لیست کامل نرم افزارهای شیمی

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Software-Related Sites

The following sites are related to software that may be of interest to computational chemists:

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

• Abbreviated Profile of Drugs (APOD) is a web-based decision and prediction program for drug discovery -http://www.ApodVision.com
   
• Accelrys- Molecular modeling, simulation, and informatics software for life and material sciences --http://www.accelrys.com/
   
• ACD/logP Freeware http://www.acdlabs.com/freelogp -- download to your desktop and predict logP values from structure. 
   
• ADF, the Amsterdam Density Functional package ( http://www.scm.com/ ) for molecules and periodic systems. 
   
• ADMET Predictor - software for predicting and modeling the ADMET (Absorption, Distribution, Metabolism, Elimination, and Toxicity) of chemicals directly from molecular structure - http://www.simulations-plus.com/ 
   
• Adun - Biomolecular Simulator. The environment for developing new algorithms in molecular simulations (distributed under GPL Licence). http://diana.imim.es/Adun
   
• Advanced Chemistry Development -- http://www.acdlabs.com/ Developers of chemical property prediction software and spectroscopic databases

 

 

• AHSystems Group -- Chemistry and Physics software reseller -- http://www.ahsystem.com/
   
• Agile Molecule -- Scientific Software for Chemists. Look at the catalog at: http://www.biomolecular-modeling.com 
   
• AMBER -- Molecular Dynamics Program -- http://amber.scripps.edu/
   
• ALOGPS, CLOGP, KOWWIN ,XLOGP, IA_LOGP -- logP and logS calculator on the Internet--http://www.vcclab.org/lab/alogps
   
• AMSOL -- semiempirical quantum chemistry program (gas phase and solvation). http://amsol.chem.umn.eduand http://www.makolab.com/amsol.
   
• APBS: Adaptive Poisson-Boltzmann Solver -- Software for evaluating the electrostatic properties of nanoscale biomolecular systems -- http://apbs.sourceforge.net/ 
   
• ArgusLab 3.0 -- Molecular Modeling Software -- http://www.planaria-software.com
   
• Artificial Life software -- http://alife.santafe.edu/alife/software/ 
   
• Automatic Format conversion of Molecular Structure Files by Corina -- http://www.molecular-networks.com/online_demos/corina_demo.html
   

B

• Babel, CLOGP, KOWWIN,XLOGP, IA_LOGP http://www.vcclab.org/lab/babel 
   
• Babel-- Program designed to interconvert a number of file formats used in molecular modeling --http://www.eyesopen.com/docs/html/babel/ 
   
• Basis Set library for ab initio programs -- http://www.emsl.pnl.gov:2080/forms/basisform.html 
   
• BioSolveIT -- Software solutions for structure and ligand-based molecular design -- http://www.biosolveit.de
  • PoseView http://www.biosolveit.de/PoseView/ is a software tools to generate 2D-images (png, svg and pdf) of 3D Protein-Ligand complexes. Note that PoseView images are available for the majority of PDB-structures on the PDB web site.
  • HYDE http://www.biosolveit.de/Hyde/ in an entirely new approach to assessing binding affinities. Hyde is entirely based on physics-principles and has not been trained or calibrated on experimental data. Hyde provides visual feedback at atomic detail.
  • ReCore http://www.biosolveit.de/ReCore/ instantaneously generates scaffold replacement ideas with the objective, to leave the 'old' side chains in place. It is also applicable in fragment-merging, fragment-linking and fragment-growing scenarios.
   
   
• Bio Online -- Biopharm Industry Info and Online Store for Life Sci Software -- http://www.bio.com/ 
   

 C

• C++ Library of Genetic Algorithm Components -- http://lancet.mit.edu/ga/ 
   
• Chemical Computing Group Inc. http://www.chemcomp.com -- A leading provider of computational applications aimed at drug discovery 
   
• Chemical Markup Language -- 
  http://cml.sourceforge.net 
   
• Chemissian: quantum chemistry program for visualizing electron/spin density distribution and UV-VIS spectra, plotting molecular orbital energy level diagrams, calculating atomic orbital populations, contributions of atoms and fragments to MOs. Chemissian supports output files of US-GAMESS, PC-GAMESS/Firefly and Gaussian quantum chemistry software packages -- http://www.chemissian.com/. 
   
