Mac OS X Applications D-I
Dalton :- Molecular electronic structure
- 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 :- Data analysis and visualisation
- 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.
DataGraph:- 2D data analysis and plotting
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.
DataTank :- Data analysis and visualisation
Daylight :- High performance cheminformatics toolkit
DelPhi:- Solves Poisson_Boltzmann equation
Runs on Macintosh. Executable is also provided.The PowerPC Mac executable version of delphi is dynamically linked to IBM XL compiler libraries. It will not run unless you have these libraries on your local system. Intel Mac version - runs on Macintosh with Intel processor. Executable is also provided.
Dilutions:- iPhone app that helps perform Serial Dilutions and make SDS-PAGE gel
DINO :- Molecular visualisation
Dirac:- Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations
The DIRAC program computes molecular properties using relativistic quantum chemical methods.
New features in [DIRAC12](http://diracprogram.org/features/) (released 12/12/12)
* 2-component relativistic Effective Core Potentials (ECPs)
* London Atomic Orbitals (LAOs) at the DFT level
* Simple magnetic balance for NMR shieldings
* LAO current densities
* Overlap diagnostic for TD-DFT calculations of excitation energies
* Pipek-Mezey localization by trust-region optimization
* Long-range MP2/short-range DFT
* Atomic start guess for SCF calculations
* MP2 natural orbitals
* Complex/Damped DFT response module
* New Lanczos algorithm for relativistic Algebraic Diagrammatic Construction (ADC)
New features in DIRAC10 (released 10/10/10)
* Kramers-restricted MCSCF
* RELADC for correlated calculations of single/double ionization spectra
* large-scale parallel CI (LUCITA/KRCI)
* intermediate Hamiltonian formalism for Fock-space CCSD
* interface to MRCC (see http://tc03.fkt.bme.hu/)
* frozen density embedding
* 2c X2C+AMFI for 2-electron spin-orbit corrections (spin-same orbit[SSO]/spin other-orbit[SOO])
* Molecular properties:
* HF/KS excitation energies
* KS response with noncollinear spin polarization and full derivative of functionals
* linear response functions at imaginary frequencies
* more efficient KS DFT code
* London orbitals for HF NMR shieldings
* visualization of unperturbed and perturbed densities
* projection analysis of expectation values
* expectation values/transition moments KRCI/GOSCI
Features in DIRAC08
* Methods available:
* Density Functional Theory
* Coupled Cluster
* Configuration Interaction
* Møller-Plesset Perturbation Theory
* Hamiltonians available:
* 4c Dirac-Coulomb (includes scalar relativistic effects and spin-own-orbit coupling)
* 4c Dirac-Coulomb-Gaunt (includes also spin-other-orbit coupling) (only HF)
* 4c spin-free Dirac-Coulomb (scalar relativistic effects only)
* 4c Levy-Leblond (nonrelativistic)
* 2c X2C, the one-step exact two-component Hamiltonian
* 2c BSS, the two-step exact two-component Hamiltonian (= DKH(infinity,0))
* Molecular properties:
* Up to quadratic response properties at the Hartree-Fock and DFT level
* First order properties with MP2
* Core excitation energies in the static exchange (STEX) approximation.
* Single/Double Ionization energies and spectra at the ADC(3)/ADC(2x) level of theory.
* Full symmetry handling for linear molecules (otherwise up to D2h)
* Parallelization using MPI library calls (MPI should be preinstalled)
* Some of the new features of DIRAC08:
* A one-step exact two-component Hamiltonian (X2C)
* Relativistic Green's function (propagator) module RELADC for the calculation of ionization energies
* Possibility to include the Gaunt interaction in HF calculations
* Implementation of several new density functionals
* Linear and quadratic response DFT
* Addition of the latest Dyall basis sets and more non-relativistic basis sets to the basis library
* Analysis by means of fragment orbitals
* New parallelization of the MOLTRA module with reduced I/O
* Parallelization of the LUCITA CI module
DiscoveryGate :-Online searching
Distillation Designer:- McCabe-Thiele method for designing binary distillation systems.
- 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.
DivCon MOE GUI
The integration provides a unique tool for accuarate quantum mechanical data to be calculated using QuantumBio's proprietary toolkit and visually displayed through the MOE database. Obtained data from the MOE/DivCon GUI is comparative to other techniques users accomplish in MOE. QuantumBio's interface makes setting up calculations easy and straightforward.
DL Visualize:- visualisation of materials structures and properties
beta port to Mac OS X (uses Darwin Unix OS core).
