Quick Links

Aabel :- Data Analysis

Aabel is a new, and recently updated high performance data management, processing, & charting application for Mac OS X. It provides a superb visual front-end to high-performance statistical data analysis. It has over 200 data presentation styles and is capable of handling very large data sets. There is a great review of Aabel 2.0 on MacResearch.
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Abinit :- Density Function Theory

Abinit is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave basis. ABINIT also includes options to optimize the geometry according to the DFT forces and stresses, or to perform molecular dynamics simulations using these forces, or to generate dynamical matrices, Born effective charges, and dielectric tensors. Excited states can be computed within the Time-Dependent Density Functional Theory (for molecules), or within Many-Body Perturbation Theory (the GW approximation). In addition to the main ABINIT code, different utility programs are provided

ADF2006 :- Density Function Theory

ADF2006.01 has been updated by Scientific Computing and Modelling, the OS X port of its quantum chemistry software is the first time ADF has been made available on the Mac platform. The release means chemists can now perform complex quantum chemical calculations using Density Functional Theory (DFT).

The Intel Mac release of ADF represents a new milestone in ease of use. Although ADF has been capable of running in parallel for as long as anyone can remember, until now this has involved installing extra software (eg.PVM) and careful configuration of one's run time environment. The Intel Mac release of ADF2006.01 has been linked with OpenMPI, and configures itself automatically at run time, so when you run it on a 4 processor Mac Pro, it will run on all 4 cores in parallel. No need to install additional libraries, or configure your environment.
There is also a benchmark comparison on MacResearch comparing various hardware configurations, needless to say the new Intel Macs look great.


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ALOGPS 2.1 :- LogP and LogS prediction

The ALOGPS 2.1 Applet provides interactive on-line prediction of logP, water solubility and pKa(s) of compounds for drug design (ADME/T and HTS) and environmental chemistry studies. In addition to the ALOGPS 2.1 logP and logW it also displays values calculated with Interactive Analysis LogP and LogW, Pharma Algorithms LogP, LogW and pKa, COSMOfrag logP, Quantum Pharmaceuticals QlogP, Molinspiration logP, KOWWIN logP and XLOGP programs. The requests are sent to the corresponding servers and the results are displayed in the applet.
A standalone version of ALOGPS is also available for MacOSX, Linux and Windows platforms from the Virtual Computational Chemistry Laboratory site.

AMBER :- Biomolecular force field

AMBER Instructions for getting AMBER 8 to run under MacOSX and on a G5 cluster.
Amber 9 should function "out of the box" on Macintosh, both with G4/G5 and Intel chips.
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

AMBIT :-Chemoinformatics system

AmbitDiscovery is part of the AMBIT project, a software for chemoinformatic data management, is an outcome of the LRI project: ‘Building blocks for a future (Q)SAR ((Quantitative) Structure Activity Relationship) decision support system. Since the software goal is to support decisions, including chemical grouping and QSAR applicability domain appraisal, the name AMBIT was chosen meaning ‘an area in which something acts or operates or has power or control’. The AMBIT software is available online and as a stand-alone application for beta testing. AmbitDiscovery is an user-friendly stand alone open source Java application, which estimates applicability domain of QSAR models by various methods, it uses the CDK for structure visualisation and seems to function fine under Mac OS X.

The full AMBIT data management system has a modular structure and is implemented in two versions: stand-alone and web-based (http://ambit.acad.bg ). It is written in Java to be platform independent and its cheminformatics functionality relies on the open source Java library – The Chemistry Development Kit. The database uses the MySQLdatabase, an open source relational database for speed and convenient access to disparate data sources. The chemical structures are stored in Chemical Markup Language (CML) the acknowledged method of encoding chemical data in XML. The choice of CML as the internal format makes the database independent of the software that is able to access it. Whilst it has not been tested on Mac OS X the developers would be very keen to hear about peoples experiences and seem very responsive.

AstexViewer :- Java molecule viewer

AstexViewer A Java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page with web page controls and as a desktop application.

