Dalton :- Molecular electronic structure

Dalton is a powerful molecular electronic structure program, with an extensive functional for the calculation of molecular properties at the HF, DFT, MCSCF, and CC levels of theory.
  • First- and second-order methods for geometry optimizations
  • Robust second-order methods for locating transition states
  • Constrained geometry optimizations; bonds, angles and dihedral angles can be fixed during optimizations
  • General numerical derivatives that automatically makes use of the highest order analytical derivative available
  • HF and DFT code direct and parallel using replication of Fock matrices using either MPI or PVM3 for message passing
  • Effective core-potentials (ECPs)

Data Desk :- Data analysis and visualisation

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    DataGraph:- 2D data analysis and plotting

    At the recent WWDC 2006 there was a discussion about the need for a simple 2D plotting tool, to meet this need David Adalsteinsson the author of the scientific visualisation tool DataTank has created DataGraph (formally known as DataPlot) a great new 2D plotting tool with the design philosophy "Simple and Powerful Plotting". I've written a review for MacResearch and you can read a copy here.

    A DataGraph.framework can be downloaded here. This allows you to use DataGraph as a graphing engine in your own program. This is works independent of DataGraph, but you need a license in order to make use of it.

    DataTank :- Data analysis and visualisation

    DataTank is designed for scientific visualization, data mining and algorithm development, but it is flexible enough to be used for a variety of other uses as well. DataTank enables interactive exploration of large data sets. Variables and relationships are defined graphically and built in modules can be combined with your own modules. DataTank will manage memory and perform incremental evaluation, treating data sets with millions of data points and hundreds of thousands of entries the same way as a simple data set that is typed in manually. To make this possible DataTank uses caching extensively, both in memory and on disk..

    Daylight :- High performance cheminformatics toolkit

    Daylight The Daylight toolkit and high performance cheminformatics database have been ported to MacOSX and is now available. The Daylight Toolkit is a programming library that provides all functions needed for chemical information processing and substructure pattern searching along with fingerprinting and similarity capabilities.

    DINO :- Molecular visualisation

    DINO is a realtime 3D visualization program for structural biology data. It runs under X-Windows and uses OpenGL. DINO aims to visualize all this structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines).

    DiscoveryGate :-Online searching

    Fully Tiger compatible, DiscoveryGate from MDL offers scientists broader access to a structure-searchable online platform for integrated researching of databases, journal articles, patent publications and reference works.

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    EasyChem :-Structure drawing

    The open source EasyChem is designed to draw chemical molecules in an intuitive way, with a very high quality (designed for book-publishing). Exporting is done to various formats (PostScript, Fig, LaTeX, etc.) to help you integrate your drawing in any software you use.
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    Eden :- Electron density

    Eden is an implementation of the holographic method to recover the electron density distribution of molecules within a crystal.

    EON :- Compare molecular electrostatics

    EON is an electrostatics comparison program - it compares electrostatic potential maps of aligned molecules and determines the Tanimoto measures for the comparison. Thus databases of molecules can be screened for electrostatic similarity to a lead compound. Since the input molecules must already be aligned, EON is suitable for analyzing the output structures from programs such as ROCS, thus yielding compounds with similar shape and electrostatics. EON should contribute significantly to lead generation and library desigm.
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    European Molecular Biology Open Software Suite (EMBOSS)

    EMBOSS the European Molecular Biology Open Software Suite is a package of over 100 high-quality FREE Open Source software for sequence analysis.

