|  ACD(Advanced Chemistry Development) - In addition to the acclaimed freeware PC Chemical Drawing package ChemSketch, and their popular Naming, NMR, and physicochemical prediction software, Advanced Chemistry Development offers powerful manipulation and database tools for NMR, HPLC, MS, and IR/UV-VIS. The search capabilities of these packages includes full- and substructure searching capability.
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| ActivityBase - ID Business Solutions Limited activity data management and analysis program.  |
| Afferent Systems, Inc. - Afferent Systems offers an integrated solution for combinatorial chemistry informatics, including instrument control and product data generation, access, and storage, all optionally using an Oracle-based enterprise-wide database. - Product : Afferent version 3, Afferent Structure, Afferent Analytical, Afferent Synthesis(Win95/NT). |
| AG ComputerChemie der MLU Halle-Wittenberg - StrucEu - a universal graphical interface for structural chemistry |
| AIMPAC - This is the official download page for the AIMPAC suite of software applications. The previous system, which involved e-mailing the sourcecode to those who wanted it, is no longer being provided. This webpage will provide easy downloading of the sourcecode needed to run the AIMPAC programs, plus helpful information |
| AM-Technologies- The software company, American Molecular Technologies Inc., was founded in March 1994 and its primary mission is to develop and market most sophisticated software and solutions for molecular design work in the pharmaceutical, chemical and biotechnology industries for the purpose of designing novel chemical entities. - Product : GALAXY SOFTWARE Summary, AM 2000 / MACROMODELING SOFTWARE. LIBCOM SOFTWARE |
| 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. The current version of this package is AMBER ver 5 which is sold for UCSF by Oxford Molecular, subject to a licensing agreement as described below. The code is written in Fortran and C and requires approximately 65 megabytes of disk space. AMBER is developed in an active collaboration of Peter Kollman and the Kollman group at UCSF, Dave Case at The Scripps Research Institute, Ken Merz at Penn State, David Ferguson at the University of Minnesota, Tom Darden at NIEHS, and Dave Pearlman at Vertex Pharmaceuticals. |
| AMMP and Dynama Homepage - AMMP is our local molecular mechanics and dynamics program. Dynama is a fast docking program which uses the FFT to calculate the interaction energy between two molecules without cutoffs or other aphysical approximations. |
| ArgusLab Homepage - ArgusLab is a molecular modeling program for Windows 95/98 and NT 4.0. ArgusLab consists of a user interface that supports OpenGL graphics display of molecule structures and runs quantum mechanical calculations using the Argus compute server. The Argus compute server is constructed using the Microsoft Component Object Model (COM).download |
| ARP/wARP - A program for the refinement of protein structures that combines in an iterative manner the reciprocal space structure factor refinement with updating of the model in real space. |
| ASAD Homepage - ASAD (A Self-contained Atmospheric chemistry code) is a package that has been developed for integrating chemical schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations. |
| AutoDock - AutoDock is a suite of programs designed to predict the bound conformation(s) of a flexible ligand to a macromolecular target of known structure, like an enzyme or DNA. AutoDock has also been used in the prediction of the structure of protein-protein complexes. AutoDock has found application in the computer-aided design of bioactive compounds and in the prediction of peptide binding to antibodies. AutoDock How to-linux |
| ATMOL - written by D. Moncrieff and V.R. Saunders. ATMOL is an integrated suite of programs for the calculation of SCF, MCSCF and CI wavefunctions and their properties. |
| Babel - Babel is a program designed to interconvert a number of file formats currently used in molecular modeling. |
| BioByte - Dr. Corwin Hansch, Professor Emeritus at Pomona College in California, and Dr. Albert Leo, Adjunct Professor at that institution, have formed a company to develop and support computer software which can be of use in the design of pharmaceuticals and pesticides as well as in the study of environmental toxicology. Product : ClogP, CQSAR |