The following pages from the Astex websiteshow examples of the use of AstexViewer™ for displaying protein/ligand complexes.

  • An applet using the internal Java graphical user interface.

  • An applet using HTML and Javascript controls.

  • An example that displays multiple structures.


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Atom in a Box :- Visualise atomic orbitals

Atom in a box a scientific and educational program that aids in visualizing the Hydrogenic atomic orbitals, a prime and otherwise unwieldy example of quantum mechanics.

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Atomic Mac :- Periodic table

Atomic Mac A periodic table of elements. In addition to the usual information found in such programs, The Atomic Mac also contains a wealth of nuclear information on each isotope, including half life, decay mode, and daughter products.

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AtVol :-Atomic vol clac

AtVol performs atomic volume calculations by separating each atom from neighboring atoms where their van der Waals spheres join and performing Monte Carlo integration to estimate the volume

AutoDock :- Docking tool

AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Updated to version 4 August 2007.
AutoDock actually consists of three separate programs: AutoDock performs the docking of the ligand to a set of grids describing the target protein; AutoGrid pre-calculates these grids; and AutoTors sets up which bonds will treated as rotatable in the ligand. This now includes the graphical front-end of AutoDock and AutoGrid, called AutoDockTools (ADT) for Mac OS X.

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Avogadro:- Advanced molecule editor

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture. Avogadro is based on top of existing chemistry software, including Open Babel. In the future, it will offer strong scripting abilities to allow for automated demos, submission of calculations to local computational resources, and user-defined customization.

Bioclipse :- Chemoinformatics platform

Bioclipse 1.1.1 beta now supports MacOSX.

Bioclipse is a free, open source, workbench for chemo- and bioinformatics with powerful editing and visualization capabilities for molecules, sequences, proteins, spectra etc. The major features are:

  • Import and export in various file formats

  • Visual editing of molecular 2D-structures

  • 3D-visualization of molecules and proteins

  • Editing and visualization of sequences and features (DNA, RNA, proteins etc)

  • Graphing and editing of various types of spectra, e. g. NMR, MS

  • Retrieval of resources (sequences, proteins, etc) from public data repositories

  • Scripting of 3D-visualizations with syntax highlighting and content assistance

  • PDB-editor with syntax highlighting for working with PDB files

  • CMLRSS-viewer for downloading chemical content published on the web using RSS-feeds

  • Chemtree for displaying a hierarchical view of molecular and macromolecular substructures

  • Visualization of syandard chemical properties

  • Powerful scripting language based on Mozilla Rhino for automating tasks

  • Integrated, searchable help-system

  • Connection with external programs, e. g. PyMol

Bioclipse is a rich client, which means it is run on your local computer but also gives the possibility to communicate with servers for data retrieval and computational services. The powerful plugin architecture is based on Eclipse, and results in a responsive, integrated user interface designed for simple and intuitive operations that at the same time is easy to extend with custom functionality.

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biOpen :-Sequence analysis and visualisation

biOpen is a new and unique sequence analysis and structure visualization software based on dynamic integration of analysis tools.

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BioX :- Bioinformatics tool

BioX takes advantage of the Unix underpinnings of Mac OS X by using command line sequence analysis tools from the ebiotools package (which contains software from the EMBOSS project, among others). By presenting these Unix tools in the form of a Mac application, BioX leverages the best of both worlds.

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BLAST from Apple :- Sequence analysis

BLAST This version has been optimised by Apple to afford a considerable speed improvement

BLAST from WU :- Sequence analysis

Washington University BLAST (WU BLAST) version 2.0 is a powerful software package for gene and protein identification, using sensitive, selective and rapid similarity searches of protein and nucleotide sequence databases. The feature list for WU BLAST 2.0 is long and continues to expand. Much of this is outlined here. A complete suite of search programs (blastp, blastn, blastx, tblastn and tblastx) is included in the package, along with database management and support programs that include nrdb, patdb, xdformat, xdget, seg, dust and xnu.
WU BLAST is neither a re-hashed nor “Mac-ified” version of NCBI BLAST, although WU BLAST is in many ways easier to use. WU BLAST shares essentially no code with NCBI BLAST, except for some portions that both packages copied from the public domain ungapped BLAST 1.4 (W. Gish, unpublished).

