Welcome to NetSci's
List of CADD/CAMM Software

Notice: Statements and opinions made for the products within this listing were supplied by their owners. Network Science Corporation assumes no responsibility for the content of these listings. All product and company names mentioned in this publication are patents, trademarks, registered trademarks or servicemarks of their respective holders.

The Software Section of NetSci is accessed by hundreds of scientists every week. Our goal is to make this resource as comprehensive as possible. If your software program is not included, please send e-mail with a brief description, the categories under which your program should appear, the platforms supported, and contact information.

For programs currently listed in NetSci, please check the table and description and notify us of any changes or additions.

[A, B, C ] -- [D, E, F ] -- [G, H, I ] -- [J, K, L ]
[M, N, O ] -- [P, Q, R ] -- [S, T, U ] --
[V, W ] -- [X, Y, Z]




--- A, B, C ---





 

ADAPT (Automated Data Analysis using Pattern Recognition Toolkit)





 

Alchemy III and Alchemy 2000 is a desktop molecular modeling system for PC (DOS and Windows) and Macintosh (Alchemy III only) computers. Provides structure building, comparison, optimization (modified SYBYL energy minimizer) and display. Available from Tripos, Inc.





 

Anaconda - an interactive molecular similarity program for visual comparison of surface properties and pharmacophore discovery originally marketed by Oxford Molecular Group. The program is no longer supported.





 

Apex-3D is a rule-based QSAR program developed by Biosym Technologies in conjunction with V. E. Golender and A. B. Rozenblit. The program is no longer available.





 

ArgusLab : Planaria Software freely distributes its molecular modeling and drug-design program, ArgusLab to anyone who desires a license. It is used world-wide in teaching and industry for teaching, spectroscopy, graphics & visualization, drug-docking, and high-level ab initio calculations. It is available at http://www.arguslab.com





 

AutoDock is an automated ligand to protein docking program.





 

CAChe - a powerful 3-D visualization of molecules, including complex derived data, with an intuitive interface. CAChe is designed to work the way experimental chemists work. Simply identify properties of interest using the standard menu interface and 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. CAChe and a variety of add-on products are available from the CAChe software division of Fujitsu





 

Catalyst Environment for combinatorial chemistry from Accelrys has the following modules:

HipHop identifies pharmacophoric hypotheses common across a series of HTS `hits'. These models are also used to perform feature-based alignments that can be used subsequently in the development of QSAR's and other interpretive models. HipHop matches chemical features, such as surface-accessible hydrophobes, surface-accessible hydrogen bond donors/acceptors, charged/ionizable groups, and features defined by users.

Catalyst/SHAPE provides access to a series of 3D shape descriptors for library evaluation and design. Once a desired shape model has been identified, it can be used to find additional molecular templates possessing a similar shape (accounting for conformational flexibility) that can be used in a lead optimization process.

Catalyst/INFO builds and administers databases of 3D structures from corporate or project data. Full 3D conformational models are generated via the ConFirm technology, which explores energetically accessible conformations that span a compound's flexibility. Catalyst is integrated with MDL ISIS to facilate the use of in-house information.

DBServer provides client-server support for databases of 3D conformational models, as well as access to data stored in ORACLE databases. Such data handling methods are necessary to handle the large quantities of property and structural data common to combinatorial approaches.

The Catalyst Environment is available from Accelrys





 

CAVEAT accomplishes a number of tasks to assist in the structure-based design of molecules





 

CAVITY is a program designed to evaluate the shape of active sites. It has been compiled for and runs on ESV, SGI Iris, and Sun workstations. A paper describing CAVITY can be found in J. Comp.-Aided Mol. Des.,4: 337-354 (1990). Contact:

Garland Marshall
Center for Molecular Design
Washington University
One Brookings Drive
St. Louis, MO 63130 USA
Tel: 314-935-4673
Fax: 314-935-4979
E-mail: garland@ibc.wustl.edu




 

Cerius2 is a software environment designed to facilitate the chemical computing needs of R&D organizations. With Cerius2, scientists are able to apply the predictive power of computational chemistry to the critical issues in their research. WIth Cerius2 users can visualize structures, predict the properties and behavior of chemical systems, refine structural models, and integrate in-house computational codes in a commercial software environment. The Cerius2 environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. CADD modeling components include:

C2*Alignment aligns sets of molecules, using automated or manual methods, for easy comparison during the study of drug candidates.