• Chemistry Software and Information Resources (CSIR) -- http://www.csir.org/index.html 
   
• ChemTK -- a cheminformatics toolkit for Windows --http://www.atomseek.com/Chemistry/Software/Cheminformatics/ChemTK_L96475/
   
• Chimera -- package for molecular modeling: atom-type identification, association of structures with sequence alignments, and interactive contouring of volume data (for example, electron density or electrostatic potential). Results from several molecular dynamics programs and from DOCK can be viewed and analyzed. Free for academia. -- http://www.cgl.ucsf.edu/chimera/
   
• CLIFF -- is a powerful program which provides a series of functionality, which goes beyond a simple conversion tool: -- http://www.mol-net.de/
   
• CMDBioscience, LLC -- CMD bioscience ( http://www.cmdbioscience.com/ ) specializes in the use of novel proprietary computational methods to model and engineer clinically important protein-protein and protein-peptide interactions. Our Affinity algorithm is designed to predict protein-protein / protein-peptide binding affinities; it is fast enough for use as a scoring function and will be made freely available to the academic community. Other key, proprietary computational tools employed by scientists at CMD Bioscience include Ensemble and Transcend. These groundbreaking search algorithms, when interfaced with Affinity, allow CMD scientists to efficiently design novel peptides and proteins 
   
• CompuChem -- http://www.compuchem.com/ 
   
• Computational Chemistry -- http://www.computational-chemistry.co.uk/ Providing excellent software for research and higher education. 
   
• Computational Science and Engineering Online --( http://cse-online.net ) - An innovative web-based Grid-enabled environment for molecular modeling and simulation 
   
• COSMOlogic -- Software for Life Sciences, Chemical Engineering and Quantum Chemistry.http://www.cosmologic.de: COSMOtherm (quantitative calculation of solvation mixture thermodynamics based on quantum chemistry), COSMOfrag (a tool that performs the rapid, automated fragmentwise construction of approximate sigma-profiles of larger molecules), COSMOsim (uses COSMO-RS method to assess crucial information for most ADME properties), COSMOmic (describes micelles or biomembranes) and distribution of other computational chemistry packages. 
   
• Culgi BV -- http://www.culgi.com/ is dedicated to provide the chemical and pharmaceutical industry with revolutionary modelling tools for the rational design of soft matter formulations. Our flagship product is theChemistry Unified Language Interface modelling library. 
   

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  لیست کامل، نرم افزار، شیمی، لیست نرم افزارهای کاربردی، نرم افزارهای شیمی کوانتوم، نرم افزارها، لینک های پر کاربرد شیمی، نرم افزارهای نایاب شیمی، نرم افزارهای جالب، کاربردی ترین نرم افزارها، نرم افزار

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D

• DiscoveryGate - Online access to integrated primary literature, secondary databases, and authoritative reference works http://www.discoverygate.com
   
• DeMon DFT Package-- http://www.demon-software.com/public_html/index.html
   
• Dragon--able to calculate 4885 molecular descriptors, it has a nice interface and runs on Windows and Linux PC's -- http://www.talete.mi.it/
   
• DSMM: a Database of Simulated Molecular Motions-- http://projects.villa-bosch.de/mcm/database/dsmm
   

E

• Elsevier MDL - scientific content, informatics framework and workflow applications that accelerate successful life sciences R&D by improving the speed and quality of scientists' decision making -- http://www.mdl.com

 

 F

• FlexX -- Fast Flexible Docking Software http://www.biosolveit.de/flexx 
   
• Force Field Explorer -- http://dasher.wustl.edu/ffe/ 
   
• FORTRAN-90 Tutorial -- http://www.cs.utk.edu/~london/MPPopt/additional.html 
   

http://www.cs.mtu.edu/~shene/COURSES/cs201/NOTES/fortran.html 

 

G

• GAMESS ab initio program, and information on http://www.msg.ameslab.gov/ --http://www.msg.ameslab.gov/GAMESS/GAMESS.html 
   

Mark Gordon's Research Group. There is also PC GAMES: http://phys069b-2.chem.msu.ru/gran/gamess/. 