BLAST from NCBI :- Sequence analysis

This is the NCBI version of BLAST

BndLst :- List interatomic interactions

Bndlst reads a PDB format file and for each atom prints a list of covalent and H-bonded neighboring atoms, along with several atomic properties. It is useful in building scripts which process atomic structures

CAChe :- Molecular Modelling

CAChe is molecular modelling software that aids researchers in studying and modeling structures and reactions. CAChe allows visualization of molecules in 3D, searching for conformations, analyzing chemical reactivity and predicting properties of compounds on desktop computer.

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CaGe :- Graph theory for molecules

CaGe is an Open Source software package, implemented in C and Java. CaGe's task is to generate mathematical graphs of different types -- often types that relate to interesting chemical molecules -- and allow the user to view selected graphs in various ways or save them in several formats. If you have a normal, fairly modern UNIX system with Java, you can probably run CaGe.

CATVS :- Chemoinformatics

The Cactvs Chemoinformatics Toolkit for Mac OS X is being developed.

CCP4 :- Crystallography programs

CCP4 The CCP4 program suite is a collection of disparate programs covering most of the computations required for macromolecular crystallography. They have been collected and developed under the auspices of the Collaborative Computing Project Number 4, in Protein Crystallography, supported by the UK Science and Engineering Research Council (serc) since 1979 and currently the Biotechnology and Biological Sciences Research Council (bbsrc), and coordinated at Daresbury Laboratory. An excellent description of how to install together with a great selection of crystallography tools is available from the W.G.Scott research group here .

Ch :- Programming

Ch is a superset of C/C++ interpreter for cross platform numerical computing and 2D/3D plotting. Ch supports ISO C standard (C90), major new features in C99, classes in C++, POSIX, X/Motif, Windows, OpenGL, ODBC, GTK+, C LAPACK, CGI, XML, 2D/3D graphical plotting, advanced numerical computing, and shell programming. Moreover, Ch has many salient features from other languages and software packages.
C is for low-level system programming and embedded systems; C++ for large-scale projects; Ch for platform-independent script computing. C/Ch/C++ allow users to use one language, anywhere and everywhere, for any programming tasks

CDK :- Chemistry Development Kit

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It is now developed by more than 20 developers all over the world and used in more than 10 different academic as well as industrial projects world wide.

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Checkmol/Matchmol :- Molecular functional group analysis

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. Output can be either clear text (English or German), a bitstring or its ASCII representation, or a set of special 8-character codes. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option.

Another output option of checkmol is a set of statistical values derived from a given molecule, which can also be used for quick retrieval from a database. These values include: the number of atoms, bonds, and rings, the number of differently hybridized carbon, oxgen, and nitrogen atoms, the number of C=O double bonds, the number of rings of different sizes, the number of rings containing nitrogen, oxygen, sulfur, the number of aromatic rings, the number of heterocyclic rings, etc. The combination of all of these values for a given molecule represents some kind of "fingerprint" which is useful for rapid pre-selection in a database structure/substructure search prior to a full atom-by-atom match (see below).

Matchmol complements the capabilities of checkmol. It compares two (or more) molecular structures and determines whether one of them is a substructure of the other one. This is done by a full atom-by-atom comparison of the input structures. Thus, matchmol can be used as a back-end program for structure/substructure search operations in chemical database.

Note: if you are running MacOS X, use the following command:
fpc checkmol.pas -S2 -Tdarwin

Chem4-D :- Drawing Package

Chemistry 4-D Draw is a chemistry program written in Java combining the most advanced technologies in structure drawing.
Chemistry 4-D Draw Modules
NamExpert that understands IUPAC nomenclature rules. If you enter an IUPAC chemical name, it creates the corresponding structure
    Chem4D Graph module that creates multi-line graphs of different styles. It supports non-linear and linear curve fitting, response curve fitting and data analysis.
The program allows you to create high-quality structures simply by entering molecular names. It assigns systematic names to structures. It includes a full set of tools for drawing, text and structure editing, and labeling.