DOCK:- Docking tool
DRAWxtl:- Crystal structure display
EasyChem :-Structure drawing
eBioTools:- a compilation of bioinformatics software
The included programs can be run from the command line in the Terminal program. If you are interested in something that is more easy to use, please take a look at our program eBioX, which works as a graphical interface for eBioTools.
eBioX:- GUI for EBioTools
Eden :- Electron density
Eden is crystallographic real-space electron-density refinement and optimization program that produces electron density maps with minimal model bias in a robust manner. This program improves macromolecular crystallographic electron density maps in a maximally unbiased manner. There are now two versions of eden, "seden" and "deden." seden is compiled with single-precision fftw libs, and is faster and less memory-intensive. deden is double- precision and is possibly more accurate (but in practice the differences appear insignificant). ieden is a new python Tkinter-based GUI. Type "eden" or "seden" to invoke single-precision eden, "ieden" for the GUI, and "deden" for double-precision eden. GUI users need to define the environment variable EDITOR, eg: export EDITOR='see' or setenv EDITOR vim.
Elemental:- Chemical Drawing
Use templates of common substructures to build complex compounds more quickly
Add user defined substructures to the list of templates to create compounds of similar structure
Export created molecules as mol files to other applications
Violations of allowed valence are automatically flagged up
Flexibility to select any element from the periodic table
Build reactions using the drawing tool.
There is a brief review of Elemental here.
EleMints:- iPhone periodic table
Calculator, and more.
EON :- Compare molecular electrostatics
European Molecular Biology Open Software Suite (EMBOSS)
EMAN :-Reconstruct 3D images from EM-pics
Evince :-Data analysis
FAF-Drugs2:- This is a package for in silico ADMET filtering
Fconv:- Molecular file manipulations
- Fconv is a command-line tool for several tasks concerning manipulating, converting, and analyzing data from different file formats.
- - Convert pdb to mol2 files
- Extract ligands from pdb files as mol2 files
- Correct errors in pdb files
- Reset atom types to many different atom type definitions (e.g. TRIPOS / SYBYL)
- Add missing hydrogens
- Merge or split multimol2 files
- Build the unit cell for a crystal structure
- Calculate the number of freely rotatable bonds, molecular weights, exact RMSD values, and other properties
- Convert Autodock dlg files to mol2 files (with or without reference)
- Convert sdf files to mol2 files
- Convert cif files to mol2 files
- Substructure searches
FieldAlign :- Align electrostatic fields
- Increase their understanding of where and how their lead molecules bind to their protein targets
- Perfect the design of new lead compounds, exploring a range of lead optimization ideas
- Prioritize syntheses and reduce time by avoiding making dead-end or uninformative compounds
- Optimize the design of a focused library for synthesis or initial screening
- Screen small libraries of compounds looking for a backup series with more structural diversity
There is a review of FieldAlign here
FieldTemplater :- Pharmacophore generator
FieldView:- View molecular electrostatics
Using FieldView you will be able to:
- Create and modify structures using the in-built molecular editor
- Automatically convert structures from 2D to a minimized 3D conformation
- Clone and compare molecules side by side or overlaid using Cresset’s unique Field technology
- Understand how a compound’s activity, ADME and toxicity properties vary with their molecular Fields
- View virtual screening results, such as those from FieldScreen, comparing 2D structures with a 3D overlay showing all the Fields of every ligand
- Filter molecules based on the exact mix of properties you need
There is a review of FieldView here
FileMaker :- Powerful and easy to build Database
- 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.
Filter:- Rapid filtering of structures
FILTER is a very fast molecular filtering and selection application. It uses a combination of physical property calculations and functional group knowledge to remove undesirable compounds before they enter experimental or virtual screening. Undesirable properties may include: toxic functionalities, a high likelihood of binding covalently with the target protein, interfering with the experimental assay, and/or a low probability of oral bioavailability.
Fitted:- Flexible molecular docking
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
Filter-it:- molecule filter
Filter-it™ is a command-line program for filtering molecules with unwanted properties out of a set of molecules. The program comes with a number of pre-programmed molecular properties that can be used for filtering.