C2*Analog Builder is used to specify combinatorial libraries and select fragments/reagents based on their diversity. You can generate sets of congeneric analogs that can be rapidly screened to identify drug candidates. Libraries can be imported from the Accelrys Project Library for diversity analysis.

C2*CAVEAT identifies molecular frameworks from which novel active lead candidates can be designed de novo. Clustering and filtering tools facilitate the rapid testing of new ideas and in turn allow you to focus on the best leads.

C2*DBAccess provides direct access to structural databases (Catalyst and MDL ISIS) for use in modeling experiments. Hits can be browsed in 2D or 3D.

C2*Diversity analyzes chemical diversity to design and evaluate compound libraries and reagent sets for combinatorial chemistry. You are able to intelligently sample all potential drug candidates so that a reduced set can be synthesized and screened. PDF datasheet.

C2*FieldFit provides algorithms for aligning molecules in a receptor binding site. Alignments are based up principal moments of inertia or electrostatic moments rather than common subgraphs.

C2*GA utilizes the breakthrough technology of Genetic Algorithms to evolve a family of predictive models, which helps you develop QSAR models from receptor surface and other data, leading to faster screening of drug candidates.

C2*Ludi is ade novo drug design tool. It can be used to design novel molecules from a library of templates and to simulate screening.

C2*MFA performs field-based 3D QSAR and visualization. You can predict the activities of new molecules based on the geometric properties of existing compounds.

C2*QSAR+ provides a wide range of regression and analysis technologies integrated in a `chemically aware' molecular spreadsheet. Existing data can be used to predict the activities of novel drug candidates.

C2*Visualizer provides a comprehensive modeling environment for building, editing and visualizing models of molecular structure as well as the core requirements to run Cerius2 applications modules. PDF Datasheet.

The Cerius2 environment is available from Accelrys





 

Chem3D Pro - Molecular modeling program gives chemists instant access to the 3rd Dimension. Gain insight into molecular behavior by rotating and visualizing 5000+ atom models in color. Performs real-time animation, energy minimization and molecular dynamic calculations. Build your own models in Chem3D or convert a 2D structure to 3D just copy in a structure from ChemDraw. Chem3D is available from CambridgeSoft





 

Hypercube's ChemPlus consists of several modules: distinct programs which interact with HyperChem. Communication between the ChemPlus modules and HyperChem takes place transparently via Dynamic Data Exchange. The ChemPlus Manager attaches these modules to appropriate places in HyperChem's menus, so that you can launch them straight from HyperChem. This close integration makes ChemPlus easy to incorporate into your normal use of HyperChem.





 

Chem-X was developed by Chemical Design Ltd. and is no longer available.





 

CLIP was created, developed and extensively tested at the Institute of Medicinal Chemistry of the University of Lausanne. CLIP is a package with the following capabilities:

  • 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)

Information about CLIP, publications can be found on the web at URL:http://www-ict.unil.ch/ict/clip/docs/clip.html





 

CODESSA is an advanced, fully featured quantitative structure/activity relationship (QSAR) program that ties information from AMPAC with experimental information. Together these programs allow researchers to answer the questions that are important to their efforts, whether they be academic or commercial. A number of papers have already been published showing the efficacy of CODESSA and AMPAC in predicting such macroscopic chemical properties as gas chromatography retention indices, polymer glass transition temperatures, critical micelle concentration, toxicity, boiling/meliting points, and flash points. CODESSA is the result of a joint effort between Semichem and Professors Alan Katritzky (U. of Florida) and Mati Karelson (U. of Tartu, Estonia). CODESSA runs on UNIX, MacOS and Windows operating systems. Contact

Semichem, Inc.
7204 Mullen
Shawnee, KS 66216 USA
Tel: 913-268-3271
Fax: 913-268-3445
http://www.semichem.com




--- D, E, F ---





 

DEREK for Windows is a rule-based expert system that predicts the toxicological hazard of chemicals based on an analysis of their molecular structure. The software uses structure activity relationships (SAR or structural alerts) and gives some consideration to physicochemical properties to derive its predictions. All outcomes are peer reviewed by expert toxicologists and are supported by literature references. Alerts cover a wide range of toxicological end points, including carcinogenicity, mutagenicity, and skin sensitisation. All the tools are provided for users to add their own in-house alerts. DEREK for Windows is supported on NT and 2000.

