Macs in Chemistry

Insanely great science

Mac OS X Applications J-M

Jamberoo:- Molecular Editor

Jamberoo (former JMolEditor) is a java program for displaying, analyzing, editing, converting, and animating molecular systems.Supported file types






GromacsGro files
Mopac 2002
Log file



xyz file

JAMMING:- 3D Protein analysis

Although several approaches based on physics principles (e.g., electrostatics) have been reported to identify critical residues from the three dimensional structure of proteins (3), there is a limited accessibility to software aimed to identify critical residues from protein structures. Network analysis on the other hand has been recently shown to be succesfull and complementary to protein sequence-based approaches, JAMMING provides a means to identify critical residues from protein 3D structures Efficient identification of critical residues based only on protein structure by network analysis Cusack M, Thibert B, Bredesen DE and del Rio G. 2007. PLoS ONE 2(5):e421

JChem :- Java chemoinformatcs toolkit

JChem Modules:
JChem Base: adds a chemical interface to corporate databases, which can be applied for combined SQL and structural queries; imports/exports molecules, substructures, or reactions in standard formats (Molfile, SD file, RD file, SMILES, SMARTS, etc.).
JChem Cartridge: adds chemical knowledge to the Oracle platform giving automatic access to Oracle's security, scalability, and replication features.
Standardier: structure canonicalization tool converting molecules from different formats into standard representation.
Screen: screening based on pharmacophore or chemical fingerprints or other descriptors.
Reactor: generating reaction products from reaction equations and reactants.
Fragmenter: generating building blocks based on Recap rules from molecule libraries.
Serial Molecule Generator: transforming molecules by a sequence of user-defined transformations.
Chemical Term Evaluator: evaluating chemical expressions.
JKlustor: clustering and diversity calculations based on molecular fingerprints or other properties

Also a review of
Instant JChem

JChem 3.2.1 has been released.
For the list of changes please see:

J-ICE:- Interface for Crystallographic and Electronic Properties.

J-ICE ia a Jmol Interface for Crystallographic and Electronic Properties.

J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), Gaussian09 (G03), GROMACS, QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats.
You can try it out online
J-ICE: a new Jmol interface for handling and visualizing Crystallographic and Electronics properties, P. Canepa, R.M. Hanson, P. Ugliengo, M. Alfredsson J. Appl. Cryst., (2011), 44" [doi]

Jmol :-Molecule viewer

Jmol is a Java molecular viewer for three-dimensional chemical structures. Features include reading a variety of file types and output from quantum chemistry programs, and animation of multi-frame files and computed normal modes from quantum programs. Also available as an applet. Jmol is a fully compatible replacement for rasmol/chime in that it will use rasmol/chime scripts

JSDraw:- Javascript chemisty library

JSDraw™ is a chemical structure editor/viewer built in 100% Javascript, running on all platforms, including Windows, Mac, Linux, iPad/iPhone, Android tablets/phones and Chromebooks.

Now includes a spreadsheet.

jVisualizer :- NMR analysis

jVisualizer for analysing and visualising first-order NMR coupling patterns.

Ketcher:- Chemical drawing

Ketcher is a javascript based chemical drawing package.

Standalone mode

Ketcher supports the standalone mode in which no server support is required. In this mode, SMILES loading and automatic layout are not available.

Scalable Vector Graphics (SVG) for rendering

Ketcher uses SVG to achieve the highest quality in-browser chemical structure rendering. SVG standard is supported by most modern browsers and provides smooth and light-weight drawing.

Note: Internet Explorer through version 8 does not support SVG. IE rendering is based on VML (Vector Markup Language) instead.

SMILES strings

SMILES is a compact format for chemical structure representation. Ketcher provides you with the ability to load and save structures in this useful format.

Automatic layout (clean up)

The server-side structure layout algorithm is developed on C++ as a part of the Indigo toolkit. It provides fast 2D structure representations that satisfy common chemical drawing standards.

Other features

Hotkeys. For a more rapid and convenient way of structure drawing, Ketcher offers a variety of hot keys. See Editing Tips for the list of hot keys.

Stereochemistry. Ketcher provides complete stereochemistry support during the editing, loading, and saving of chemical structures.

Undo/Redo. Ketcher stores a full history of performed actions, and the user can rollback to any previous state.

In-place atom editing. Ketcher allows for the direct input of atom labels and charges. See Editing Tips for details.

Molfiles support. In addition to SMILES strings, Ketcher also supports Molfile saving and loading.

Kinemage :-Protein structure analysis

Kinemage have a variety of very useful bits of software for investigating protein structure Mage a 3D display program, KiNG, Rduce, Probe, Dang

KiSTheIP:- Kinetic and Statistical Thermodynamical Package

KiSThelP is a cross-platform free open-source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, NWChem). Some key features are:

  • gas-phase molecular thermodynamic properties (offering hindered rotor treatment)
  • thermal equilibrium constants
  • transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart)
  • RRKM rate constants, for elementary reactions with well-defined barriers.

KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the GUI and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D-plots, exporting images and data files.

KNIME:- Data Exploration platform

  • KNIME, pronounced, is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models.

KnowledgeMiner :- A self-organising data mining tool

KnowledgeMiner A self-organising data mining tool

LabCal:- iPhone app to calculate molarity

The Laboratory Calculator is an utility to calculate the molarity, to convert gram and mole and to compute dilutions of stock solutions.