    ChemLabNotebook :- Electronic Notebook

    ChemLabNotebook is an electronic laboratory notebook for chemists. The notebook consists of two databases: the notebook itself and a built-in reagents database. The reagents database contains the structures, name, MWt, density and safety information on over 13,000 compounds that can be used as reagents. Entering the name of a reagent into the notebook causes the rest of the information to be "looked up" from the reagents database. The notebook also provides links to Chemdraw for calculation of MWt, formula etc. Users can add 10 records you will then need a password to add further experiments.

    ChemLab :- Lab Expt simulation

    Model ChemLab is a unique product incorporating both an interactive simulation and a lab notebook workspace with separate areas for theory, procedures and student observations. Commonly used lab equipment and procedures are used to simulate the steps involved in performing an experiment. Users step-through the actual lab procedure while interacting with animated equipment in a way that is similar to the real lab experience.
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    Chenomx :- NMR analysis

    Chenomx Chenomx provides a set of powerful software applications that allow you to quickly identify and quantify metabolites in NMR spectra based on validated compound signatures. The products include Chenomx NMR suite, Chenomx Profiler and Chenomx Signature Builder.

    ChemBioDraw :- Drawing Package

    ChemBiodraw 11.0 The best chemistry drawing package is now available for MacOSX available from Cambridgesoft. They also supply browser plugins that allow almost all the desktop functionality to be accessed from within a web browser. Here is a review I wrote describing the latest version.
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    ChemKey :- Chemistry reference

    ChemKey is a desktop chemistry refererence database containing over 90,000 records collected over 40 years covering all aspects of chemistry.

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    ChemSpotlight :- Chemistry aware spotlight plugin

    ChemSpotlight is a Spotlight metadata importer plugin for Mac OS X 10.4 Tiger written by Geoff Hutchison, which reads common chemical file formats (MDL .mol, .mdl, .sd, .sdf, Tripos .mol2, Protein Data Bank .pdb, Chemical Markup Language .cml, and XYZ) using the Open Babel chemistry library. It is provided as a Universal Binary for PowerPC and Intel, for optimized performance on both. ChemSpotlight indexes chemistry files, adds molecular formulas (complete with subscripts in the Finder), molecular weight, and a variety of other information for Spotlight searches and "Get Info" windows. iBabel can be used to search this information.
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    ChemTree :- Recursive partioning

    ChemTree is now available for MacOSX, it is a statistical analysis software based on recursive partitioning, that facilitates intelligent, target specific compound selection for High Throughput Screening (HTS). The software takes the compound structures and results from a screen, generates a model that predicts the results based on molecular features, and applies that model to untested compounds.
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    Chemical Thesaurus :- Chemical Information

    The Chemical Thesaurus from meta-synthesis is a great collection of free chemical information, slides and gadgets

    Chenomx NMR Suite :- Integrated suite of NMR tools

    Chenomx NMR suite is an integrated suite of tools that allow you to easily identify and quantify metabolites in NMR spectra.
    Chenomx Profiler offers you a broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum.
    Chenomx Signature Builder was developed to address a recurring customer request: the capability to add custom compounds to a Compound Library. Signature builder allows a user to create a signature that models the compound of interest.
    Chenomx Spin Simulator is a simple yet powerful tool for creating simulations of NMR spectra, based on user-defined spin systems, coupling relationships and reference spectra. You can use these simulations as starting points for creating your own compound signatures based on fundamentals of NMR theory.
    Chenomx Library Manager allows you to create and manage Compound Sets for use in Profiler. Compound Sets can contain any compound signatures in your library, including those from the Chenomx library as well as those that you create with Compound Builder.
    Chenomx Processor allows a variety of native spectrum formats to be converted into the Chenomx file format. These include:
    • Varian
    • Bruker
    • JCAMP (Version 5.0 and above)
    In addition, Processor allows users to identify or manually override the automatically determined parameters for the Chemical Shift Indicator. Processor can also be used to determine and set a variety of properties for the spectrum, such as pH.