For further information contact:

Nicole McSweeney
LHASA Limited
School of Chemistry
University of Leeds
Leeds LS2 9JT
United Kingdom
Tel: +44 (0)113 233 6531
Fax: +44 (0)113 233 6535
E-mail: lukinfo@mi.leeds.ac.uk




 

DOCK is a suite of programs used to produce a negative image of a biomacromolecular surface. This image is matched to positive images of putative ligands of known 3-D structure. Molecules which fit the receptor are scored and saved in PDB format. The program has been used to propose novel compounds of pharmaceutical interest. Graphical user interface must be supplied from external programs. Contact: I.D. Kuntz, University of California, Dept. Pharmaceutical Chemistry, San Francisco, CA 94143-0446 USA, Tel: +1-415-476-1937, Fax: +1-415-476-0688 or visit the DOCK homepage.





 

DockingServer is an internet service that calculates the site, geometry and energy of small molecules interacting with proteins. You can dock your ligands to your proteins (see Flexible ligand docking) and analyze their interaction in 5 easy steps. The DockingServer is offered to everyone in the field of molecular modeling from beginners to professionals. DockingServer can be used for molecular docking and thorough analysis of single ligands or for high throughput docking of sdf files.





 

eHiTS is a flexible ligand-docking package that is fully automated, making it suitable for high throughput screening applications. It is not limited to a predetermined discrete set of dihedral angles. Version 4.3 includes improved multithreading computations, decreasing over all wait times for dockings. eHiTS is available for Linux and SGI platforms. Contact SimBioSys, http://www.simbiosys.ca.





 

FRED is an accurate and extremely fast docking program. For every ligand, FRED exhaustively searches all possible poses within a protein active site, filtering for shape complementarity and pharmacophoric features before evaluating with several scoring functions (ChemScore, PLP, ScreenScore, ChemGauss, PBSA).

FRED uses a systematic search algorithm, accurately predicting binding modes in a reproducible manner, unlike many other docking programs, which use stochastic methods. Despite being exhaustive, FRED is extremely fast, out-performing all competitive methods; FRED docks about a dozen ligand conformers per second per processor. Furthermore, FRED will perform constrained docking, wherein certain pharmacophoric features are guaranteed to be in specific regions of the active site, allowing scientists to take advantage of known structure activity relationships.

Key new features in FRED 2.1 include:

  • the use of multiple scoring functions during pose selection. This consensus pose selection significantly improves the likelihood that the ligand is placed in the correct binding mode;
  • a more accurate version of the ChemGauss scoring function with significantly better hydrogen-bond perception;
  • customizable scoring functions and flexible consensus scoring methods;
  • greatly expanded documentation; and
  • docking analysis tools for investigating how various parameter settings affect the reproduction of known structures of ligand-receptor complexes.

For further information and graphics, etc., please contact:

George Vacek
VP Marketing and Business Development
OpenEye Scientific Software
3600 Cerrillos Road, Suite 1107
Santa Fe, NM 87507
505-473-7385
FAX: 505-473-0833
business@eyesopen.com
http://www.eyesopen.com




--- G, H, I ---





 

GERM (Genetically Evolved Receptor Models) is used to develop three-dimensional atom-based models of previously uncharacterized receptor sites starting from a small structure-activity model of active and inactive compounds.





 

Glide is a fast and accurate docking program that addresses a number of problems, ranging from fast database screening to highly accurate docking. The hierarchical filters in Glide ensure a fast and efficient reduction of large data sets to the few drug candidates that bind best with the target. Glide is available from Schrödinger



 

GMMX is available as part of PCModel, a structure building, manipulation and minimization program which is available from Serena Software. Contact:

Kevin Gilbert
PO Box 3076
Bloomington, IN 47402 USA
Tel: +1-812-333-0823
Fax: +1-812-332-0877
E-mail gilbert@iubacs.bitnet




 

GOLD is a program for calculating the docking modes of small molecules into protein-binding sites. It features a genetic algorithm for protein-ligand docking, full ligand and partial protein flexibility, choice of scoring functions, and a number of constraints to allow greater control over the output solutions. The software is available for Windows and UNIX. Contact Cambridge Crystallographic Data Centre at http://www.ccdc.cam.ac.uk.