| Biomer - Biomer is online java applet, model builders for polynucleotides (DNA/RNA), polysaccharides and proteins, interactive molecule editor, AMBER force-field based geometry optimization, simulated annealing with molecular dynamics, and the ability to save gif, jpeg, and ppm images |
| CAChe-Fujitsu - CAChe is designed to work the way experimental chemists work. Identify properties of interest using a simple menu interface. CAChe computes the properties using its extensive built-in library of computational chemistry tools. Every tool can be calibrated to experimental data to improve the accuracy of predicted results. Product :CAChe, CAChe for medicinal chemists, Dgauss, Winmopac |
| CambridgeSoft Home Page - software for chemists including CS ChemOffice, CS ChemDraw, CS Chem3D, and CS ChemFinder for Macintosh, Windows, and UNIX platforms. |
| CHARMM Home Page - CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations. The CHARMMDevelopment Project involves a network of developers in the United States and elsewhere working with Professor Karplus and his group at Harvard to develop and maintain the CHARMM program. The current released version of CHARMM is version 27b1. If you are running an earlier version, you should consider upgrading. Academic users can obtain CHARMM by contacting TheCHARMM Development Project. |
| ChemInnovation Software - is a leading provider of chemistry graphics and nomenclature software. - Product : Chemistry 4-D Draw(TM),NamExpert(TM), Nomenclator(TM), PowerRef(TM), ChemSite(TM) , NamExpert and Nomenclator Add-ons for CS ChemDraw (TM), Chemistry 4-D Nomenclator Database and Chemistry 4-D Database |
| Chem-It - Chem-It is freeware program for the novice chemistry student. The current version includes an interactive periodic table, conversion charts, and much more. |
| Chemland - educational java applets (about 40) explaining many principles in chemistry |
| Chempak - Sophisticated estimation techniques yield accurate profiles for vapor pressure, specific volume, specific heats, enthalpy, entropy, latent heat, viscosity, conductivity, surface tension versus temperature and pressure |
| Chempen3 - This is a program for building 3D molecular structures, analyzing molecular geometry and reaction energetics, and for exploring molecular mechanics. This is a fully functional 60 day trial versions of ChemPen and ChemPen3D |
| Chemware - download chemistry shareware for high school students and teachers. |
| CLIP(Computed Lipophilicity Properties) - Computation and representation of the Molecular Lipophilicity Potential (MLP) on the solvent-accessible surface of molecules and macromolecules, Calculation of n-octanol/water partition coefficients (log Poct) from the MLP on the solvent-accessible surface; Calculation of virtual log P values for individual conformers, and exploration of the lipophilicity range accessible to a compound; Computation and representation of the MLP in a given region of space around molecules and macromolecules; Computation and incorporation of the MLP into Comparative Molecular Field Analysis (CoMFA) |
| CompuDrug - Presentation of software predicting physico-chemical parameters (pKalc, PrologP and PrologD), metabolism pathways (MetabolExpert), toxic effects (HazardExpert) of compounds and assisting in HPLC method development (EluEx). |
| CTW Associate Inc. - DTW Associates, Inc. is primarily a provider of PC-Based software for the "practicing" scientists and engineers who work in the Chemicals and Allied Products Industries. Product : Polymer-Design Tools PC-based software for Computer-aided design, development and selection of polymers, uses Quantitative Structure-Property Relationship (QSPR) Methods in estimating properties of homopolymers and copolymers.PPP Handbook is an electronic handbook for properties of polymers. Formu-Tools is the most advanced PC-Based software now commercially available for formulation work. |
| Daylight Chemical Information Systems, Inc. -Daylight Chemical Information Systems. Inc. develops and distributes software tools (ToolKits) for creation of chemical information systems. |
| DL-POLY - Molecular dynamics package |
| DockVision - DockVision is a revolutionary new docking package created by scientists for scientists. By including Monte Carlo, Genetic Algorithm, and database screening docking algorithms in one complete docking package, DockVision increases your capability to generate laudable results. |
| DomainFinder - DomainFinder is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are
- computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes
- ease of use: a state-of-the-art graphical user interface
