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.
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
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
OpenMM:- MM Library
OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding. Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available.
M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande. “Accelerating Molecular Dynamic Simulation on Graphics Processing Units.” J. Comp. Chem., (2009), 30(6):864-872, available at: http://www3.interscience.wiley.com/journal/121677402/abstract
ORCA:- General purpose tool for quantum chemistry
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.
OSRA:- Optical Structure Recognition
OSRA is a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES (Simplified Molecular Input Line Entry Specification - see http://en.wikipedia.org/wiki/SMILES) or SD file - a computer recognizable molecular structure format. OSRA can read a document in any of the over 90 graphical formats parseable by ImageMagick.
Partek :- Data analysis
Partek A leading provider
of pattern recognition software, data mining and
interactive visualisation tools plan to support Mac
OSX.
PC GAMESS/Firefly :- Computational Chemistry package
As of
February 23, 2009, the PC GAMESSFirefly team is proud
to announce the availability of the first official
release of the PC GAMESS/Firefly
package for Mac
OS X/Intel platform.
List of some key features:
Free and fast! Proven reliability and performance of Windows/Linux PC GAMESS/Firefly.
Feature rich - supports all the functionality of Windows/Linux-based PC GAMESS/Firefly.
Runs on Mac OS X 10.4.x (Tiger) and 10.5.x (Leopard).
Parallel jobs run on SMP/multi-core hardware without additional software.
Installation is straightforward with a native DMG installer. New drag and drop job submission applications make running jobs significantly easier and more intuitive than most other ab-initio computational chemistry programs on the Mac platform. Just drag and drop your input file on to the appropriate run application for the number of CPU cores desired (or double-click and select) and your job will simply launch and open the output in a suitable text editor. All the necessary output files that may be needed for future follow-up jobs are automatically delivered to the input file directory. Everything is intended to be Mac friendly including a set of Mac-specific step by step Quick Start and Complete install and usage guides that should cover 90%+ of all potential questions for new users.
A batch job submission application and a STOP-FIREFLY-JOBS application which allows multiple job management.
A good set of third-party Mac native graphical applications is available to prepare input jobs as well as to visualize the output of those runs (e.g., WebMO). Most visualization tools that are not available natively for Mac work fine through Darwine or Crossover Wine.
There is an active community of Mac beta testers and Firefly community users to answer questions for new users.
List of some key features:
Free and fast! Proven reliability and performance of Windows/Linux PC GAMESS/Firefly.
Feature rich - supports all the functionality of Windows/Linux-based PC GAMESS/Firefly.
Runs on Mac OS X 10.4.x (Tiger) and 10.5.x (Leopard).
Parallel jobs run on SMP/multi-core hardware without additional software.
Installation is straightforward with a native DMG installer. New drag and drop job submission applications make running jobs significantly easier and more intuitive than most other ab-initio computational chemistry programs on the Mac platform. Just drag and drop your input file on to the appropriate run application for the number of CPU cores desired (or double-click and select) and your job will simply launch and open the output in a suitable text editor. All the necessary output files that may be needed for future follow-up jobs are automatically delivered to the input file directory. Everything is intended to be Mac friendly including a set of Mac-specific step by step Quick Start and Complete install and usage guides that should cover 90%+ of all potential questions for new users.
A batch job submission application and a STOP-FIREFLY-JOBS application which allows multiple job management.
A good set of third-party Mac native graphical applications is available to prepare input jobs as well as to visualize the output of those runs (e.g., WebMO). Most visualization tools that are not available natively for Mac work fine through Darwine or Crossover Wine.
There is an active community of Mac beta testers and Firefly community users to answer questions for new users.
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.
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
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.
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
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
Pooch :- Cluster computing on Mac
It is of
course worth bearing in mind how easy it is to set up
small Mac clusters, Dauger Research
provides a 3
step recipe for setting up a cluster using
Pooch.
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
PSI3:- Quantum Chemistry
The
PSI3 suite of quantum chemical programs
is designed for efficient, high-accuracy
calculations of properties of small to
medium-sized molecules. The package's current
capabilities include a variety of Hartree-Fock,
coupled cluster, complete-active-space
self-consistent-field, and multi-reference
configuration interaction models. Molecular
point-group symmetry is utilized throughout to
maximize efficiency. The latest version of the
code, PSI 3.4, rests upon a completely rewritten
infrastructure relative to previous versions of
the package. Non-standard computations are
possible using a customizable input format.
Package highlights include:
- Arbitrarily high angular momentum levels in integrals and derivative integrals. (Up to m-type functions have been tested.)
- Coupled cluster methods including CC2, CCSD, CCSD(T), and CC3 with RHF, ROHF, UHF, and Brueckner orbitals.
- Determinant-based CI including CASSCF, RAS-CI, and Full CI.
- Multithreaded integral-direct SCF, MP2, and MP2-R12.
- Excited state methods: CIS, CIS(D), RPA, EOM-CCSD, and CC3.
- Analytic energy gradients for CCSD with RHF, ROHF, and UHF orbitals.
- Coupled cluster linear response methods for static and dynamic polarizabilities and optical rotation.
- Diagonal Born-Oppenheimer correction (DBOC) for RHF, ROHF, UHF, and CI wave functions.
PSILO :- Macomolecular Database
PSILO is
a database system that provides an easily accessible,
consolidated repository for proprietary and
non-proprietary macromolecular and protein-ligand
structural information. It offers research
organizations a means to systematically register,
annotate, track and disseminate both experimental and
computational macromolecular structural data. PSILO
provides powerful bioinformatics and cheminformatics
search, analysis and visualization capabilities
through a web browser interface. For more information
on PSILO please visit the web site at:
http://www.chemcomp.com/psilo-info.htm
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
If you would like to enable the use of plugins in PyMol read this tutorial here