  GRID is a computational procedure for detecting energetically favorable binding sites on molecules of known structure. It may be used to study arrays of molecules in membranes and crystals or macromolecules such as proteins. The energies are calculated as the electrostatic, hydrogen-bond and Lennard Jones interactions of a specific probe group with the target structure. GRID can distinguish between selective binding sites for different probes. Input for GRIN is prepared and checked by GRID. Display of results is through output files produced by GRID. The programs are written in Fortran 77 and run on all computer systems. Contact:

Peter Goodford
Molecular Discovery Ltd.
West Way House
Elms Parade
Oxford OX2 9LL, England
Tel: +44-993-830385
Fax: +44-295-269206
http://www.moldiscovery.com/




 

HASL the Hypothetical Active Site Lattice program. HASL modeling is accomplished through the intermediate conversion of a molecule to a set of regularly-spaced points (lattice) defined by Cartesian coordinates (x,y,z) and atom type. In this way individual molecules can be compared to one another, and their lattices merged to form a composite description called the HASL. The activity (ED50, pKi, etc.) of each molecule is distributed among the points in the HASL in such a way that the sum of the partial activity values associated with a set of points belonging to each molecule is equal to the activity for that molecule. The result is a model of the active (receptor) site consisting of points in space capable of predicting the activities of as yet untested molecules. A recent innovation, the construction of a predictive 3D-pharmacophore, is based on the selective editing of a HASL model. Recent investigations have shown that HASL modeling of data sets previously analyzed using the popular 3D-QSAR technique, CoMFA (Tripos), has resulted in similar degrees of predictivity and insight into active site binding. This observation is not unsurprising, since CoMFA, like HASL, relies on the deconvolution of a complex 3D problem into equidistant points in space. While CoMFA examines the effects (steric and electrostatic) outside the molecule, HASL focusses on a heuristic inspection of atom types within the Vander Waal's domain of the molecule.

HASL runs on PC-DOS, PC-Windows. The program can be ordered from:

Arthur Doweyko, President
Hypothesis Software
PO Box 237
Long Valley, NJ 07853-0237
or e-mail Arthur Doweyko at adoweyko@comcast.net




 

HINT (Hydrophobic INTeractions) a program for calculating and visualizing hydrophobic and hydrophobic interactions of biomolecular species is available from eduSoft.





 

HyperChem contains extensive facilities for building, manipulating, and visualizing molecules coupled to molecular mechanics and semi-empirical and an initio quantum mechanics programs that carry out simulations. You can carry out many different varieties of energy minimization (geometry optimization) and molecular dynamics calculation to obtain insight into molecular structure and flexibility. You can also compute and analyze IR and UV spectra. TheSGI version of HyperChem contains additional features.ChemPlus is available as an add-on to HyperChem for Windows.HyperChem Lite, Release 1.0 for Windows, brings a research level molecular modeling tool to the PC desktop. http://www.hyper.com/





 

Impact is a molecular mechanics program specifically designed to handle large macromolecular simulations. The program effortlessly treats simulations on ligand-protein systems in solvation or in vacuo enabling the study of large systems in a timely manner. Impact is available from Schrödinger



 

Insight II is a 3D graphical environment for molecular modeling. Its user interface enables the seamless flow of data between a wide range of scientific applications. The Insight II environment integrates builder modules, development tools, force fields, simulation and visualization tools with tools specifically developed for applications in the life and materials sciences. The programs are available from Accelrys.





 

INTERCHEM is a molecular modeling system designed for use on Silicon Graphics workstations. It includes facilities for handling and display of small molecules and large bio-molecules. Building new structures is made easy by a library of 380 pre-optimized (MOPAC) fragments. It incorporates a molecular mechanics program PIFF (written by Armin Widmer, Sandoz A.G.), which provides rapid optimization of structures. Structure files may be read into the program in SYBYL, BIOSYM, Cambridge Crystallographic Database XR and native INTERCHEM formats. The Proteins Package provides selective editing, display and highlighting of special features, investigation of homology, prediction of protein secondary structure, prediction of important sites, etc. The Crystal Structure package allows reading of files in Cambridge XR format, display of unit cells, the replication of the asymmetric unit necessary to fill a 3X3X3 nest of unit cells. Other programs included in INTERCHEM are PROTEINS, CONVERT, PRESTO, and THREEDOM. Contact:

Peter Bladon
Dept of Pure and Applied Chemistry
The University of Strathclyde
Glasgow G1 1X1, Scotland UK
Phone: 41-552-4400
Fax: 41-552-5664
e-mail: cbas25@vaxa.strath.ac.uk@nsf-relay-ac.uk




--- J, K, L ---





 

Liaison is a new program for fast estimation of free energy of binding between a receptor and a ligand. The free energy of binding can be approximated by an equation in which only the free and bound states of the ligand are calculated. The method combines high-level molecular mechanics calculations with experimental data to build a scoring function for the evaluation of ligand-receptor binding free energies. Liaison is availble from Schrödinger.