    EMAN :-Reconstruct 3D images from EM-pics

    EMAN is a software to reconstruct 3D images from EM-pics. There are also a number of other structural biology applications available here

    Evince :-Data analysis

    Evince newly developed java based platform for advanced data analysis. The software can be used for design of compound libraries and contains a combination of multivariate statistical algorithms such as PCA and PLS and interactive visualisations. For example can data be imported in .sdf format and molecule structures shown in 3D together with results from multivariate modelling.
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    FileMaker :- Powerful and easy to build Database

      Folding@Home :- Protein folding

      Folding@Home is a distributed computing project looking at protein folding -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world.
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      FRED :- Molecular docking

      Based on an original scientific perspective and efficient computational algorithms,FRED is an accurate and extremely fast docking program. With equivalent resolution settings, FRED will out-perform all known docking programs, typically examining about a dozen ligand conformers in a second. For each, FRED exhaustively examines all possible poses within the protein active site, filtering for shape complementarity and pharmacophoric features before scoring with more traditional functions.

      GAMESS :- Ab Initio

      The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. GAMESS is a program for ab initio molecular quantum chemistry. Briefly, GAMESS can compute SCF wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF. Correlation corrections to these SCF wavefunctions include Configuration Interaction, second order Perturbation Theory, and Coupled-Cluster approaches, as well as the Density Functional Theory approximation. Nuclear gradients are available, for automatic geometry optimization, transition state searches, or reaction path following. Computation of the energy hessian permits prediction of vibrational frequencies, with IR or Raman intensities. Solvent effects may be modeled by the discrete Effective Fragment Potentials, or continuum models such as the Polarizable Continuum Model. Numerous relativistic computations are available, including third order Douglas-Kroll scalar corrections, and various spin-orbit coupling options. The Fragment Molecular Orbital method permits use of many of these sophisticated treatments to be used on very large systems, by dividing the computation into small fragments.
      A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials, so all elements up to Radon may be included in molecules. Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolPlt program for the Macintosh, are available for viewing of the final results.

      Gaussian 03M :- Structural Modelling

      Gaussian 03M is a complete implementation of the popular Gaussian electronic structure modeling program for the Mac OS X environment. Also GaussView a full featured graphical user interface is now available for MacOSX.
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      GDIS :- Molecular Display

      GDIS is a GTK based program for the display and manipulation of isolated molecules and periodic systems. It is in development, but is nonetheless quite functional. It has the following features:
      • Support for many common file formats (eg CIF, PDB, XTL, XYZ).
      • OpenGL rendering.
      • Assorted tools for visualization (measurements, ribbons, polyhedral display).
      • Useful manipulation tools, including matrix transformations and supercell construction.
      • Powerful surface generation and crystal morphology tools.
      • Diffraction pattern generation and plotting.
      • Animation and movie generation for multi-frame files.
      • Analysis of Molecular Dynamics simulations.

      Ghemical :- Molecular modelling

      Ghemical is a computational chemistry software package released under GNU GPL. Requires X11.

      GROMACS :- Molecular dynamics

      GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. See also Tips to compile gromacs on MacOSX or download a binary here

      GSAS :- Solid and Powder diffraction analysis

      GSAS is a set of programs for the processing and analysis of both single crystal and powder diffraction data obtained with x-rays or neutrons. It is capable of handling all of these types of data simultaneously for a given structural problem. In addition, it can handle powder diffraction data from a mixture of phases refining structural parameters for each phase.

      GULP :- Solid and Polymer modelling

      GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids). The focus of the code is on analytical solutions, through the use of lattice dynamics, where possible, rather than on molecular dynamics. A variety of force fields can be used within GULP spanning the shell model for ionic materials, molecular mechanics for organic systems, the embedded atom model for metals and the reactive REBO potential for hydrocarbons. Analytic derivatives are included up to at least second order for most force fields, and to third order for many.
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      Scientific details about GULP can be found in the following papers:
      1. GULP - a computer program for the symmetry adapted simulation of solids, J.D. Gale, JCS Faraday Trans., 93, 629 (1997)
      2. Empirical potential derivation for ionic materials, J.D. Gale, Phil. Mag. B, 73, 3, (1996)
      3. The General Utility Lattice Program, J.D. Gale and A.L. Rohl, Mol. Simul., 29, 291 (2003)

      Hibridon:- Solve inelastic collisions.

