Mac OS X Applications

• 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's dynamic plots and tables show patterns and structure among several variables. Rotating plots and sliders use animation to reveal aspects of your data that static plots cannot show. Changing the color, symbol and selection state of datapoints instantly changes all plots to show patterns, clusters, and outliers. Hot Set selections restrict displays to subsets of your data with a single click.

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.

• Boiling Point Graph showing Vapour-Liquid Compositions.
• q-Line calculation from component thermodynamic properties.
• Manually defining the minimum reflux ratio.
• Loading of Data files.
• Plot of Reflux versus stages to help determine the optimal value.
• Drag and Drop graphs direct to desktop.
• Configurable printing of the 3 Graphs
• Much better checking of input data before the McCabe-Thiele graph can be plotted.

• If you need to build a custom database but don't want the overhead of learning SQL then you should seriously look at FileMaker. Many custom solutions are available and the built in scripting language allows you to build very sophisticated solutions easily.

FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds with the protein side-chains.

• FITTED is a suite of programs (FITTED, ProCESS and SMART)
• Fully automated and flexible docking program
• Uses an evolutionary algorithm
• Semi-flexible protein docking with flexible waters
• Has the ability to consider water molecules displaceable
• Different docking modes available: Dock, Filter, SAR, VS and Score
• Runs on Linux, Mac and Windows
• Accuracy and speed

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.

• Gabedit can Creates input file for GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, PCGamess and Q-Chem.
• Gabedit can graphically display a variety of Gamess-US, Gaussian, Molcas, Molpro, MPQC, OpenMopac, PCGamess, Q-Chem and (partially) ADF calculation results, including the following

• • Molecular orbitals.
• • Surfaces from the electron density, electrostatic potential, NMR shielding density, and other properties.
• • Surfaces may be displayed in solid, translucent and wire mesh modes. they are can be colorcoded by a separate property.
• • Contours (colorcoded), Planes colorcoded, Dipole. XYZ axes and the principal axes of the molecule.
• • Animation of the normal modes corresponding to vibrational frequencies.
• • Animation of the rotation of geometry, surfaces, contours, planes colorcoded, xyz and the principal axes of the molecule.
• • Animation of contours, Animation of planes colorcoded.

• Gabedit can display UV-Vis, IR and Raman computed spectra.
• Gabedit can generate a povray file for geometry (including hydrogen's bond),surfaces (including colorcoded surfaces), contours, planes colorcoded.
• Gabedit can save picture in BMP, JPEG, PNG, PPM and PS format.
• Gabedit can generate automatically a series of pictures for animation (vibration, geometry convergence, rotation, contours, planes colorcoded).
• Simulated Annealing with Molecular Dynamics is implemented in Gabedit (using Amber 99 molecular mechanics parameters).

• 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.

The concept of HADDOCK is described in the following paper:

• Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003).
  HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125, 1731-1737.

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.

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.