretation of results and computer based learning are the three unique features of OpenMol that distinguish it from all other programs in the field. The concept of OpenMol is based on the fundamental ideas of two software concepts, the (rule based) expert system and the abstract data type model. These together lead to the syntheses of knowledge engineering and numerical data processing and give birth to intelligent software. The rigorous use of these concepts has led to a more fexible program, which is easier for a novice to use but also, through the possibility of rapid prototyping and symbolic manipulation, for an expert to exploit as an important working tool. Abstract data types are at the core of object-oriented technology, allowing for flexibility but preserving the efficiency of numerical operations. gOpenMol is the graphics interface to the OpenMol set of programs. gOpenMol can also be used for the analysis and display of molecular dynamics trajectories and the display of molecular orbitals, electron densities and electrostatic potentials from programs like the GaussianXX.

targetenvironment:

contact:

mail to

keyword:

comments:

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SCWRL.C

url:

http://www.cmpharm.ucsf.edu/~dunbrack/#scwrl

abstract:

SCWRL.C is a program for using the backbone-dependent rotamer library to place sidechains on a backbone template and perform a search on alternate rotamers to remove steric conflicts

targetenvironment:

contact:

, mail to

keyword:

comments:

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UniChem

url:

http://www.cray.com/apps/UNICHEM/Mainpage.html

abstract:

A package with a graphics front-end for structure input and visualizations of electron density, electrostatic potentials, molecular orbitals, and molecular surfaces from quantum applications. Dgauss for density functional theory calculations with nonlocal SCF corrections and geometry optimization. CADPAC for ab initio calculations. MNDO93 for semiempirical molecular orbital calculations. Interface to Gaussian 92 quantum chemistry program.

targetenvironment:

contact:

Cray Research, Inc., mail to sgustaf@rhea.cray.com

keyword:

comments:

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WIZARD

url:

http://mercury.aichem.arizona.edu/wizard.html

abstract:

WIZARD is a conformational analysis program based on the AI techniques of theorem proving. This method begins with a set of axioms of conformational analysis and a set of structural postulates, and applies them to a a given molecule to derive a set of conformations.

targetenvironment:

contact:

mail to pat@mercury.aichem.arizona.edu

keyword:

comments:

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Databases of molecular structures

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Cambridge Structural Database

url:

http://csdvx2.ccdc.cam.ac.uk

abstract:

Database with more than 130,000 X-ray structures of low-molecular-weight organic and organometallic compounds. QUEST for data retrieval using connectivity and text searching. QUEST3D for 3D structure searching. PLUTO for stick, ball-and-stick, and space-filling plots of retrieved 3D structures. GSTAT for statistical summaries of molecular geometrical data retrieved by QUEST, and VISTA for interactive statistical analysis. BUILDER converts structures to CSD format. The CSD is also available in MACCS and UNITY formats.

targetenvironment:

contact:

Cambridge Crystallographic Data Centre, mail to software@crystallography.chemistry.cambridge.ac.uk

keyword:

comments:

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Current Facts in Chemistry

url:

http://www.beilstein.com

abstract:

Database of 2D structures, data, and reactions.

targetenvironment:

contact:

Beilstein Information Systems, Inc., mail to helpdesk@beilstein.com(Germany)

keyword:

comments:

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GenBank

url:

ftp://ncbi.nlm.nih.gov (130.14.25.1)

abstract:

targetenvironment:

contact:

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health.

keyword:

comments:

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ISIS

url:

http://www.mdli.com/isishome.html

abstract:

ISIS, MDL's Integrated Scientific Information System, is a client-server software system consisting primarily of ISIS/Draw, ISIS/Base, and ISIS/Host. To meet different customers' needs, MDL packages ISIS as ISIS/Development, ISIS/Chemistry, ISIS/Life Science, and ISIS/Retrieval.

targetenvironment:

contact:

MDL Information Systems, In., mail to techsupp@mdli.com

keyword:

comments:

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Look

url:

http://www.mag.com/products/look/Look2.0.html

abstract:

Look is an integrated protein research tool designed to bring structural insight to molecular biology. Look allows you to search databases, perform analyses, model structures, and visualize data from your own experiments. Combining these into a single package allows a scientist to focus on their own experiments, leaving computer issues like file formats to the computer itself.

