NAND :- Molecular simulation

NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular system

NMRNotebook :- NMR analysis

NMRtec have an NMRnotebook, is a new NMR software package for processing, analysing and managing NMR data. It is especially designed for chemists, biochemists and spectroscopists dealing with NMR. It allows you to perform state of the art 1D and 2D NMR data processing by just a few mouse clicks.
interfaceNnb

NWChem :- High performance comp chem

NWChem is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters. It aims to be scalable both in its ability to treat large problems efficiently, and in its usage of available parallel computing resources. NWChem has been developed by the Molecular Sciences Software group of the Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL).

NMRPipe :-NMR analysis

NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. It is currently used in over 300 academic and commercial laboratories.

NMRViewJ :-NMR analysis

NMRViewJ software for the visualisation and analysis of NMR data.

nuccyl :-PyMOL helper

nuccyl is a Perl program that allows PyMOL, a powerful open-source molecular modeling system, to display atomic models of nucleic acids in a highly simplified representation

Numerical Tools :-Binaries for a range of packages

Numerical tools binaries, source and installation instructions for Fortran, MPL, Octave, Cactus, Globus, TINKER and more

O :- crystallographic modeling tool

O is a macromolecular crystallographic modeling tool. It can be used to build, modify and analyze macromolecular structures, there is also a unix beginners installation guide here

OpenBabel :- Chemoinformatics

OpenBabel is a community-driven scientific project including both cross-platform programs and a developer library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file formats and data, Open Babel includes two components, a command-line utility and a C++ library. iBabel is a Mac OS X graphical user interface for OpenBabel

OMEGA :- Conformational analysis

Designed for use with the large libraries required for computer-aided drug design, OMEGA generates multi-conformer structure databases with unprecedented speed and reliability. Conformational expansion of drug-like molecules can be performed in fractions of a second, yielding a throughput of hundreds of thousands of compounds per processor per day. Scientists at AstraZeneca found OMEGA to be more reliable in reproducing crystal structures than programs taking orders of magnitude more time [1]. Researchers at Vertex concluded, "Omega achieves the best balance between speed and performance among the programs examined, and it appears to be the most suitable tool for conformational analysis on large chemical databases."

OnScreen DNA :- DNA visulisation

OnScreen DNA™ is geared towards, but not restricted to, high school and college students and teachers. The program has been designed, first of all, to allow students to become completely at home with the essential details of DNA's three-dimensional double helix structure.

OpenDX :-Data analysis

OpenDX is a uniquely powerful, full-featured open source software package for the visualization of scientific, engineering and analytical data. Downloadable binaries are available from VIS Inc.

Partek :- Data analysis

Partek A leading provider of pattern recognition software, data mining and interactive visualisation tools plan to support Mac OSX.

PCModel :-Molecular modelling

PCModel 9 is available for MacOSX, it is designed for research chemists build, minimise and manipulate multiple structures. A variety of forcefields are supported, conformational searching is biult in and there is an interface to Gaussian and Games. They also supply Orbdraw for displaying molecular orbitals and Vibrate for visualise normal vibrational modes.

Peacock :- Mass spec tool

Peacock is an application that can be used to interpret gas-chromatography/mass-spectrometry (GC/MS) data files.

Here is a quick overview of what you can do with Peacock.
  • Read NetCDF GC/MS files
  • Identify peaks in chromatograms
  • Identify compounds associated with peaks
  • Make a summary of all your analyses

Periodic Table

Periodic Table A user configurable Periodic Table.
basictable-eu

PerlMol :- Chemoinformatics

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging". The PerlMol toolkit provides objects and methods for representing molecules, atoms, and bonds in Perl; doing substructure matching; and reading and writing files in various formats.

Polyxmass :- Mass Spec analysis

Polyxmass is a collection of programs that integrate into a mass spectrometry data simulation/analysis framework. The molecular objects that are dealt with are polymers. Because the user can define brand new polymers, the program is not targetted at any specific polymer in particular. Indeed, after having defined the basic protein or saccharide chemistry, the user can start using the polyxmass programs on proteinaceous or saccharidic polymer sequences

PMV :-Molecule viewer

PMV A Python based Molecular Viewer

proFit :-Data analysis

pro Fit An excellent data analysis and graphing package has been update to version 6.0.6

Protein Dynamics :- Molecular simulations

Protein Dynamics The program simulates the dynamic behavior of proteins, DNA, and RNA, using the AMBER force field. It allows the user to view molecules, create and modify molecules, and run energy minimization and dynamics simulations

PFAAT :-Sequence alignment

Protein Family Alignment Annotation Tool (PFAAT) Pfaat is a Java-based protein sequence alignment application designed to facilitate the analysis, curation, and annotation of large protein sequence families has recently been updated

PyMOL :-Molecule viewer

PyMOL A 3D molecule viewer, PyMOL is a powerful molecular graphics package for structural biology and other sciences. This interactive system is fully scriptable using the Python computing language, sponsored and supported by users.
If you would like to enable the use of plugins in PyMol read this tutorial here