Mac OS X Applications T-Z

Tessellator :- Molecular volume visualisation

Tessellator is an application for the tessellation of 3D volume in and around biological molecules. It creates Tcl script files which are run within VMD to visualize volumes in context with their associated molecular structures

Theseus:- Superimpose macromolecules

Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. By downweighting variable regions of the superposition and by correcting for correlations among atoms, the ML superpositioning method produces much more accurate results.
When superpositioning macromolecules with different residue sequences, other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel maximum likelihood superposition algorithm that includes all of the data.

Empirical Bayes hierarchical models for regularizing maximum likelihood estimation in the matrix Gaussian Procrustes problem.
Theobald, Douglas L. & Wuttke, Deborah S. (2006a) PNAS 103(49):18521-18527

THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures.
Theobald, Douglas L. & Wuttke, Deborah S. (2006b) Bioinformatics 22(17):2171-2172
Supplementary Materials for Theobald and Wuttke 2006b.

Accurate structural correlations from maximum likelihood superpositions.
Theobald, Douglas L. & Wuttke, Deborah S. (2008) PLOS Computational Biology 4(2):e43

TINKER :-Molecular modelling

TINKER a molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for polypeptides. TINKER has the ability to use any of several common parameter sets, such as AMBER-95, CHARMM22, MM2(1991), MM3(2000), OPLS-AA and OPLS-UA.

Tonto :- Quantum Chemistry

Tonto is a free package for doing quantum chemistry simulations. The main objective of Tonto is to be simple--simple to understand, simple to use, and most importantly, simple to hack

TmoleX :- GUI for Turbomole

COSMOlogic provides a graphical user interface for Turbomole, TmoleX 2.1, as a cost-free add on for the Windows, Linux and MacOS X version of Turbomole 6.0.

Tox_Tree:-Toxic Hazard Estimation by decision tree approach

Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported - they could be entered by SMILES, or by using the built-in 2D structure diagram editor.

TRANSITION STATE TOOLS FOR VASP

The TRANSITION STATE TOOLS FOR VASP

Nudged Elastic Band: method for finding reaction pathways between two stable states.
Dimer: method for finding reaction pathways when only one state is known.
Lanczos: provides an alternative way to find the lowest mode and find saddle points.
Dynamical Matrix: uses finite difference to find normal modes and reaction prefactors.
Bader: analysis of charge density grids to find charges and dipole moments of atoms in molecules

TurboMole :- DFT & ab initio Quantum Chemistry

TURBOMOLE is one of the fastest and most stable quantum chemistry codes available. With over 20 years of development on HF, DFT and MP2, its RI-DFT method is up to 10 times faster than many comparable codes. TURBOMOLE was developed by Prof. Ahlrich's group at the University of Karlsruhe to deal with practical applications and large systems (> 100 atoms), and to create accurate COSMO (input) files for COSMOtherm.

For further details see:
*TURBOMOLE*: http://www.cosmologic.de/index.php?cosId=3050&crId=3

Unicon:- Cheminformatics toolkit

UNICON is a command-line tool to cope with common cheminformatics tasks. The functionality of UNICON ranges from file conversion between standard formats SDF, MOL2, SMILES, and PDB via the generation of 2D structure coordinates and 3D structures to the enumeration of tautomeric forms, protonation states and conformer ensembles.

UnityMol :- Molecular viewer/Editor

UnityMol is a molecular editor, viewer and prototyping platform, coded in C# with the Unity3D game engine. It was developed by Marc Baaden's team at the LBT laboratory at the IBPC institute of CNRS in Paris. UnityMol includes HyperBalls designed to visualize molecular structures using GPU graphics card capabilities based on shaders (GLSL or Cg). UnityMol can currently read Protein Data Bank (PDB) files, Cytoscape networks, OpenDX potential maps and Wavefront OBJ meshes. In its latest version, called SweetUnityMol, we added specific functionalities to visualize sugar molecules.