- export of results for visualization and further analysis (VRML, PDB, and MMTK object format)
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| DRAGON (National Institute for Medical Research, London) - A program for protein modelling that uses distance geometry to predict the tertiary structure of a small soluble protein given its sequence, secondary structure, and possibly a set of distance restraints. |
| DSSP - The DSSP (Definition of Secondary Structure of Proteins) 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. |
| Easybabel - A windows front end for the Babel program. It simplifies the procedure of converting one format to another using the common windows interface. (requires the original Babel for Dos). |
| Edusoft - HINT!®(Hydropathic INTeractions) is a novel empirical molecular modeling system with new methods for de novo drug design and protein or nucleic acid structural analysis. The HINT model and algorithms are being developed by Drs. Glen Kellogg and Donald Abraham of theMedicinal Chemistry Department at Virginia Commonwealth University in Richmond. HINT!® translates the well-developed Medicinal Chemistry and QSAR formalism of LogP and hydrophobicity into an interaction model for all biomolecular systems based on the experimental data from solvent partitioning. The partition coefficient (LogP) is a thermodynamic parameter that, because of its unprocessed and unbiased experimental nature, encodes all non-covalent interactions in the biological environment as well as solvent effects and entropy. HINT® calculates 3D hydropathy fields that are useful as tools for 3D QSAR (e.g., CoMFA in Sybyl-compatible versions of HINT). HINT calculates 3D hydropathicinteraction maps that are uniquely instructive for understanding biomacromolecular structure: substrate/inhibitor/drug binding to proteins and nucleotides, protein subunit interactions, and protein folding.Molconn-Z is the standard program for generation of Molecular Connectivity, Shape, and Information Indices for Quantitative Structure Activity Relationship (QSAR) Analyses. New parameters and concepts of QSAR, including the E-State, have been introduced first in Molconn-Z. |
| EGO - EGO is a program to perform molecular dynamics simulations on parallel as well as on sequential computers at Bayerish Acadamie of Science, Munich, Germany (Unix and PC (with GNU-c compiler); free downloadable). |
| Environmental Science Center - The Environmental Science Center (ESC) ofSyracuse Research Corporation (SRC), is a world leader in scholarly research in environmental chemistry, toxicology and risk assessment. - Product : KowWin, AopWin,HenryWin, MPBPVP, BioWin, PcKoc, WsKow, Hydro, EPI Suite, DermWin, ECOSAR,Bcfwin |
| EQS4WIN - EQS4WIN program calculates chemical equilibrium compositions for a broad range of systems, based on the algorithms of Smith and Missen. |
| Espoir (Univ. du Maine-France) - A special purpose Reverse Monte Carlo code for ab initio crystal structure determination |
| Fantom - The main purpose of the program FANTOM (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. |
| FlexX - FlexX is a program for automatic prediction of receptor-ligand interactions |
| FTDock - FTDock is a software package consisting of the main docking program plus one preprocessor and one postprocessor. The primary program, called FTDOCK, accepts two PDB format structure files as input and performs rigid-body docking. The Fourier correlation algorithm used by FTDOCK takes advantage of the fast Fourier transform (FFT) to scan rapidly the translational binding space of two rigid molecules. |
| GeneMine Home Page - GeneMine is the first expert bioinformatics data mining system to automatically query multiple independent sources. GeneMine￠â has been designed to provide users with a set of features that can be readily customized to their specifications. |
| gHemical - Ghemical is a computational chemistry software package and it can do all-atom molecular mechanics. Geometry optimization, molecular dynamics and some visualization tools are available. |
| GRASS - This tool is designed to facilitate the study of macromolecular function by mapping a number of structural, chemical, and biological properties onto various representations of molecular structure (molecular surfaces, wire frame, CPK spheres, or backbone tracing ribbons). |
