Mac OS X Applications T-Z
Tessellator :- Molecular volume visualisation
Theseus:- Superimpose macromolecules
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
Tonto :- Quantum Chemistry
TmoleX :- GUI for Turbomole
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
For further details see:
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
VaspView:-A visualization package for examining output files generated by VASP
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
- 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.
Viewmol :-Molecule viewer
VMD :-Molecule viewer
You can also use VMD as the molecular visualiser for the molecular dynamics package NAMD
Vortex:- Cheminformatics Data Analysis
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.
WebMo:- Front end to Computational Chem
- 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
Widgets :- A collection of widgets
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 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
X-score :-Calc binding affinity
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
You can read more about Yasara in these peer reviewed journals.
Zem:- Molecular Editor
Zephyr:- Molecular Mechanics
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
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.