      Hibridon, a program package to solve the close-coupled equations which occur in the quantum treatment of inelastic atomic and molecular collisions. Gas-phase scattering, photodissociation, collisions of atoms and/or molecules with flat surfaces, and bound states of weakly-bound complexes can be treated.

      HKL-2000 :- Structural Biology

      HKL-2000, a new program package based on the original HKL Suite, is the premier software of choice for structural biology. Analysis of the Protein Data Bank (PDB) shows that nearly 80% of all entries were processed with the HKL/HKL-2000 package and it is now available for MacOSX.

      HyperChem :- Molecular modelling

      HyperChem is now available for MacOSX, OpenGL graphics for sophisticated rendering of molecules and properties, Full range of molecular mechanics and quantum mechanics methods., Protein and DNA capabilities for modeling and manipulation with PDB files. Scripting capabilities to automate and your molecular modeling workflow.Molecular dynamics, Langevin dynamics and Monte Carlo statistical mechanics. Spectral computations including vibrational analysis and excited electronic states.
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      iBabel :- Molecular file conversion and viewer

      iBabel 2.1.1 is an AppleScript Studio application that provides a graphical interface for the command line-driven file conversion application OpenBabel. The update requires the installation of OpenBabel 2.0, and includes additional file conversions as well as very fast similarity and sub-structure based searching. Structures can be viewed in 2D or 3D as appropriate using the embedded Jmol or JChempaint applets. Now uses ChemSpotlight to search chemical content on your hard drive.

      iChem :- Periodic table

      iChem written in Cocoa for Mac OS X exclusively, iChem is a full-featured periodic table and molecular weight calculator.
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      ICM-Browser :- Structural Biology

      ICM-Browser, a new product in the ICM family from Molsoft, provides a biologist or a chemist with direct access to the treasures of structural biology and protein families. It reads PDB files or alignment files directly from the database web-sites and provides rich professional molecular graphics environment with powerful representations of proteins, DNA and RNA, and multiple sequence alignment.
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      IGOR Pro :- Data analysis

      IGOR Pro is an interactive environment for experimentation with scientific and engineering data and for the production of publication-quality graphs and page layouts.
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      iMass :- Molecular mass calculator

      iMass a molecular mass calculator, a periodic table of the elements, an isotope distribution graph and a calculator that computes elemental compositions matching a given mass. iMass understands complex chemical formulas as well as user defined abbreviations for commonly used formulas.
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      iMol :-Molecular viewer

      iMol is a free molecular visualisation program written in Object C and using OpenGL for the graphics so no need for X-windows, the author Piotr Rotkiewicz is looking for feedback. Updated May 24 2007.
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      InDigestion :- Proteomic tool

      InDigestion is a handy Mac OS X application for calculating protein properties used in proteomics. Currently it calculates molecular weights of intact proteins, performs enzymatic digests, and creates hydrophobicity plots. InDigestion is created using the BioCocoa framework.

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      InforSense KDE :- Data analysis

      InforSense KDE is an Integrative Analytics platform used for seamless integration of all data types, for improved decision-making across life sciences research. BioSense Grid adds a service-based high-performance environment for creating bioinformatics applications

      iNMR :-NMR analysis

      iNMR is now a universal binary, the only NMR tool designed specifically for the Mac. This fantastic tool for the processing and analysis of NMR data in a Mac environment has beeen updated to version 2.2.22. It can import SwaN-MR, JCAMP-DX, Bruker (Aspect, Win-NMR, XWin-NMR, TopSpin), Varian, SpinSight, Tecmag, Jeol Delta, GE Medical, Siemens. Other formats can be converted indirectly, via SwaN-MR or Jeol Delta. Other importing filters can be added at no additional cost. iNMR is a product by nucleomatica.
      The website also includes a wealth of information including       tutorials and visual guides

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