| GROMACS Home Page - GROMACS is a set of molecular dynamics code and analysis tools which is available from the GROMACS website Features of the software include: The GROMACS code runs your simulations *blazingly fast* on all UNIX platforms. The code is especially well-tuned for pipelined architectures, such as MIPS R8000, HP:PA-RISC, Intel i860 etc. |
| GROMOS96 - This is a general-purpose molecular dynamics simulation package |
| HBPLUS - HBPLUS is a hydrogen bond calculation program from University College Londen. |
| HOLE - HOLE : A Program for the Analysis of the Pore Dimensions of Ion Channel Structural Models. |
| HotDock - HotDock allows to load arbitrary 3D-molecular structures, visualizes them in different common representations and interactively simulates a docking process. By means of a collision detection based on the structural properties of the loaded molecules, the program supports protein-ligand docking, but may also be used to simulate protein-protein docking as well. The tool is designed to teach, visualize and communicate results in chemistry and structural biology. |
| Hypercube Home Page - Molecular Modeling Program based PC, SGI -Hyperchem v6.0, ChemPlus v1.6, HyperNMR v2.0 - Hyperspin (Hyperchem conformational search add-on) |
| Hypothetical Active Site Lattice - HASL is 3D-QSAR software designed to run on the PC. Correlates structure to binding activity for up to 400 molecules |
| INTERPROBE - The main function of INTERPROBE CHEMICAL SERVICES is the provision of quality computer software for the handling of chemical structure information. - Product : INTERCHEM, PRESTO, CHEMSPREAD,THREEDOM, CONVERT, AUTOBUILD, PROTEINS, FINDSEQUENCE, PIFF, ICMECH,STRAUSS, DATABASES |
| JEEP - A free, easy to use first-principles electronic structure program. |
| K2d - 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. |
| LIGPLOT - LIGPLOT automatically generates schematic diagrams of protein-ligand interactions for a given PDB file. The interactions shown are those mediated by hydrogen bonds and by hydrophobic contacts. |
| LOOK Homepage - LookTM is a unique software tool specifically designed to bring structural insight to molecular biology. As sequences are loaded into the Look￠â sequence window, the alignment is automatically generated by the Needleman-Wunsch algorithm and measurements of the quality of a matchup are based on a similarity matrix. The Look￠â interface has been designed to provide the expert user with immediate access to integrated sequence and structure information concerning a given protein. |
| MDL Information Systems, Inc. - We are the recognized leader in discovery informatics for the life science and chemical industries. Our software, content, and services provide the enterprise framework for identifying successful new products. We are an international business headquartered in San Leandro, California with offices worldwide. MDL is a wholly owned subsidiary of Elsevier Science, Inc. - Service list - Chemscape: Web access to structures and data, Cheshire for ISIS: Environment for structure manipulation and analysis, ISIS for Microsoft Excel: Spreadsheet access to structures and data, ISIS: Integrated Scientific Information System, Central Library: Enterprise-wide information management for parallel and combinatorial synthesis, Project Library: Desktop information management for parallel and combinatorial synthesis, Reagent Selector: Chemists' tool for selecting reagents, Assay Explorer: Flexible biological data management system, ISIS Beilstein Interface: ISIS access to Beilstein database, LitLink Server: One-click access to the primary literature, Reaction Browser: Reaction database search system, Reaction Web: Web-based access to chemical reactions,SCULPT: 3D structural visualization and analysis, Spotfire: Multi-dimensional, interactive data visualization, OHS Safety Series: Environmental, health, and safety data management, Available Chemicals Directory (ACD): Database of chemicals and their suppliers, Available Chemicals Directory-Screening Compounds (ACD-SC), SMART: Sample Management and Reagent Tracking system, Comprehensive Medicinal Chemistry (CMC): Biologically active compounds, MDL Drug Data Report (MDDR): Patent literature coverage, Metabolite: Metabolism information system, Toxicity: Toxic properties of chemical substances, ChemInform Reaction Library: Solution-phase synthetic methodology, Comprehensive Heterocyclic Chemistry (CHC), Current Synthetic Methodology (CSM): New representative synthetic methodology, ORGSYN: Organic Syntheses, RX-JSM: Journal of Synthetic Methods, Reference Library of Synthetic Methodology (RefLib): Collection of representative novel syntheses, Solid-Phase Organic REactions (SPORE): Solid-phase synthetic methodology, THEILHEIMER: Synthetic Methods of Organic Chemistry, MDL File Formats: Published formats for chemical structures, reactions, and data