targetenvironment:

contact:

Molecular Applications Group, mail to info@mag.com

keyword:

comments:

---

MAG

url:

http://www.mag.com/products/KnowPack.html

abstract:

MAG provides researchers with Knowledge Packages: integrated databases of structure, sequence and literature information, customized for your protein family. Knowledge Packages give researchers a head start in getting the right information.

targetenvironment:

contact:

Molecular Applications Group, mail to info@mag.com

keyword:

comments:

---

Protein Data Bank

url:

http://www.pdb.bnl.gov, ftp and gopher://pdb.pdb.bnl.gov (130.199.144.1)

abstract:

Database of more than 3000 sets of atomic coordinates of proteins and other macromolecules, such as nucleic acids and carbohydrates, derived from X-ray crystallography, NMR spectroscopy, and modeling. Procheck for evaluation of stereochemical quality of protein structures. BLDKIT for model building. BENDER for bent wire models. CONECT generates full connectivity from atomic coordinates from printed stereo molecular graphics.

targetenvironment:

contact:

Protein Data Bank, Chemistry Department, Building 555, Brookhaven National Laboratory, mail to pdb@bnl.gov

keyword:

comments:

---

SCOP

url:

http://scop.mrc-lmb.cam.ac.uk/scop/

abstract:

Structural Classification of Proteins. Nearly all proteins have structural similarities with other proteins and, in some of these cases, share a common evolutionary origin. The scop database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

targetenvironment:

contact:

Dr. Tim Hubbard, Centre for Protein Engineering, Medical Research Council Centre, mail to th@mrccpe.cam.ac.uk

keyword:

comments:

---

Molecular graphics

---

Ball & Stick

url:

ftp://ftp.unilinz.ac.at

abstract:

targetenvironment:

contact:

Cherwell Scientific Publishing, mail to csp@netcom.com

keyword:

comments:

---

CAP

url:

http://bond.caltech.edu/index.html

abstract:

The Chemistry Animation Project presents CAPseries, a collection of multimedia products for use in high school and introductory college chemistry classrooms. Animated using state-of-the-art computer hardware and software, each product offers insight into chemical phenomena for teacher and pupil alike, with intuitive 3-D models and computer-calculated accuracy. Under the direction of Professor of Chemistry Nathan S. Lewis, CAP is chemistry for students by students. For product availibility, comments, and new title announcements, see appropriate section in this URL.

targetenvironment:

contact:

, mail to

keyword:

comments:

---

Chemscape

url:

http://www.mdli.com/chemscape/index.html

abstract:

The Chemscape Product Line provides two powerful capabilities: rendering of 2D and 3D chemical and biological structures within a Web page or table (via our Chime plug-in) and a high performance, client-server structure search system which provides full ISIS structure and text search capabilities within a Web browser (via Chemscape Chime Pro and Chemscape Server.)

targetenvironment:

contact:

mail to techsupp@mdli.com

keyword:

comments:

---

FLEX

url:

ftp://perutz.scripps.edu (137.131.152.27)

abstract:

Molecular graphics of molecular models and MD trajectories.

targetenvironment:

contact:

Dr. Michael Pique, Research Institute of Scripps Clinic,, mail to mp@scripps.edu

keyword:

comments:

---

GRASP

url:

ftp://cumbnd.bioc.columbia.edu (128.59.96.103)/grasp

abstract:

Molecular graphics.

targetenvironment:

contact:

Dr. Anthony Nicholls, Department of Biochemistry and Molecular Biophysics, Columbia University. Mail to nicholls@cuhhca.hhmi.clumbia.edu

keyword:

comments:

---

Imdad

url:

http://www.mag.com/products/imdad/imdad.html

abstract:

Imdad is a versatile and easy to use research and teaching tool designed to satisfy your macromolecular modeling needs. Imdad enables you to interactively display, analyze and print molecular structures - in one comprehensive, user-friendly package.

targetenvironment:

contact:

Molecular Applications Group, mail to info@mag.com

keyword:

comments:

---

ISIS/Draw

url:

http://www.mdli.com/idraw.html

abstract:

ISIS/Draw is a remarkable chemical drawing program that functions like an extension of a chemist's own mind: It knows that a letter is an atom with valence limits; that a line is a bond that attaches at correct lengths and angles; and that double bonds or aromatic ring systems are dynamic, changing with attachments made to the ring. You can draw the most complicated structures rapidly and intuitively; use these drawings to build databases of reactions and 2D and 3D molecules; and query these databases with flexible features that allow you to define variable or partial structures -- a bond as double, single, or aromatic; an atom as any atom on a given list. All of this and more quickly becomes second nature with ISIS/Draw, so that you can focus on chemistry and not on the computer. ISIS/Draw has a user-tested interface and is the only tool you will ever need for chemical drawing. Manufacturer: MDL Information Systems, In. http://www.mdli.com/mdlhome.html

targetenvironment:

contact:

http://www.mdli.com/offices.html

keyword:

comments:

Free Software

---

Kinemage

url:

gopher://orion.oac.uci.edu:1071/11/protein/Kinemage.

abstract:

targetenvironment:

contact:

Protein Science, mail to prosci@u.washington.edu

keyword:

comments:

---

MidasPlus

url:

http://www.cgl.ucsf.edu/midasplus.html

abstract:

MidasPlus (Molecular Interactive Display and Simulation) is used extensively for the display and manipulation of macromolecules. Features of MidasPlus include the selective display of protein and nucleic acid structures, display of several types of molecular surfaces including van der Waals, solvent accessible, and space filling images with shadows, ability to depict protein secondary structure using ``ribbon'' drawings, viewing of images in three dimensions using stereo glasses, and easy interactive adjustment of various viewing parameters.

targetenvironment:

contact:

Dr. Tom Ferrin, Department of Pharmaceutical Chemistry, University of California, mail to tef@cgl.ucsf.edu, midas@cgl.ucsf.edu

keyword:

comments:

---

Molecules-3D Pro

url:

http://synapse.bio.com/cgi-bin/bio1/product/2000290?se=hcdTc8jF&pg=398

abstract:

Step up to Molecules-3D Pro - the advanced 3D Molecular Model Building System.

targetenvironment:

contact:

Molecular Arts Corporation, mail to sales@bio.com

keyword:

comments:

---

Nano Vision

url:

http://www.acs.org/, http://pubs.acs.org

abstract:

A 3D visualization program capable of rotating molecules with up to 32,000 atoms, for the Macinton. Stick and space-filling displays. Analytical Chemistry by Open Learning (ACOL) for computer-aided teaching. ChemStock for managing database of laboratory chemicals. DESIGN-EASE for factorial design. DESIGN-EXPERT for multiple response optimization. EndLink to capture bibliographic data from on-line services. EndNote and EndNote Plus for creating database of bibliographic information in conjunction with word processing. EQUIL for aqueous solution equilibrium calculations. Gardner's Chemical Names and Trade Names database. Grant Tracker. Instant EPA's Air Toxics, Integrated Risk Information System, and Pesticide Facts database. IR Mentor for spectral interpretation. IR SearchMaster to manage data libraries. LabADVISOR information database on regulated chemicals. Origin for scientific graphics and data analysis (under Windows). PCNONLIN for pharmacokinetic models. PeakFit for deconvolution. SpecTool for managing spectral data. TableCurve for curve fitting. Un-Scan-It for entering x, y data into Pcs and Macintosh. UniVersions for unit conversion and physical constant database.

targetenvironment:

contact:

ACS Software, American Chemical Society

keyword:

comments:

---

ORTEP_for_Mac

url:

ftp://infomeister.osc.edu, gopher://infomeister.osc.edu (port 70 or 73)

abstract:

targetenvironment:

contact:

Ohio Supercomputer Center, mail to jkl@osc.edu, jkl@ohstpy.bitnet

keyword:

comments:

---

ORTEP

url:

http://www.ornl.gov/ortep/ortep.html

abstract:

The Oak Ridge Thermal Ellipsoid Plot (ORTEP) program is a computer program, written in Fortran, for drawing crystal structure illustrations. Ball-and-stick type illustrations of a quality suitable for publication are produced with either spheres or thermal-motion probability ellipsoids, derived from anisotropic temperature factor parameters, on the atomic sites. The program also produces stereoscopic pairs of illustrations which aid in the visualization of complex arrangements of atoms and their correlated thermal motion patterns.

targetenvironment:

contact:

Mail to

keyword:

comments:

---

Pluton

url:

ftp://xraysoft.chem.ruu.nl/pub/dec5000/pluton/

abstract:

PLUTON is a program for interactive molecular graphics. It is designed for use in a crystallographic context. However, it can be used for the display and analyses of molecules in an orthogonal (Angstrom) coordinate system as well. Various hardware/software/graphics platforms are supported. The programs may be used free of charge in non-profit organisations.

targetenvironment:

contact:

, mail to

keyword:

comments:

---

RasMol

url:

http://chpc06.ch.unito.it/rasmol.html, ftp://ftp.dcs.ed.ac.uk/export/rasmol/, ftp://ftp.dcs.ed.ac.uk/home/ftp/pub/rasmol

abstract:

RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

targetenvironment:

contact:

Dr. Roger Sayle, Glaxo Research and Development, ros@dcs.ed.ac.uk, mail to ras32425@ggr.co.uk

keyword:

comments:

---

RASTER3D

url:

http://www.bmsc.washington.edu/raster3d/raster3d.html ftp://stanzi.bchem.washington.edu/pub/raster3d/raster3d.html

abstract:

Raster3D is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, and cylinders with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from Brookhaven PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in Per Kraulis' program Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

targetenvironment:

contact:

Dr. Ethan A. Merritt, Department of Biological Structure SM-20, University of Washington, mail to merritt@xray.bchem.washington.edu

keyword:

comments:

---

SciAn

url:

ftp://ftp.scri.fsu.edu

abstract:

Scientific visualization and animation program that can be applied to molecules.

targetenvironment:

contact:

Dr. Eric Pepke, Supercomputer Research Institute, Florida State University, mail to pepke@scri.fsu.edu

keyword:

comments:

---

Xmol

url:

http://www.arc.umn.edu/GVL/software/xmol/XMol.html, ftp://ftp.msc.edu/pub/xmol

abstract:

Molecular graphics from molfiles produced in Alchemy, Brookhaven PDB, CHEMLAB-II, Gaussian, MOLSIM, and MSCI's XYZ formats.

targetenvironment:

contact:

Minnesota Supercomputer Center, Inc., mail to xmol@msc.edu, doherty@msc.edu

keyword:

comments:

---

Quantitative structure-property relationships and statistics

---

2 Dimensional Finite Difference Hartree-Fock Program

url:

http://laaksonen.csc.fi/num2d.html

abstract:

A Numerical Hartree-Fock Program for Diatomic Molecules http://laaksonen.csc.fi/2d/support/messages.htmls

targetenvironment:

contact:

Supporthttp://laaksonen.csc.fi/2d/support/messages.htmls

keyword:

comments:

---

DSSP--Definition of Secondary Structure of Proteins

url:

http://www.sander.embl-heidelberg.de/dssp/

abstract:

The DSSP program defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in Protein Data Bank format. The program does NOT PREDICT protein structure. According to the Science Citation Index (July 1995), the program has been cited in the scientific literature more than 1000 times.

targetenvironment:

keyword:

comments:

Executables of the DSSP program are available from http://www.embl-heidelberg.de/dssp/ or from ftp.embl-heidelberg.de (192.54.41.33). Free academic use. For an academic source code license or for a commercial license go to http://www.embl-heidelberg.de/dssp/ or write to Chris Sander / email: sander@embl-heidelberg.de

---

HINT

url:

http://www.i2020.net/edusoft/hint.html

abstract:

Hydropathic INTeraction by empirical calculation of atomistic hydrophobicity of molecules. Grid points based on energetics of hydrophobic and hydrophilic fields can be used for contouring a hydrophobic space and for scoring ligand-macromolecule and macromolecule-macromolecule interactions.

targetenvironment:

contact:

eduSoft LC, mail to haney@netcom.com

keyword:

comments:

---

JMP

url:

http://www.sas.com, ftp://ftp.sas.com

abstract:

Statistical analysis using spreadsheet format; experimental design. Demonstration version available.

targetenvironment:

contact:

SAS Institute Inc., mail to support@unx.sas.com

keyword:

comments:

---

K2D

url:

http://www.embl-heidelberg.de/~andrade/k2d.html

abstract:

Protein secondary structure prediction from CD spectra. You can either use k2d via a web server or get the program and run it on your machine.

targetenvironment:

contact:

Mail to andrade@embl-heidelberg.de

keyword:

comments:

---

MARDIGRAS (Matrix Analysis of Relaxation for DIscerning the Geometry of an Aqueous Structure)

url:

http://picasso.ucsf.edu/mardi.html

abstract:

MARDIGRAS is a FORTRAN program for calculating proton-proton distances from cross-peak intensities measured from a 2D NOE experiment.

targetenvironment:

contact:

Thomas James, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143-0446, fax: 415.476.8780, mail to james@picasso.ucsf.edu

keyword:

comments:

---

SigmaStat

url:

http://www.jandel.com

abstract:

Statistical modeling. SigmaPlot for graphing. SigmaScan/Image for image processing. TableCurve 2D for curve fitting. TableCurve 3D for fitting surfaces to x, y, z data. Mocha for image analysis. PeakFit for deconvoluting curves.

targetenvironment:

contact:

Jandel Scientific Software, mail to sales@jandel.com

keyword:

comments:

---

XNMR

url:

http://acp5.chemie.uni-kl.de/seimet/xnmr_english.html

abstract:

is a X11/Motif based program for processing and simulating exchange broadened NMR spectra. Processing is only possible with data coming from Bruker NMR spectrometers. Simulating, of course, is independent from the spectrometer type. XNMR should run on any platform with at least X11R4 and Motif 1.1. If possible, newer versions of X11 and Motif should be used. XNMR is Shareware.

targetenvironment:

contact:

, mail to

keyword:

comments:

---

Other Applications

---

Artificial Life Software

url:

http://alife.santafe.edu/alife/software/

abstract:

targetenvironment:

contact:

, mail to

keyword:

comments:

---

Apex-3D

url:

http://www.cerf.net:80/biosym/index.html

abstract:

The Apex-3D expert system assists you in designing novel drugs, pesticides, odorants, and other bioactive chemical substances. Apex-3D employs advanced statistical techniques and 3D pattern-matching algorithms to draw generalizations from existing chemical and biological data, and then generates activity predictions from those generalizations.

targetenvironment:

contact:

Valery Golender, mail to valery-g@dcl.co.il

keyword:

comments:

---

Babel

url:

http://mercury.aichem.arizona.edu/develop.txt

abstract:

Babel is a program designed to interconvert a number of file formats currently used in molecular modeling.

targetenvironment:

The program is available for Unix (AIX, Ultrix, Sun-OS, Convex, SGI, Cray, Linux), MS-DOS, and on Macs running at least System 7.0.

contact:

Mail to babel@mercury.aichem.arizona.edu

keyword:

comments:

---

BBDEP96.C

url:

http://www.cmpharm.ucsf.edu/~dunbrack/#bbdep96

abstract:

BBDEP96.C is a program for calculating dihedrals, evaluating x-ray and NMR structure quality, and for predicting sidechain dihedrals from the backbone-dependent rotamer library.

targetenvironment:

contact:

, mail to

keyword:

comments:

---

BIOPROP

url:

ftp://berkeley.edu/pub

abstract:

Dr. Steven M. Muskal's program for neural network simulator for protein conformation prediction and other data analysis. BLSS for statistics.

targetenvironment:

contact:

Office of Technology Licensing, University of California, mail to domino@uclink2.berkeley.edu

keyword:

comments:

---

BioWorld Online

url:

http://www.cartermill.com

abstract:

Bioworld Today daily fax biotechnology newsletter. BEST North America database with research profiles, patents, and facilities of more than 125 universities and research institutions and five U.S. federal agencies.

targetenvironment:

contact:

Cartermill Inc., mail to info@bestpl.hcf.jhu.edu

keyword:

comments:

---

CACTVS

url:

http://schiele.organik.uni-erlangen.de/cactvs/index.html

abstract:

The CACTVS system is a research project aiming to change the ways of doing computational chemistry. CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type.

targetenvironment:

contact:

Mail to wdi@eros.ccc.uni-erlangen.de

keyword:

comments:

---

CCP4

url:

ftp://gserv1.dl.ac.uk/pub/ccp4

abstract:

Suite of almost 100 protein crystallography programs for data processing, scaling, Patterson seardch and refinement, isomorphous and molecular replacement, structure refinment, such as PROLSQ, phase improvement (solvent flattening and symmetry averaging), and presentation of results, such as SURFACE for accessible surface area.

targetenvironment:

contact:

Dr. David Love, SERC Daresbury Laboratory, mail to ccp4@daresbury.ac.uk

keyword:

comments:

---

ChemFinder

url:

http://www.camsoft.com/

abstract:

Chemical information management. CambridgeSoft Corporation

targetenvironment:

contact:

CambridgeSoft Corporation.

keyword:

comments:

---

Chemistry 4D-Draw

url:

http://www.cheminnovation.com

abstract:

Chemical structure drawing (formerly ChemNameStru); the NameExpert module converts IUPAC names to 2D structure drawings.

targetenvironment:

contact:

ChemInnovation Software, mail to cis@cheminnovation.com

keyword:

comments:

---

ChemStructure

url:

http://megalon.megalon.com, gopher://gopher.megalon.com, ftp://ftp.megalon.com

abstract:

2D chemical structure drawing. Compounds database with chemical structure of 27,000 organic compounds. Unistat for statistical analysis. Helix Systems' ResearchStation for electronic notebook integration of data from multiple applications.

targetenvironment:

Pcs (Windows)

contact:

Megalon S.A., mail to info@megalon.com

keyword:

comments:

---

CORINA

url:

http://schiele.organik.uni-erlangen.de/services/3d.html

abstract:

CORINA is the currently most capable program worldwide for the quick generation of good 3D coordinates for drug-sized chemical structures of almost any kind, including compounds with large rings, metal complexes and strained cages. Corina is a non-interactive model builder. It uses ring patterns and pseudo forcefield optimization to compute PCs and Sun.

targetenvironment:

contact:

Dr. Johann Gasteiger, Computer-Chemie-Centrum, Universitat Erlangen-Nurnberg, mail to gasteiger@eros.ccc.uni-erlangen.de christof@eros.ccc.uni-erlangen.de

keyword:

comments:

---

gluplot

url:

ftp://ftp.stat.ucla.edu

abstract:

Gopher server with software related to statistics.

targetenvironment:

contact:

Dr. Jan De Leeuw, University of California, mail to deleeuw@math.ucla.edu

keyword:

comments:

---

Gopher

url:

ftp://boombox.micro.umn.edu (132.84.132.2)

abstract:

Internet client/server for a distributed information delivery system.

targetenvironment:

contact:

Internet Gopher Developers, mail to gopher@boombox.micro.umn.edu

keyword:

comments:

---

ISIS Add-ins

url:

http://www.mdli.com/addin.html

abstract:

The ISIS Add-in Manager delivers a framework for run-time extensions to ISIS/Draw or ISIS/Base for Windows and Macintosh.

targetenvironment:

Free Software

contact:

MDL Information Systems, In., http://www.mdli.com/mdlhome.htmlMail to techsupp@mdli.com

keyword:

comments:

---

Mathematica

url:

http://www.wri.com/mathsource.html, ftp://mathsource.wri.com, gopher://mathsource.wri.com

abstract:

Mathematical modeling.

targetenvironment:

Pcs (DOS and Windows), Macintosh, and UNIX workstations.

contact:

Wolfram Research, Inc., mail to info@wri.com, support-euro@wri.com (U.K.)

keyword:

comments:

---

MDL Chemscape Chime

url:

http://www.mdli.com/chemscape/chime/chime.html

abstract:

Chemscape Chime is a Netscape Navigator plug-in that allows scientists to view chemical information directly on a Netscape Navigator HTML page. Chime supports most of the popular structure display formats that scientists use including MDL Information Systems, Inc. Molfile and many of the popular 3D display formats such as the Brookhaven Protein Databank (PDB) format (3D rendering and RasMol scripting code courtesy of Roger Sayle.)