 

• Gaussian Inc. -- http://www.gaussian.com 
   
• gOpenMol -- http://www.csc.fi/gopenmol/ 
   
• Grace5.1.5: A WYSIWYG 2D plotting tool for the X Window System and M*tif --- http://plasma-gate.weizmann.ac.il/Grace/ 
   
• Gromacs MD Software -- http://www.gromacs.org/ 
   
• Guide to Available Mathematical Software (GAMS) -- http://gams.nist.gov/ 
   

H

• H-bonds: packages that display H-bons and more -- 
  AUTODOCK: http://autodock.scripps.edu/
  MOLEKEL: http://www.cscs.ch/molekel/>
  SWISS-PDB VIEWER: http://www.expasy.org/spdbv/ 
   
• HYPERCUBE. INC. -- http://www.hyper.com/
  HyperChem package: Computational methods include molecular mechanics, molecular dynamics, and semi-empirical and ab-initio molecular orbital methods, as well as density functional theory. HyperChem is applicable to macromolecules as well as small molecules and is scriptable. 
   

I,J,K

• ImageWave EHS Enterprise Software Solution - http://www.imagewave.com. This EHS solution provides MSDS Management (MSDSFinder), Environmental Reporting (including SARA 313 and Tier II), Container Labeling, MSDS Authoring, MSDS directory, MSDS Scanning/Updating Service and more. 
   
• IQmol open-source molecular editor and vizualization package -- http://www.iqmol.org/. Runs on OS X, Windows and Linux. 
   
• JOELib -- An open source computational chemistry package written in Java http://joelib.sourceforge.net/ 
   
• Jmol -- A free open source molecule viewer http://jmol.sourceforge.net/ 
   

L

• Lammps--is a classical molecular dynamics (MD) code created for simulating molecular and atomic systems such as proteins in solution, liquid-crystals, polymers, zeolites, or simple Lenard-Jonesium --http://lammps.sandia.gov/ 
   
• Leadscope, Inc. -- chemoinformatics software and databases: FDA Toxicity Database, FDA SAR Genetox Database, Predictive Data Miner and more (see the Website: http://www.leadscope.com for a full list of products and services). 
   
• Linux Scientific Software -- http://www.redbrick.dcu.ie/~noel/linux4chemistry/ 
   
• LSD program -- Logic for Structure Determination, searches the molecular structures that are compatible with NMR spectroscopic data http://www.univ-reims.fr/Labos/UPRESA6013/GNOSIE/LSD/ 
   

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  لیست کامل، نرم افزار، شیمی، لیست نرم افزارهای کاربردی، نرم افزارهای شیمی کوانتوم، نرم افزارها، لینک های پر کاربرد شیمی، نرم افزارهای نایاب شیمی، نرم افزارهای جالب، کاربردی ترین نرم افزارها، نرم افزار

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M

• Marvin Applets and Marvin Beans 2.10.5, JChem and JKlustor 1.7.3
  • - Marvin Applets and JavaBeans support drawing/displaying chemical structures and handling molecule objects.
  • - JChem provides chemical database searching capabilities by integration into relational database engines supporting SQL.
  • - JKlustor is a software for diversity calculations and clustering, which can generate and apply 2D molecular fingerprints.
  http://www.chemaxon.com/marvin/jnlp/index.html
  http://www.chemaxon.com/marvin/doc/for-mac-users.html
  http://www.jchem.com/doc/user/
  http://www.jchem.com/changes.html
  http://www.jchem.com/doc/admin/JKlustor.html
  http://www.chemaxon.com/marvin/demos.html
  http://www.jchem.com/examples.html
   
• MDL QSAR - Comprehensive QSAR modeling system --http://www.mdl.com/products/predictive/qsar/index.jsp 
   
• MicroSimulations -- http://www.microsimulations.com/ 
   
• MIPSIM: is a computational system for the automatic exploration of biomolecular similarities on the basis of molecular interaction potentials -- http://cbbl.imim.es:8080/cbbl/publications-new/decaceres00/?searchterm=mipsim 
   
• Mol2Mol: molecule file conversion,manipulation and utility program -- http://www.gunda.hu/mol2mol/index.html 
   
• MOLCAS -- quantum chemistry software package http://molcas.org or http://www.teokem.lu.se/molcas/. 
   
