QuantumBio :- QuantumMechanics

QuantumBio provides Pharmaceutical and Biotech companies with fast Quantum Mechanical (QM) solutions for Lead Optimization

Q-Chem :- Ab Initio

Q-Chem the latest version of a modern ab initio electronic structure program, is capable of performing first principles calculations on both the ground and excited states of molecules

Rasmol :-Molecule viewer

Rasmol A 3D molecule viewer ported to Mac OS X

Raster 3D :- Molecule images

Raster3D - is a set of tools for generating high quality raster images of proteins or other molecules. The core program renders spheres, triangles, cylinders, and quadric surfaces with specular highlighting, Phong shading, and shadowing. It uses an efficient software Z-buffer algorithm which is independent of any graphics hardware. Ancillary programs process atomic coordinates from PDB files into rendering descriptions for pictures composed of ribbons, space-filling atoms, bonds, ball+stick, etc. Raster3D can also be used to render pictures composed in other programs such as Molscript in glorious 3D with highlights, shadowing, etc. Output is to pixel image files with 24 bits of color information per pixel.

Ribbons :- Molecule viewer

Ribbons A popular molecular graphics program.

From Clipboard

ROCS :- Molecular shape comparison

ROCS is a shape comparison program, based on the idea that molecules have similar shape if their volumes overlay well and any volume mismatch is a measure of dissimilarity. ROCS uses a smooth Gaussian function to represent the molecular volume, so it is possible to routinely minimize to the best global match. ROCS is capable of processing 600-800 comparisons each second, making it is possible to search multi-conformer representations of corporate collections in a day on a single processor to find compounds with similar shape to a lead compound.

SciFinder :- Scientific literature search

SciFinder is now MacOSX native!! it is an easy to use desktop research tool that allows you to explore research topics, browse scientific journals, and stay up to date on today's most recent scientific developments. With SciFinder, no special training is needed. You simply point and click to access more than 19 million abstracts and 35 million substances.

Scilab :- Numerical analysis

Scilab Scilab is a scientific software package for numerical computations in a user-friendly environment

SciPy :- Numerical analysis

ScilPy (pronounced "Sigh Pie") is open-source software for mathematics, science, and engineering. It is also the name of a very popular conference on scientific programming with Python. The core library is NumPy which provides convenient and fast N-dimensional array manipulation. The SciPy library is built to work with NumPy arrays, and provides many user-friendly and efficient numerical routines such as routines for numerical integration and optimization. Together, they run on all popular operating systems, are quick to install, and are free of charge. NumPy and SciPy are easy to use, but powerful enough to be depended upon by some of the world's leading scientists and engineers. If you need to manipulate numbers on a computer and display or publish the results, give SciPy a try!

SemiChem :-QSAR

SemiChem report that the semiempirical quantum mechanical program Ampac and advanced, fully featured quantitative structure/activity relationship (QSAR) program Codessa are available for MacOSX

Siesta :-ab initio simulation of solids

Siesta (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

Smell-o-mints :- Periodic table

Smell-o-mints is a Periodic table of the elements for the Macintosh. It's not as full-featured as a lot of other Periodic tables out there, but it's free and looks very nice.

smi23D:- Convert SMILES to 3D structures

smi23d consists of two programs that can be used to convert one or more SMILES strings to 3D. The first step uses a program called smisdf which generates a set of rough 3D coordinates using an iterative refinement procedure. These coordinates are then optimized with a MMFF94 force field by mengine to generate a reasonable 3D structure. In addition to generating an optimized structure, the code can optinally calculate some molecular properties such as XlogP, dipole moment and vibrational properties. By default these are not calculated. The resultant coordinates are written in SD format.

The source code for the programs can be obtained from the CICC-Grid Sourceforge SVN repository and binary builds are available for Intel Mac OS X.

Sparky :-NMR analysis

Sparky is a graphical NMR assignment and integration program for proteins, nucleic acids, and other polymers. For more information about what Sparky does look at the introduction in the manual.
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Spartan :- Molecular modelling

Spartan 04 is the most sophisticated version offered. The latest Spartan release offers all features and methods included in the Spartan Essential Edition, and in collaboration with Q-Chem, provides a full range of post-Hartree-Fock methods including Density Functional, Moller Plesset (new RI-MP2), Thermochemistry recipes (including the new T1 procedure), and an assortment of Advanced Correlated approaches.

SQLGrinder :- SQL tool

SQLGrinder If you need a tool to access any database that has a JDBC driver (Oracle, Sybase, mySQL, postgresql etc) I highly reccomend this tool, it is a native Cocoa application that has applescript support.

Sugarmagnolia :- Carbohydrate Mass Spec

SugarMagnolia, a freeware program to use as an aid when interpreting mass spectrometric data from carbohydrates. It can calulate the molecular weight of carbohydrates, calculate fragment ions (B-, C-, Y-, and Z-type ions), modify the complete molecule or, modify individual residues, save and print sequences.

Swiss-Pdb Viewer :-Molecule viewer

Swiss-PdbViewer a carbonised version is available in alpha form