Updated 20 Jan 2017

USPEX :- Universal Structure Predictor: Evolutionary Xtallography

USPEX Universal Structure Predictor: Evolutionary Xtallography

VarSeq:- Analysis of gene sequences

VarSeq designed from the ground up for your computer. All types of next-generation sequencing data are supported. With VarSeq, whole exome and whole genome data are no longer solely in the domain of cloud compute clusters and bioinformatics core labs. It doesn't matter if you have 10 variants or 10 million, you can now make sense of this mountain of data on your desktop.

VASP :- Vienna Ab-Initio Simulation Package

VASP is a Fortran90 plane-wave DFT code which can be run as a single-cpu or MPI-parallel code. It runs on many platforms, too many in fact for the VASP group to test and support VASP on all of them. Peter Klaver ported VASP to MacOSX using LAM-MPI and the IBM XLF/XLC compilers for MacOSX (now using gcc instead of XLC for MacOSX 10.4 'Tiger'). Performance is excellent and he has written a 'How to install+run VASP for dummies' instruction

VaspView:-A visualization package for examining output files generated by VASP

VaspView is a scientific visualization package for examining output files generated by the Vienna Ab-initio Simulation Package (VASP), a package for performing ab-initio quantum-mechanical molecular dynamics using pseudopotentials and a plane wave basis set. The project was initiated when a chemical engineering professor requested assitance in visualizing output files produced by the above package. It displays iso-surfaces and slices of a three-dimensional data set, along with the atoms that make up the molecule the calculations were performed for, and allows symbolic bonds to be inserted between them.

VEGA:- QSAR modelling

Virtual models for property Evaluation of chemicals within a Global Architecture (VEGA), Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes. QSAR models can be used to predict the property of a chemical compound, using information obtained from its structure.

Vesta :- Molecular Visualisation

VESTA is a 3D visualization program for structural models and 3D grid data such as electron/nuclear densities. Some of the novel features of VESTA are listed below.

Deal with structural models and volumetric data at the same window.
Support multiple tabs corresponding to files.
Support multiple windows with more than two tabs in the same process.
Deal with virtually unlimited number of objects such as atoms, bonds polyhedra, and polygons on isosurfaces (theoretical limit on 32bit operating system is 1,073,741,823)
Support lattice transformation from conventional to non-conventional lattice by using matrix. The transformation matrix is also used to create superlattice and sublattice.
Visualize interatomic distances and bond angles that are restrained in Rietveld analysis with RIETAN-FP.
Transparent isosurfaces can be overlap with structural models.
Isosurface can be colored on the basis of another physical quantity.
Arithmetic operations among multiple volumetric data files.
High quality smooth rendering of isosurfaces and sections.
Export high-resolution graphic images exceeding Video card limitation.
Free for non-commercial use.

Vibrate:- visualizing the normal vibrational modes of a molecule.

Vibrate is a program for visualizing the normal vibrational modes of a molecule. Vibrate can read files generated by Gaussian (G03, G98, G94 and G92), Gamess, Jaguar, ADF, Turbomole, Hondo, Ampac, Mopac and Pcmodel and display the computed vibrational spectrum. The user can then select a vibration to display by pointing to one of the spectral lines and an animated display of the vibrating molecule will be displayed. Up to four vibrations can be displayed at one time and the structures can be rotated about any axis. The vibrational spectrum can be printed along with a vector display of the currently active vibrational modes, and image files can be output for PovRay.

Viewmol :-Molecule viewer

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results

VMD :-Molecule viewer

VMD 1.9 is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X,and now uses native windowing and hardware acceleration. The vmd-xplor package is a combination of VMD with the xplor structure determination package

You can also use VMD as the molecular visualiser for the molecular dynamics package NAMD

Vortex:- Cheminformatics Data Analysis

Vortex can import files in a variety of formats, it provides depiction and structure based searching, together with property calculations tightly integrated with excellent charting and analysis tools. There is a review of Vortex here.

V_Sim

V_Sim visualizes atomic structures such as crystals, grain boundaries and so on (from many file formats, binary or plain text). The rendering is done in 3D with coloured sphere to represent the atoms. The user can interact through many functions to choose the view, load densities, draw planes etc.

v_sim-paths

WebMo:- Front end to Computational Chem

WebMO is a free World Wide Web-based interface to computational chemistry packages.