 

Ludi provides a tool which can quickly generate a series of potential binding compounds for a given ligand binding site on a protein. The knowledge-based system chooses fragments from a library based on their ability to bind to portions of the binding site through hydrogen bonding and lipophilic interactions. Ludi is available from Accelrys Inc.





--- M, N, O ---





 

MacroModel - With a large selection of force fields and advanced methods for conformational analysis, molecular dynamics, and free energy calculations, MacroModel is one of the most trusted names in molecular mechanics. MacroModel is especially well suited for general-purpose molecular mechanics for small and medium-sized organic molecules in both gas and solution phases.

Schrödinger, Inc.
1500 S.W. First Avenue, Suite 1180
Portland, OR 97201-5815
Phone: +1 503 299-1150
Fax: +1 503 299-4532
email: info@schrodinger.com
http://www.schrodinger.com




 

MCSS/Hook characterizes an active site's ability to bind ligands using energetics calculated via CHARMm. Strongly bound ligands are linked together automatically to provide de novo suggestions for drug candidates. The program is available from Accelrys Inc. as a part of the QUANTA modeling package.





 

METEOR originally resulted from a three year research project to develop a computer system for the intelligent prediction of the metabolic fate of xenobiotic chemicals. The software is continually developed alongside experts from various industry and academic sectors, with knowledge of biotransformations covering phase I and phase II metabolism. The software predicts the metabolic fate of a parent compound, and it also evaluates the likelihood that each predicted metabolite could be found in vivo. This evaluation considers physicochemical parameters, such as logP. Metabolites can be restricted to those most likely to be of interest by user defined controls. These include:

  • Selection of confidence levels for metabolite generation
  • Sequence termination at excretable metabolites.
  • External link to ClogP
  • The potential to make species specific predictions
  • Restriction to either Phase I or Phase II processes

The report for a query compound contains specific literature references, and links to external commercial metabolism databases are available. METEOR can also perform alongside DEREK for Windows, allowing a fast assessment of the likelihood of potential metabolites being toxic.

For further information contact:

Nicole McSweeney
LHASA Limited
School of Chemistry
University of Leeds
Leeds LS2 9JT
United Kingdom
Tel: +44 (0)113 233 6531
Fax: +44 (0)113 233 6535
E-mail: lukinfo@mi.leeds.ac.uk
http://www.chem.leeds.ac.uk /luk




 

MOE (Molecular Operating Environment) Chemical Computing Group Inc. (http://www.chemcomp.com) has created a very unique tool for Drug Discovery researchers. MOE's uniqueness is due to SVL - Scientific Vector Language which lays at the heart of the package. SVL is a next generation high-performance data-parallel language. Due to the incorporation of SVL, MOE can be used in any combination of 3 ways:

  1. Out-of-the-box: MOE contains a robust set of built-in applications in the areas of High Throughput Screening Data Analysis, Combinatorial Chemistry Library Design, Protein & Homology Modeling, and QSAR as well as traditional modeling and simulation.
  2. Customizable functionality: As most of MOE's built-in functionality is coded in SVL, you receive the actual source code and hence are able to fully customize features ranging from additions to the Graphical User Interface to changes in the specifics of the algorithms.
  3. Prototyping: The package includes SVL therefore the user is able to quickly prototype ideas and papers at a speed and in a manner not currently available anywhere.

In addition, due to SVL, Chemical Computing Group is able to quickly turnout upgrades and new modules to ensure that you have a software package that keeps pace with advances in science. SVL also allows MOE to be a true cross-platform software currently running native on Sun, SGI, Windows NT, Windows XP, Mac OS X and DEC Alpha NT. This marriage of unique architecture and platform independence makes MOE the ideal corporate deployment vehicle. One that can change and grow as your science changes and grows. Please see: http://www.chemcomp.com for more product information or contact Chemical Computing Group at: info@chemcomp.com.