- by scientists who analyse data from powder diffraction, chromatography, photoluminescence and photoelectron spectroscopy, infrared and Raman spectroscopy, and other experimental techniques,
- to fit peaks – bell-shaped functions (Gaussian, Lorentzian, Voigt, Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic, etc.),
Folding@Home :- Protein folding
Force Field Explorer:- Graphical user interface to TINKER
FORECASTER :- Includes programs for drug discovery and process chemistry
1. FITTED, a docking program
2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically
3. CONVERT, a program that converts 2D molecules to energy-minimized 3D molecules (adds hydrogens, generates tautomers and protomers)
4. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues
5. REDUCE, a program that filters using descriptors and functionnal groups
6. REACT, a program that performs combinatorial chemistry in silico from user-defined chemical schemes
7. IMPACTS, a sites of metabolism prediction program (CYP 450)
8. ACE, a program that predicts the stereochemical outcome of reactions
All the programs are integrated into a new web-based graphical interface that allows complete automation of the different workflows.
You can read more details here, Integrating Medicinal Chemistry, Organic/Combinatorial Chemistry, and Computational Chemistry for the Discovery of Selective Estrogen Receptor Modulators with Forecaster, a Novel Platform for Drug Discovery
ForgeV10:- SAR analysis and ligand design
forgeV10 takes advantage of Cresset’s patented ligand comparison method to align, score and compare molecules from a biological viewpoint
It is designed to
- Decipher complex SAR and communicate the results
- Design better molecules based on predictions you can trust
- Prepare detailed pharmacophores
- Virtually screen 10 000 compounds on your desktop
- Generate ADME and off target activity profiles.
FOX:- ab initio structure determination from powder diffraction
- a versatile description of the crystal contents: either isolated atoms , molecules described using a bond length, bond angles and dihedral angles, and polyhedra for inorganic compounds. You can describe your structure by using any combination of groups of atoms, using a chemist's or crystallographer knowledge about the connectivity in your sample to constrain possible solutions..
- an automatic correction for special positions and shared atoms between polyhedra, suitable for global optimization algorithms.
- the ability to use simultaneously multiple powder patterns (X-rays, neutrons), as well as single crystal data (e.g. extracted from a powder pattern)
- smart global optimization algorithms which can get out of false minima.
FRED :- Molecular docking
Gabedit:-Graphical user interface to computational chemistry package
It can display a variety of calculation results including support for most major molecular file formats. The advanced "Molecule Builder" allows to rapidly sketch in molecules and examine them in 3D. Graphics can be exported to various formats, including animations.
- 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).
- It works under Windows, Linux, Mac OSX11 and other UNIX OS.
GAMESS :- Ab Initio
A variety of molecular properties, ranging from simple dipole moments to frequency dependent hyperpolarizabilities may be computed. Many basis sets are stored internally, together with effective core potentials, so all elements up to Radon may be included in molecules. Most computations can be performed using direct techniques, or in parallel on appropriate hardware. Graphics programs, particularly the MacMolPlt program for the Macintosh, are available for viewing of the final results.
GamessQ:- A companion to GAMESS and MacMolPlt
GAMGI:- Molecule Viewer
GAMGI aims to be useful for: 1) the scientific community working in atomistic modelling, who needs a graphic interface to build and analyse atomic structures; 2) the scientific community at large, who needs a graphic interface to study atomic structures and to prepare images for presentation
GAMMA:- NMR C++ library
GAMMA is a C++ library expressly for simulation of Magnetic Resonance experiments. It was written by Scott A. Smith and Tilo Levante under the guideance of B.H. Meier and R.R. Ernst at the ETH in Zürich, as described in the article
"Computer Simulations in Magnetic Resonance.
An Object Oriented Programming Approach",
S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst,
J. Magn. Reson., 106a,
Gaussian 09M :- Ab initio Structural Modelling
GaussView:- Gaussian viewer
GDIS :- Molecular Display
- 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.
Ghemical :- Molecular modelling
Graphite - LifeExplorer: Protein/DNA modeling
Graphite - LifeExplorer is a tool for modelling DNA, the tool generates DNA along a Bézier curve, open or closed, allows fine-tuning of atoms' position and, most importantly, exports to PDB. This software allows to model in 3D assemblies of proteins and DNA. Its main feature is the capability to create 3D models of DNA in a highly intuitive manner. To date, the modeling and visualization tool allows to: - import PDB files - create isosurface of molecular object - highlight residues of interest - calculate distance between residues pairs - import and export in 3D formats - model DNA and export the result in PDB - visualize a 3D scene with Level of Detail - explore a scene with real-time ambient occlusion - import a file with x,y,z coordinates and convert it into a DNA representation.
You can see a it in action here
GridChem client:- Desktop client for Computational Chemistry Grid
The "Computational Chemistry Grid" (CCG) is a virtual organization that provides access to high performance computing resources for computational chemistry with distributed support and services, intuitive interfaces and measurable quality of service. The CCG client, GridChem, is a Java desktop application that provides an interface to integrate the hardware, software and middleware resources necessary to solve quantum chemistry problems using grid technologies.