targetenvironment:

contact:

MDL Information Systems, In., mail to techsupp@mdli.com

keyword:

comments:

Free Software

---

Molecule Editor entirely written in Java

url:

http://www.chem.leeds.ac.uk/ICAMS/people/denis/moledit.html

abstract:

You may also download the 1800 or so lines of commented java code and modify and use them for any non-commercial puposes (for commercial uses, please ask the author). Also available is the source code for the standalone version. Molecule Editor does not do anything but draw a molecule. You cannot save into a file, print or send the drawn molecule to a modelling package etc... Molecule Editor is just a molecule drawing module for some WebChem software that other people will write in the future or have started writing already.

targetenvironment:

contact:

Mail to denis@mi.leeds.ac.uk

keyword:

comments:

---

MORASS

url:

http://www.nmr.utmb.edu

abstract:

Hybrid matrix NOE structural refinement.

targetenvironment:

contact:

Dr. David Gorenstein, University of Texas Medical Branch at Galveston, mail to bruce@dggin1.utmb.edu

keyword:

comments:

---

Mosaic

url:

ftp://ftp.ncsa.uiuc.edu (141.142.20.50)

abstract:

Communication of text and graphics files between computers using World Wide Web servers.

targetenvironment:

contact:

National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, mail to orders@ncsa.uiuc.edu, alpha@ncsa.uiuc.edu

keyword:

comments:

---

MOUSE

url:

http://mercury.aichem.arizona.edu/mouse.html

abstract:

MOUSE is a program which utilizes machine learning techniques to derive rules for predicting the behavior of chemical systems. The technology in MOUSE has been applied to a number of areas, including conformational analysis and pharmacophore prediction. In learning rules of conformational analysis MOUSE operates by examining a set of crystal structures, all of which have a particular ring system in common. The program randomly selects a portion of the examples and uses these to derive rules for class membership. The remainder of the examples are then used to test the effectiveness of the learned rules.

targetenvironment:

contact:

Mail to

keyword:

comments:

---

O

url:

http://kaktus.kemi.aau.dk/, ftp://rigel.bmc.uu.se

abstract:

Molecular graphics for crystallographic determination of protein structures.

targetenvironment:

contact:

Dr. T. Alwyn Jones, mail to alwyn@xray.bmc.uu.se, gerard@xray.bmc.uu.se

keyword:

comments:

---

Photobase

url:

http://www.dcl.co.il/photobase.html

abstract:

Photobase represents a comprehensive compilation of published photochemical information. All photochemical reactions have been abstracted by a team of skilled photochemists. Substantial data is presented for each reaction. A special classification scheme is used for the systematization of reaction data.

targetenvironment:

contact:

Mail to

keyword:

comments:

---

Platon

url:

ftp://xraysoft.chem.ruu.nl/pub/dec5000/platon/

abstract:

Platon is a versatile crystallographic tool implementing a large variety of standard geometrical calculations (i.e. bonds, angles, torsions, planes, inter-molecular contacts (H-Bond analysis), Coordination etc), tests (i.e. MISSYM, VOIDS etc.), utilities (cell transformation, SHELXL input etc.), graphics (e.g automatic labelled 'ORTEP-type plots) and several filters (i.e. the DIFABS technique for empirical absorption correction (Walker & Stuart) and SQUEEZE for handling disordered solvents (= BYPASS procedure, (v.d. Sluis & Spek, Acta Cryst. (1990), A46, 194))).

targetenvironment:

contact:

, mail to

keyword:

comments:

---

XtalView

url:

ftp://ftp.sdsc.edu

abstract:

Complete package for solving X-ray crystal structures such as those of proteins. SHAPE for analyzing molecular surfaces. FLEX for displaying and animating molecular graphics.

targetenvironment:

contact:

Dr. Duncan E. McRee, Computational Center for Macromolecular Science, Research Institute of Scripps Clinc, mail to ccms-request@sdsc.edu, dem@scripps.edu

keyword:

comments:

---

nhse-librarian@netlib.org