   

Molecular Analysis Pro and Molecular Modeling Pro, developed by Norgwyn Montgomery Software Inc. are designed as analysis tools for chemists doing practical research in the relationship between properties of molecules (QSAR, QSPR etc.). Molecular Analysis Pro has three main features that aid in the discovery of these relationships:

  • calculates molecular properties from structure
  • contains statistical and graphing tools for analyzing data
  • data base storage, retrieval and manipulation capacity

Unlike general statistical packages, Molecular Analysis Pro is specialized to deal with QSAR/QSPR problems, and accomplishes these tasks easily and efficiently, with tools not found elsewhere. Molecular Analysis Pro and Molecular Modeling Pro are available from Norgwyn Montgomery Software http://www.norgwyn.com





 

Molecules-3D - is no longer available





Molecules-3D Pro - is no longer available





 

MS is no longer available from QCPE, but is a part of MSP





 

Molecular Surface Package is made up of two computer programs, MSRoll and MSDraw. The programs are written in ANSI C. Since neither currently does interactive graphics, they will run on any computer with an ANSI C compiler. MSP computes molecular surfaces, areas and volumes. Five programs provide robust, highly accurate areas and volumes and identify internal cavities. The programs are written in machine independent C. Source code is included with the license.





 

Nemesis - an interactive molecular modelling for IBM PCs, PS/2s, and compatibles running Windows 3.1, and Apple Macintosh II. The program is no longer available.





--- P, Q, R ---





 

PALLAS for WINDOWS is a collection of tools for making predictions of pKa, logP, logD values and metabolites based on the structural formulae of compounds. It has a modular structure allowing to attach each prediction module separately to the system. Modules include pKalc, EluEx, PrologP, PrologD, MetabolEx, and HazardEx.

For more information please contact CompuDrug;
Tel (650)401-5781



 

PCModel is a structure building, manipulation and display program which uses molecular mechanics and semiempirical quantum mechanics to optimize geometry. Energy routines available include MMX (an extension of MM2 and MM1) and MOPAC. Available on PC (DOS and Windows), Macintosh, SGI, Sun and IBM/RS computers.

Contact: Kevin Gilbert
Serena Software
PO Box 3076
Bloomington, IN 47402 USA
Tel: +1-812-855-1302
Fax: +1-812-332-0877
E-mail: gilbert@iubacs.bitnet




 

pKa Predictor - Schrödinger's pKa module is a highly accurate and automated tool for predicting pKa's for a wide range of molecules. The module utilizes ab initio quantum chemical methods to reliably predict pKa's in aqueous media. It employs a combination of correlated ab initio quantum chemistry, self-consistent reaction field (SCRF) continuum treatment of solvation, and systematic corrections to account for approximations in both the ab initio and continuum solvation models. Because it is based on high-level quantum mechanics, users can have confidence in the consistent quality of the results. pKa Predictor is available from Schrödinger.





 

ProChemist is a 3D molecular modeling program which includes Logp, Pka, and Solubility calculations, Qsar, and chemometrics capabilities (neuronal network and Genetic Algorithms). The program is available from Cadcom at http://pro.chemist.online.fr





 

Project Leader - Intuitive, experimental chemist's interface to computational methods. Originally developed by Oxford Molecular Group, the program is no longer available.





 

PRECLAV (PRopertyEvaluation byCLAssVariables) is a program for QSPR/QSAR calculations, available from Tarko Laszlo, Center of Organic Chemistry (CCO) - Bucharest, Romanian Academy.

  • accepts as input MOPAC v. 7.0 output files
  • analyzes molecules with maximum 99 atoms (H, C, N, O, S, P, F, Cl, Br, I, B, Si or As)
  • analyzes molecules with maximum 60 heavy atoms (C, N, O, S, P, F, Cl, Br, I, B, Si or As)
  • analyzes maximum 500 molecules (learning set + testing set)
  • calculates over 950 (global, local and grid / field) descriptors
  • calculates the aromaticity of chemical bonds by the TPA algorithm
  • calculates the logP values by a certain QSPR
  • computes the optimum value for probe atom distances
  • selects descriptors using r2 and Class functions
  • computes weighting factors by the Ordinary Least Squares Method
  • QSPR /QSAR selection is made by r2 function and r2CV / rKCV cross-validation functions
  • minimum number of predictors in final QSPR /QSAR: 3
  • maximum number of predictors in final QSPR /QSAR: 20
  • adaptable to work with user databases

PRECLAV includes a know-how procedure for the identification of testing set valuable molecules. E-mail inquiries: ltarko@cco.ro (author) or pfilip@cco.ro (general manager of CCO)





 

QikProp provides rapid ADME characteristic predictions of drug candidates. It is available from Schrödinger.