    Chimera :- Molecular viewer

    UCSF Chimera is a highly extensible, interactive molecular graphics program is available for MacOSX, both X-windows and native versions are available.
    They also have a huge collection of images and movies     available
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    Citrin :- Interactive scientific graphing and curve fitting

    Citrin 1.0: A low-cost ($120), high-performance Mac OS X universal application for interactive scientific graphing and curve fitting, providing commonly-used charts, such as scatter and line series, bar, column, area, 3-D (column, pyramid, prism, area and band), ternary scatter, pie, polar, box and whisker, histograms, probability charts, etc.; curve fitting with built-in functions, as well as a module for user-defined, non-linear curve fitting with an interactive graphical interface; flexible capabilities for applying error bars; full Unicode support, diverse graphic export formats; support for drag-and-drop; native worksheets that can import and store large data sets from diverse data formats.

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    CN3D :- Molecule viewer

    Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures from NCBI's Entrez retrieval service together with sequence data.
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    COLUMBUS :- Ab Initio calculations

    COLUMBUS is a collection of programs for high-level ab initio molecular electronic structure calculations. The programs are designed primarily for extended multi-reference (MR) calculations on electronic ground and excited states of atoms and molecules. A variety of methods, including

    • MCSCF (multiconfiguration self-consistent field)

    • MR-CISD (multireference configuration interaction with all single and double excitations),

    • MR-ACPF (multireference averaged coupled-pair-functional) and

    • MR-AQCC (multi-reference average quadratic coupled-cluster)

    CONFLEX :- Conformation searching

    CONFLEX Corporation develops and licenses the CONFLEX5™ and PARALLEL CONFLEX software packages for fast, accurate molecular conformational analysis and searching

    Coot :- Crystallographic Object Oriented Toolkit

    Coot is for model building, model completion and validation.
    Coot displays maps and models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, Ramachandran plots etc.
    For more information visit the website here

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    Crystal Explorer :- Crystal structure analysis

    CrystalExplorer is a program designed principally to calculate, display and colour the Hirshfeld surface for a chosen molecule, or cluster or atoms, within a crystal.

    What can CrystalExplorer do for you?

    CrystalExplorer can display a two dimensional representation of the Hirshfeld surface, which is referred to as a "fingerprint" of the crystal. This can help uniquely classify a crystal, even polymorphic crystals.

    The Hirshfeld surfaces in CrystalExplorer give a novel alternative view of the crystal, which may enable you to see trends that are not apparent otherwise.

    CrystalExplorer enables you to view a CIF containing multiple crystal structures, and measure distances and angles within the crystal. All molecules and surfaces are displayed in three dimensions; with rotation, translation and zooming of the viewpoint.

    CrystalExplorer is interfaced to the free software     Tonto. As a result, it can calculate SCF energies of and obtain molecular orbitals for any fragments of the crystal. Once molecular orbitals are obtained, they can be used to generate quantum mechanical isosurfaces which are then displayed.

    Crystallographic and NMR System (CNS)

    CNS A crystallographic and NMR system. An excellent description of how to install is available here. Crystallography & NMR System (CNS) is the result of an international collaborative effort among several research groups. The program has been designed to provide a flexible multi-level hierachical approach for the most commonly used algorithms in macromolecular structure determination. Highlights include heavy atom searching, experimental phasing (including MAD and MIR), density modification, crystallographic refinement with maximum likelihood targets, and NMR structure calculation using NOEs, J-coupling, chemical shift, and dipolar coupling data.

    CrystalMaker :- Crystal structure analysis

    CrystalDiffract X and CrystalMaker and Single Crystal for fully-interactive visualization and analysis of crystal and molecular structures and simulation x-ray & neutron patterns from CrystalMaker files.

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