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| MDynaMix - MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by AMBER-like force field in a periodic rectangular cell. In the case of flexible molecules the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are employed, as well as optimized Ewald sum for treatment of the electrostatic interactions. The program can be run both in sequential and parallel execution. |
| Microsimulations Home Page - Accumodel, Powerfit (Windows95/98/NT) |
| Modeller - Protein modeling |
| MOE - MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package. |
| Molecular Knowledge Systems, Inc. - Molecular Knowledge Systems, Inc. is a leading provider of computer software for physical property estimation and molecular design. Synapse - A molecular design system focusing on the generation and screening of new molecular structures. Unlike traditional molecular design software, Synapse automatically constructs new chemicals and predicts their macroscopic physical properties. A "lite version" will soon be available for download. Cranium- A physical property estimation package capable of estimating over 20 physical properties. Simply draw your molecule's structure or enter your mixture's composition and Cranium will provide rapid and accurate estimates. |
| Molecular Modeling Toolkit homepage - The Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications. Its aim is to provide researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling. |
| Molecular Simulations Inc. (MSI) Home Page- Molecular Simulations Inc., a subsidiary of Pharmacopeia, Inc., is a leading provider of molecular modeling and simulation software and services for both life and materials science research. - Product : Cerius2 Simulation environment for life and materials science, WebLab Computational science accessed from desktop personal computers, Insight II Simulation environment for life and materials science, Catalyst Modeling, hypothesis generation and structure search for drug discovery, FELIX Processing, display and analysis of NMR data, QUANTA Advanced tools for macromolecular X-ray crystallographers. |
| Molecular Surface Package - MSRoll(This program reads a protein data bank atomic coordinate file and rolls a water-sized probe over the molecule. It writes a piecewise-quartic molecular surface, a dot surface and a polyhedral surface. ), MSDraw(This program renders and plots molecular surfaces.), MSForm(This program measures protein surface shape by solid angles. It also converts a polyhedral molecular surface to a solvent-excluded density in AVS format.) |
| Molecular Ventures, Inc. - MacMolecule, PCMolecule - Molecular visualizations for students of chemistry, biology, biochemistry, cell and molecular biology, and organic chemistry. Remarkable for ease of use, speed of display, quality of visualizations, and student-centered interface design. |
| MOLGEN - The program system MOLGEN is devoted to the computation of all structural formulae (=connectivity isomers) that correspond to a given molecular formula, with (optional) further conditions (e.g. substructures). |
| MOIL (MOlecular dynamics at ILlinois) - MOIL is a molecular dynamics program available from the Computational Biology Tools page. 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. |
| MolScript - Official Homepage by Avatar Software AB, who develops, markets and distributes software for structural biology, protein NMR and bioinformatics (UNIX; free for non-profit, but license required). |
| Molsoft - MolSoft is a growing company that is devoted to the development of new software to aid in computational biology. Our ICMsoftware uses the latest and most powerful algorithms to perform complex molecular manipulations and database interactions. |
| MolSurfer - MolSurfer software is a graphical tool for studying protein-protein interfaces. It links a 2D projection of a protein-protein interface to a 3D view of the protein structures. This Java-based software uses the representation of the protein-protein interface generated by ADSI, the interface-mapping module of ADS (analytically defined surfaces) software, and WebMol, a Java-based PDB viewer. |
| NAOMI - NAOMI is a computer program system for studying the three-dimensional structure of proteins at the atomic level. |