 

QSite is a new mixed mode QM/MM program for highly accurate energy calculations of protein-ligand interactions in the active site. The program is specifically designed for proteins and allows a number of different QM/MM boundaries for residues in the active site. QSite uses the power and speed of Jaguar to perform the quantum mechanical part of the calculations and OPLS-AA to perform the molecular mechanical part of the calculations. Qsite is available from Schrödinger.





 

RASSE is a structure-based method for de novo drug design developed at Molecular Design Laboratory, Institute of Physical Chemistry, Peking University (IPC). The detailed description of methodology can be found atJ. Chem. Inf. Comput. Sci., 1996,36, 1187-1194. The program is freely distributed via anonymous ftp on the condition that an agreement is signed between IPC and the end user. If you have any questions in using RASSE or comments, please contact Prof. Luhua Lai (lai@ipc.pku.edu.cn) or Mr. Renxiao Wang (arthur@ipc.pku.edu.cn). Tel: 86-10-62751490; Fax: 86-10-62751725.

RASSE3.1 can be get by anonymous ftp to:

ftp.ipc.pku.edu.cn
cd /pub/software/rasse

three files can be found in the directory: README: This text
rasse.tar.Z: Compressed source codes of RASSE3.1
License: A License form for users

Please sign the license agreement and fax it to Prof. Luhua Lai, Institute of Physical Chemistry, Peking University, Beijing 100871, CHINA. Fax: 86-10-62751725. You will be sent the help files from the authors describing how to run RASSE.





--- S, T, U ---





 

SARvision is chemoinformatics software available from ChemAPPS. SARvision is a desktop software application that identifies chemical motifs present in chemical datasets and organizes available biological and biochemical data, such as those that may result from high throughput screening, according to the scaffolds it identifies. The program facilitates R-table generation and facilitates data reporting as well. The user can quickly navigate chemical information and create tables with the data available that can be exported into applications such as Microsoft Word and Excel. Among the new features, we have comparison of the scaffold content of different libraries, added graphical capabilities to plot properties by scaffolds. A Linux version (without GUI)for scaffold identification is also available if you let meknow you are interested. SARvision is used by chemoinformaticians, medicinal chemists, high throughput screeners and even patent agents. Contact:

Hugo O. Villar, Ph.D.
Chemapps, An Altoris Project
11575 Sorrento Valley Road 214
San Diego, CA 92121
858.259.8161 Phone
858.259.8162 Fax
www.altoris.com
www.chemapps.com




 

SCULPT the interactive molecular application program that lets a drug or protein modeler simply grab and move part of a structural model to a specific place. The program is no longer available





 

SEA is a program which aligns molecular structures based on maximizing the overlap of electrostatic potential and steric fields. The program is no longer available





 

SEAL is an alternative method for alignment of molecular structures. The program was developed by Simon K. Kearsley and Graham M. Smith at Merck Research Laboratories. The package contains three programs: PRESEAL is used for input preparation, SEAL performs the alignment calculations, and POSTSEAL is used to analyze the output files. SEAL is based on the SEA program and depends on it to do much of the basic calculations. The SEA program is contained in SEAL. SEAL is written in FORTRAN 77 and runs on SGI systems. The program was originally available from QCPE, which is no longer on-line.





 

Sprout is an interactive system that assists chemists in several steps of the structure-based rational drug design process.





 

SYBYL is a suite of molecular modeling programs for building, editing and analyzing small molecule organics, biopolymers, polymers and materials. Modules include Base SYBYL, Biopolymer, QSAR, HQSAR, CoMFA, Advanced Comp (for conformation searching and interfaces to QCPE programs). Additional functionality is also available. SYBYL is available from Tripos, Inc.





 

TOPKAT is a computer-assisted toxicology prediction program which is available from Accelrys, Inc.





 

Tsar - a fully integrated analysis package for investigation of Quantitative Structure-Activity Relationships (QSARs). Available from Accelrys, Inc.





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X-LIGAND is a tool for drug discovery that automatically fits ligand molecules to electron density of protein-ligand complexes. Thousands of possible conformations can be sampled within seconds. X-LIGAND is a part of the QUANTA molecular modeling environment from Accelrys Inc.



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