GROMACS :- Molecular dynamics
GSAS :- Solid and Powder diffraction analysis
GULP :- Solid and Polymer modelling
Scientific details about GULP can be found in the following papers:
1. GULP - a computer program for the symmetry adapted simulation of solids, J.D. Gale, JCS Faraday Trans., 93, 629 (1997)
2. Empirical potential derivation for ionic materials, J.D. Gale, Phil. Mag. B, 73, 3, (1996)
3. The General Utility Lattice Program, J.D. Gale and A.L. Rohl, Mol. Simul., 29, 291 (2003)
HADDOCK :- Molecular Docking
HADDOCK (High Ambiguity Driven biomolecular DOCKing) is an approach that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments, mutagenesis data or bioinformatic predictions. This information is introduced as Ambiguous Interaction Restraints (AIRs) to drive the docking process.
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:- Solve inelastic collisions.
HKL-2000 :- Structural Biology
Hybrid:- Ligand guided docking
HYBRID is a docking program that can utilize bound ligand information in a seamless manner. Like FRED, HYBRID performs a systematic, exhaustive, nonstochastic examination of all possible poses within the protein active site; however, instead of filtering the poses based on their shape complementarity to the active site, they are filtered on their shape and chemical complementarity to a known bound ligand.
HyperChem :- Molecular modelling
iBabel :- Molecular file conversion and viewer
Version 3.0 of iBabel is now in beta testing.
ICEDIT:- Chemical drawing java applet
ICEDIT is the new chemical structure- and reaction-editing tool developed at InfoChem following customer-specific requirements.
Features such as:
easy integration in any desktop or web application
advanced options for the definition of query features
support of complex R-group query specification
Supported Browsers: Internet Explorer 5.5 or higher, Firefox (Windows, Mac OS X, Linux), Opera, Netscape, Safari (Mac OS X)
Software: Java Runtime Environment JRE 1.1.x or higher
iChem :- Periodic table
iChemistry:- iPhone equation balancer
ICM-Modules :- Biology and Chemistry
ICM from molsoft stands for Internal Coordinate Mechanics and was first designed and built to predict low energy conformations of biomolecules. ICM also is a programming environment for various tasks in computational structural biology, sequence analysis and rational drug design.
ICM is distributed in the following packages:
- ICM-browser and ICM-browser-pro (distributed from a single package)
- ICM-chemist and ICM-chemist-pro (distributed from a single package)
- ICM-pro with options including bioinformatics, Poisson electrostatics, chemistry and cheminformatics, homology modeling, docking, virtual ligand screening (VLS).
iCut DNA:- iPhone app to search the Restriction Enzyme Database (REBASE)
IGOR Pro :- Data analysis
iMass :- Molecular mass calculator
iMol :-Molecular viewer
iMolBuilder:- iPhone application
iMolDraw :- iPhone application for chemical drawing
InDigestion :- Proteomic tool
Indigo:- Cheminformatics Toolkit
- Indigo is an organic chemistry toolkit. The code base is shared among the projects. All of the tools are written in C++, while a number of C# and Java wrappers are available.
Bingo: Cartridge for Oracle database supporting a wide range of searches in organic chemistry databases. Absolute portability, great scalability, plus unique features like:
Resonance substructure search
Tautomer substructure search with user-defined rules
Canonical (absolute) SMILES computation
Fast table update with no need to rebuild the index
Multi-threaded table indexing
Dingo: Molecule and reaction rendering library with C# wrapper and command-line utility. Best picture quality among all available products. Excellent portability. Easy SVG support. Automatic layout for SMILES-represented molecules and reactions.
Cano: Canonical SMILES computation library with C# wrapper. Unique support of tetrahedral and cis-trans stereochemistry features.
Deco: R-Group deconvolution and scaffold detection library and command-line utility. Pioneer work in computing the exact maximum common substructure of arbitrary amount of input structures.
Nucleo: Nucleotide chain handling library with Java wrapper. Includes canonical SMILES computation.
InforSense KDE :- Data analysis
iNMR :-NMR analysis
The website also includes a wealth of information including tutorials and visual guides
Instant JChem:- Desktop Chemistry Database
See also : A review of Instant JChem
Other tools from ChemAxon
IQmol:- molecular editor and visualisation
IQmol is a free open-source molecular editor and visualization package. It offers a range of features including a molecular editor, surface generation (orbitals and densities) and animations (vibrational modes and reaction pathways).