Support for Gaussian09, MOPAC 2009, Gamess 2009, Molpro 2009, NW-Chem 5.1, PC-Gamess 7.1, PQS 3.3, Q-Chem 3.2, Tinker 5.0
Users draw structures in a 3D java editor, run calculations, and view results, all from their web browser
No software to install on the client. WebMO is installed only on the single web server that runs or accesses the computational chemistry programs
All administrative tasks (user accounts, program configuration, job time limits, etc) are performed through a web browser interface
Simple enough for undergraduate computational chemistry curriculum: reasonable default values and results are presented on web pages
Flexible enough for computational chemistry research: full access to input and output files
Works fully with Internet Explorer 4.0+ (Windows), Safari (Mac), Mozilla Firefox (Windows, Mac, Linux/unix), and other browsers

WebMol:- Structure Viewr

WebMol was designed to display and analyze structural information contained in the Brookhaven Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application.

Widgets :- A collection of widgets

A collection of widgets, if you see any I've missed please let me know

Wizard:- Click and explore data analysis.

Wizard is an intuitive data analysis program for the Mac. Unlike packages like R there is no need to be able to program. Pro version allows import from SAS, Stata and SPSS.

XCrySDen:-

XCrySDen is a crystalline and molecular structure visualisation program, which aims at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.

XDrawChem :-Structure drawing

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems. It is similar in functionality to other molecule drawing programs such as ChemDraw (TM, CambridgeSoft). It can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

X-score :-Calc binding affinity

X-score is a scoring function that computes the binding affinities of ligands to a target protein (Dr. Xueliang Fang and Dr. Renxiao Wang J. Med. Chem. 2003, 46 2287) whilst it was written for SGI it compiles fine with either Apples GCC or the IBM c++ compiler.

XQuartz

XQuartz
The XQuartz project is an open-source effort to develop a version of the X.org X Window System that runs on Mac OS X. Together with supporting libraries and applications, it forms the X11.app that Apple has shipped with OS X since version 10.5. OS-X Software Updates have included some of the work done by this project, but for various reasons, Apple cannot ship the latest and greatest version. Since XQuartz package clobbers Apple's X11.app, their SU will clobber ours. Because of this, you may experience conflicts after doing a Software Update from Apple. It is suggested that you install the latest XQuartz release after installing an update to OS-X.

XYZViewer:- A program for viewing/manipulating quantum-chemistry related files.

XYZViewer version 0.97 A program for viewing/manipulating quantum-chemistry related files.

To run, double click the jar file, or from the command line: >java -jar XYZViewer.jar

Yasara:- Structure visualisation

YASARA is a high performance structure visualisation, modelling and simulation program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software . PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs (see benchmarks). You can push and pull molecules around and work with dynamic models instead of static pictures.

You can read more about Yasara in these peer reviewed journals.

Zem:- Molecular Editor

The first beta release of Zem a molecular editor is now available.

Zephyr:- Molecular Mechanics

OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface. It is built on top of the visualization tool VMD and a special version of the molecular dynamics code GROMACS. This version of GROMACS uses the OpenMM API for GPU-accelerated molecular simulations. The new release is able to run on Mac OSX and further simplifies the installation process. See the Zephyr website at http://simtk.org/home/zephyr for a list of other features that were added and to download.

With version 0.9.2, OpenMM Zephyr makes it even easier to run molecular dynamics simulations. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities on both NVIDIA and ATI GPUs. This latest version of OpenMM Zephyr has automated many of the steps for converting PDB molecule files into the format required for the simulations.

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 (2009)

Zodiac :- Human steered molecular docking

Zodiac is the result of work by Nicola Zonta on developing an environment for human steered computation approaches to drug design. The application is built upon OpenBabel and the aim is to use simple input devices to allow the user to interact with a molecule and guide it into an active site. To date they have implemented haptic device support so you can feel when the molecule bumps into the receptor, and wiimote head tracking for 3D visulisation.

The application is still in early development but already has impressive graphics capabilities. In addition Zodiac now includes a front-end to the PLANTS docking engine.

Macs in Chemistry

Insanely great science