| 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 |
| O - O is a general purpose macromolecular modelling program aimed at the field of protein crystallography. It enables the scientist to model, build and display macromolecules. O is a graphical display program built on top of a versatile database system. All molecular data is kept in this database, in a predefined datastructure. However, any data can be stored in the database. For example, data produced by associated, standalone programs can very easily be stored in the database, and used by the program, for example for colouring of atoms. |
| OpenEye Scientific Software - The goal of OpenEye is to provide tools to address the explosion of chemical data generated experimentally by focusing on those features which carry the most physical importance, i.e. electrostatics and shape of molecules, and which can be calculated at speeds sufficient for the analysis of large chemical libraries. Product :OMEGA(Rapid conformaer generation), ROCS(Shpae matching and database search), OELIB(Small molecule c++ class library), FILTER(Graph based compound eliminaion tool), ZAP(Poisson-Bolzmann electrostaics),VIDA(Compound brower and GUI tool) |
| Oxford Molecular Group - Molecular Modeling Software : UniChem,Tsar, AutoDock, Chem-X, Others (MacVector, Geneworks, PCGene, OMIGA, TOPKAT, CIS) |
| PASS online prediction - It is possible with computer program PASS (Prediction of Activity Spectra for Substances), which predicts the biological activity spectrum for a compound on the basis of its structural formula. |
| PDB WWW Home Page |
| PhDD Inc. - PhDD, Inc. has developed cutting edge technology to help manage the enormous amount of data that companies in the Life Science Industry work with. These new technologies include PhDD's BioChemServer,WebDisplay and WebDraw. They are web-based technologies that utilize the power of a platform independent system. Phdd also specializes in database design specifically for the Life Science Industry. |
| PMD (Scalable Parallel Molecular Dynamics Simulation) Home Page - 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. |
| PovChem - PovChem combines chemistry and raytracing to create high quality graphics of molecular models. |
| PDB WWW Home Page |
| PhDD WWW Homepage - PhDD stands for Pharmaceutical Design and Database. PhDD dedicates to the development of a series of platform independent software to power the pharmaceutical and chemical industry. We utilize the most advanced technology to make the research, registration and search of chemical compound, data management, and system upgrading painless to users. |
| POLYRATE Home Page - Polyrate is a computer program for the calculation of chemical reaction rates of polyatomic species (and also atoms and diatoms as special cases). |
| Princeton Simulations - software that helps chemists determine the 3-D structures of molecules. |
| PROCHECK - ProCheck Checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. - Operating Manual |
| Proteus - Software for molecular Design |
| PRPPHET Home Page - Prophet is a comprehensive data-analysis software package that makes entering, visualizing, and analyzing your data quick and easy, so you can concentrate on life science, not computer science. If you can use a mouse, you can use Prophet! (Win95/NT, Unix) |
| PTViz - PTYjz is macintosh program for illustrating the organizing principles for the periodic table. Select elements, graph properties, and print tables. |
| QCPE - QCPE promotes the practice of computational chemistry by gathering and distributing computer software for chemistry and related fields. QCPE holds approximately 772 computational chemistry systems, programs, and routines. Most programs are available in source code, and QCPE holds many of its programs in several versions for most popular computer platforms. These programs can be ordered from QCPE for a nominal distribution fee. |
| 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. |
| Sadtler Software - Free Hummel/Sadtler Polymer Database Offer, ChemWindow Spectroscopy 6.5, Sadtler Suite 1.5 , ChemWindow 6, FT-IR Databases |