• Molexel-- an interactive molecular graphics program to visualize molecular and electronic structure data from a number of electronic structure program outputs (Gaussian, Gamess, ADF...) as well as from XYZ and PDB files --http://www.cscs.ch/molekel/ 
   
• MolSoft -- http://www.molsoft.com/: Molsoft is a La Jolla, California based company that is a primary source of new breakthrough technologies in: molecular graphics and visualization, molecular modeling, docking and virtual screening, computational biology and cheminformatics.
  • ICM-Browser Molecule Visualization
    • ICM-Browser (Free Download) -- Software for browsing molecules and making fully-interactive slides for embedding in PowerPoint and the Web using ActiveiCM.
    • ICM-Browser-Pro -- A high quality visualizer and annotator for three dimensional molecular structures, sequences and alignments, chemical spreadsheets and biological data.
    • ActiveICM (Free Download) -- Enables you to view and display 3D ICM graphical slides and animations interactively inside Microsoft PowerPoint and web browsers such as Internet Explorer, Safari and Mozilla Firefox.
  • ICM-Pro and Modules Desktop Modeling
    • ICM-Pro -- Easy-to-use and complete desktop-modeling environment for a biologist or a chemist interested in molecular structure and function.
    • ICM-Homology - Modeling -- High-throuput molecular modeling, loop modeling and refinement program.
    • ICM-VLS - Virtual Ligand Screening -- A structure-based drug design program allows you to dock and score millions of compounds. An efficient and proven approach for lead discovery.
  • ICM-Chemist: Cheminformatics Tools
    • ICM-Chemist -- A standalone suite of programs for chemical drawing and editing, chemical database generation, chemical searching, clustering, and enumeration.
    • ICM-Chemist-Pro -- A standalone cheminformatics products containing a wide set of 3D chemical tools, chemical superposition, 3D interactive ligand-receptor editing, and QSAR.
  • Chemical Management Tools
    • MolCart -- MolCart allows you to store large chemical compound libraries for searching and analysis. Moreover, it uses a fast relational database which is freely available without any limitations.
    • MolCart Compounds -- MolCart Compound Database is an up-to-date collection of vendor compound databases.

 

 

• MOPAC: new features of MOPAC 2002 and LinMOPAC2.0--http://www.ccl.net/chemistry/links/software/index.shtml\ 
   

N

• NetLib -- Library of Numerical Public Domain Software -- http://www.netlib.org/ 
   
• NIST -- Guide to Available Mathematical Software -- http://gams.nist.gov/ 
   
• Numerical Recipes Home -- online version of "Numerical Recipes" -- http://www.nr.com/ 
   

O,P,Q

• ORTEP -- Plot program -- http://www.ornl.gov/ortep/ortep.html 
   
• Orbitron -- A gallery of Orbitals on Internet -- http://www.shef.ac.uk/chemistry/orbitron/ 
   
• Packmol--Creates an initial point for molecular dynamics simulations by packing molecules with a specified minimum-atom distance--http://www.ime.unicamp.br/~martinez/packmol 
   
• PGPLOT -- Graphics Subroutine Library -- http://astro.caltech.edu/~tjp/pgplot/ 
   
• Polar -- electrochemical simulation and data analysis (http://www.electrochem.net, http://www.DrHuang.com).
   
• PREMIER Biosoft -- Software for molecular biologists. http://www.premierbiosoft.com
  Real Time PCR Design, Primer and Probe Design, Cloning & Plasmid Maps, Cross Species, Species Identification, Allele Identification, SNP Detection, SNP Genotyping, DNA Methylation, FRET Probes, Microarray Software, Tissue Microarray Sofwtare, Glycan, Glycosylation, etc. 
   
• ProBis -- Protein Binding Sites Detection: http://probis.cmm.ki.si/. Algorithm for detection of structurally similar protein binding sites by local structural alignment. 
   
• Prospect 2--PROSPECT is a threading-based protein structure prediction system--http://compbio.ornl.gov/structure/prospect2/ 
   
• PyMOL-- Free and unrestricted open-source molecular graphics system -- http://pymol.sourceforge.net/ 
   
• Q-chem -- ab initio and DFT molecular modeling package http://www.q-chem.com
   
• Qmol -- An OpenGL based molecular viewer for Windows http://www.dnastar.com/products/qmol/index.html
   

R

• RASMOL -- http://www.umass.edu/microbio/rasmol 
   

S

• SageMD -- Visualizer/builder for crystal structures and interfaces. Classical MM/MD. Support for popular file formats for export/import. Extensve database of inorganic structures. Free for academia and inexpensive for industrial researchers. http://sagemd.com 
   
• Schrodinger, Inc.'s -- Computational Chemistry Software -- http://www.schrodinger.com/ 
   
• Scienomics -- http://www.scienomics.com. Software for Materials R & D, modeling and simulation. 
   