| Schrodinger, Inc. Homepage - Schrödinger, Inc. has as its goal the development and commercialization of groundbreaking new algorithms and software that will place its customers on the leading edge of computational chemical science. Schrödinger's fundamental rationale is a commitment that all of its products have quantitative and qualitative performance advantages in computational efficiency and chemical accuracy over competing products in the same class. - Product : Jaguar - our extremely fast ab initio software package, Titan - the power of Jaguar and the convenience of Spartan in one integrated package, Mopac 2000 - the giant-molecule semiempirical (including MOZYME) software package,MacroModel - our powerful molecular modeling software package, QikProp - rapid predictions for determining ADME characteristics of drug candidates,Maestro - our state-of-the-art graphical interface for molecular modeling |
| Scivision Scientific Software - SciQSAR 2D, SciQSAR 3D, SciLogP Ultar, SciPolymer, SciGlass, SciProtein, SciQSAR, Spectal Atlas, Ion Fingerprint, ONCOIS, QSARIS, TOXSYS, Alchemy 2000 |
| SCOP - 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. |
| Sculpt-Interactive Simulations Inc. |
| SDL - Software Development Lohninger, Chemometrics Consultants, Software Developers Vienna, Austria, Europe (Teach/Me, INSPECT, CLUSTER, Applicat, Randgen, TOPIX, ISEFOSS, MSLIB) |
| Semichem - Semiempirical Quantum Mechanics, Quantitative Structure/Activity Relationships (QSAR), High Quality Graphics for Input and Visualization - Product : AMPAC 6.0 with graphical user interface,CODESSA |
| Serena Software - Molecular Modeling Program : PCMODEL, GMMX, Mopac,Orbdraw, Vigrate, NMR |
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| STING (Columbia Univ.) - A tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis |
| Synopsys Scienctic System Ltd.- Accord chemical software range provides a wealth of facilities for chemical data management on client and server platforms, database products(Solid-Phase Synthesis, Metabolism, Biotransformations CD-ROM, Methods in Organic Synthesis, Biocatalysis, Protecting Groups, BIOSTER) provide you with quick and easy access to a wealth of chemical information right at your desktop. |
| TCPE - calculate online properties like critical properties, vapor pressure, density, surface tension, heat capacity, viscosity, ... just by entering the SMILES string of your compound |
| THREADER 2 Homepage - THREADER2 is a program for predicting protein tertiary structure by recognizing the correct fold from a library of alternatives. Of course if a fold similar to the native fold of the protein being predicted is not in the library, then this approach will not succeed. Fortunately, certain folds crop up time and time again, and so fold recognition methods for predicting protein structure can be very effective. |
| TINKER Molecular Modeling - The TINKER molecular modeling software is a complete package for molecular mechanics and dynamics of molecules, especially polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER/OPLS, CHARMM22, MM2, MM3, AMBER-95, ENCAD, MMFF-94, MM4 (last 3 in progress) and our own TINKER set. |
| ToPLign Homepage - Threading by Recursive Dynamic Programming [RDP] and Easy ToPLign Fold Prediction servers |
| TOPS (Dept. Biochemistry and Molecular Biology, Univ. College London) - Generates protein topology cartoons. Places circles and triangles depicting alpha-helices and beta-strands respectively giving a pictorial topological summary of any protein structure. |
| Trinity Software - Chemical Education Software - programs for chemistry, life science, and speech a nd communication . Program titles include curriculum supplements and resear ch tools for both PC and MAC computers. |
| Tripos HomePage -Tripos is a leading provider of discovery research software and services to pharmaceutical, biotechnology and other life sciences companies worldwide. - Product : SYBYL/base, Advanced Computation, MM3, AMPAC, GASP, RECEPTOR, DISCO, HQSAR, QSAR with CoMFA,Advanced CoMFA, TOPKAT, ClogP/CMR, HDisq, MOLCAD |
| UCSF MidasPlus - Molecular Display and Simulation System |
| 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. |
| Uppsala Software Factory - Software and Resources for Macromolecular Crystallography and Structural Biology (Gerard J. Kleywegt) |
| VMD : Visual Molecular Dynamics Home Page - VMD is a package for the visualization and analysis of biomolecular systems (SGI, HP-UX9 and 10, Linux, Win95/NT(coming soon)). - Download |
| WebMO - WebMO is a World Wide Web-based interface to computational chemistry packages. WebMO is available for free and can be installed on nearly any unix or Linux system. |
| WHAT IF Home page - WHAT IF is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. |
| WPDB for Windows - PDB 100 Meg Protein Database for Windows. 100 Random structures zip file included. |
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