• Scientific Computing & Modelling -- http://www.scm.com 
   
• Scientific Software Catalogue -- http://www.scitechint.com/ 
   
• Seascape -- computational science company offering software, research consulting and software services --http://www.seascapelearning.com 
   
• Simulated Annealing or Adaptive Simulated Annealing, by Lester Ingber -- http://alumni.caltech.edu/~ingber/ 
   
• Simulated Biomolecular Systems Inc. (SimBioSys (TM)) http://www.simbiosys.ca Products for the pharmaceutical industry. 
   
• SQS--is the Simple Queueing System that allows jobs to be run in sequence on a single machine --https://sourceforge.net/projects/sqs/
   
• Sunset Molecular Discovery, LLC -- http://www.sunsetmolecular.com/ -- WOMBAT-PK and WOMBAT: Pharmacokinetics and BioActivity Databases. 
   
• SWizard is a user-friendly program (OS: MS Windows NT/2000/XP) for postprocessing spectral data. A spectrum is calculated as a sum of Gaussian or/and Lorentzian bands or the mixture of these functions please checkhttp://www.sg-chem.net/swizard/ 
   
• Swiss PDF viewer--an application that provides a user friendly interface allowing to analyze several proteins at the same time -- http://www.expasy.org/spdbv/
   
• Symbolic Algebra Package -- Maple -- http://www.maplesoft.com/ 
   
• Synergy Software -- Terminal Emulators -- http://www.synergy.com/ 

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  لیست کامل، نرم افزار، شیمی، لیست نرم افزارهای کاربردی، نرم افزارهای شیمی کوانتوم، نرم افزارها، لینک های پر کاربرد شیمی، نرم افزارهای نایاب شیمی، نرم افزارهای جالب، کاربردی ترین نرم افزارها، نرم افزار

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T

• TINKER Molecular Modeling Software -- http://dasher.wustl.edu/tinker/ 
   
• Transient V2.52 -- A new reaction-diffusion equations solver -- http://transient.mkolar.org 
   
• Tripos, Inc. -- software products and services for compound research in pharmaceutical, -- http://www.tripos.combiotechnological, and related organizations worldwide 
   
• TURBOMOLE -- Program Package for ab initio Electronic Structure Calculations -- http://www.turbomole.com/ 
   

U

• UNIVIS-2000 -- Molecular Visualization Package from University of Pune. Free for Academia.http://chem.unipune.ernet.in/univis.html 
   

V

• VEGA1.4.3--program to convert, manage and visualize of 3D structures for several platforms (Win32, Linux, Irix, AmigaOs). -- http://www.ddl.unimi.it/ 
   
• VLifeMDS (www.vlifesciences.com ) (VLife Molecule Design Suite) is an integrated platform for Computer Aided Drug Design (CADD) and molecule discovery available for both Windows^® and Linux platforms. This integrated suite provides complete toolkit to scientists to perform all scientific functions required to pursue structure based as well as ligand based discovery approaches. 
   
• VMD Molecular Visualization Software -- http://www.ks.uiuc.edu/Research/vmd/
   

W

• Wavefunction -- http://www.wavefun.com/ 
   
• WHATIF - sequence analysis package -- http://swift.cmbi.kun.nl/whatif/ 
   

X,Y,Z

• ZMM Software, Inc. -- http://www.zmmsoft.com -- Molecular Modeling and Simulation Software (MVM viewer is a freeware, ZMM is a molecular modeling and simulation system that runs on Windows and Unix/Linux). 
   

 

 

A large list of links to chemistry software makers is also available athttp://www.liv.ac.uk/Chemistry/Links/softwarecomp.html -- Links for Chemists

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لیست کامل، نرم افزار، شیمی، لیست نرم افزارهای کاربردی، نرم افزارهای شیمی کوانتوم، نرم افزارها، لینک های پر کاربرد شیمی، نرم افزارهای نایاب شیمی، نرم افزارهای جالب، کاربردی ترین نرم افزارها، نرم افزار