LabCalPro:- Enhanced version of LabCal

LabCalPro is the enhanced version of LabCal. The Laboratory Calculator is an utility to calculate a molarity, to convert gram and mole and to compute dilutions of stock solutions

LabView:- Data acquisition and analysis

LabView is a graphical programming environment supporting more than 80 measurement devices, and driver software for data acquisition and instrument control, for developing custom measurement and automation systems based on Mac OS X

LAMMPS:- Molecular Dynamics

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale.
LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.
LAMMPS is distributed as an
open source code under the terms of the GPL. The current version can be downloaded here

LaTeX Chemistry Package

Chemistry packages for using with the document typesetting system LaTeX. Includes packages for reactions, molecular formulae, R and S codes, chemistry journals, symmetry elements and even to draw chemical structure

Libint:- Functions to compute two body integrals

Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. The idea of the library is to let computer write optimized code for computing such integrals. There are two primary advantages to this: much less human effort is required to write code for computing new integrals, and code can be optimized specifically for a particular computer architecture (e.g., vector processor).

Libint has been utilized to implement methods such as Hartree-Fock (HF) and Kohn-Sham density functional theory (KS DFT), second-order Moller-Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD) method, as well as explicitly correlated R12 methods.
From the compilation notes:-
MacOS X (versions 10.1 and 10.2) seems to set stacksize limit too low for the library generators to run properly. Use unlimit to increase the limit and then proceed with compilation
On Intel Xeon and Pentium4 systems we obtain significantly higher performance with Intel C/C++ compilers. In the latest test we compared Intel C/C++ compiler (version 7.1) against GNU gcc compiler (versions 3.2 and 3.3). libint performs at least 10% better with the former compiler. The recommended compiler options are -O3 -xW -tpp7.

LiBMCS:- Clusters based on maximum common substructure

LibraryMCS clusters a set of chemical structures on a structural basis. Structures that share a common substructure are clustered together. The common substructure is identified by the clustering program, and it is always the largest one among all substructures found in the structure set. Such substructure is called the Maximum Common Substructure (MCS). No predefined fragments are applied in finding the MCS.

Ligand Scout:-

LigandScout is a software tool that allows to rapidly and transparently derive 3D pharmacophores from structural data of macromolecule/ligand complexes in a fully automated and convenient way.

LigBuilder: Build ligands for protein active sites

I recently came across a program called LigBuilder developed at the Molecular Design Laboratory, it is a multiple-purposed program written for structure-based drug design procedure. Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket and subsequently screen them.

To quote from the website:-

"(1) The program analyzes the binding pocket of the target protein and derives the key interaction sites. A pharmacophore model is suggested and it could be applied to 3D database searching.
(2) User can choose either growing strategy or linking strategy to develop ligand molecules.

(3) Molecules are constructed by using fragments as building blocks. Various kinds of structural manipulation are provided, such as growing, linking, and mutation. On-the-fly minimization of conformation is performed during the building-up procedure. While the target protein is kept rigid, flexibility of the ligand molecules is considered.

(4) Molecules are evolved by Genetic Algorithm. The fitness score of a molecule is evaluated by considering its chemical viability as well as binding affinity.

(5) Chemical rules for judging "drug-likeness" are applied to screen the resultant molecules. Chemical stability, synthesis feasibility, and toxicity can also be taken into account by defining "forbidden structure" libraries.

(6) All the input and output molecules are in popular format, i.e. protein in PDB format and ligand in Sybyl Mol2 format. The program is very easy to use and maintain."

LigBuilder is written in ANSI C++ language and has been tested on UNIX and LINUX but not MacOSX, I've downloaded the siource and with minor modificartions got it to run under MacOSX.

For more detailed description of LigBuilder, please refer to: Wang, R.; Gao, Y.; Lai, L. "LigBuilder: A Multiple-Purpose Program for Structure-Based Drug Design", J.Mol.Model., 2000, 6, 498-516.

Instructions for running LigBuilder under MacOSX.

Download LigBuilder

A folder called LigBuilderv1.2 will be created in 'Downloads' in that folder you should find

bin/ default working directory
pocket/ source codes of POCKET module
grow/ source codes of GROW module
link/ source codes of LINK module
process/ source codes of PROCESS module
parameter/ necessary parameters
example/ test examples
manual/ user manual in HTML
fragment.mdb/ building-block fragment library
forbidden.mdb/ forbidden substructure library
toxicity.mdb/ toxic substructure library

LigBuilder has four main modules, i.e. POCKET, GROW, LINK, and PROCESS. You need to compile them respectively. You can do this by simply entering each subdirectory, i.e. "pocket/", "grow/", "link/", and "process/", and typing "make" to run the Makefile scripts. The scripts will compile the source codes automatically and generate the executable codes. The default C++ compiler assigned in the Makefile script is SGI "CC" compiler. To compile under MacOSX you should open the "MakeFile" in a text editor (i used BBEdit) and modify the first line in the "Makefile" scripts as "CC = g++" before compiling. You need to do this in each of the POCKET, GROW, LINK, and PROCESS folders.

Now open a terminal window and cd to the LigBuilderv1.2 folder

>cd /Downloads/LigBuilderv1.2/

Now cd to each of the POCKET, GROW, LINK, and PROCESS folders in turn and run make and then copy the resulting executable to usr/local/bin, you will need the admin password.

>cd pocket/
g++ -c -o main.o main.c
g++ -c -o parameter.o parameter.c
g++ -c -o protein.o protein.c
g++ -c -o ligand.o ligand.c
g++ -c -o pocket.o pocket.c
g++ -c -o misc.o misc.c
g++ main.o parameter.o protein.o ligand.o pocket.o misc.o -o pocket -lm

>sudo cp pocket /usr/local/bin/pocket

>cd ..
>cd grow/
g++ -c -o main_grow.o main_grow.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o grow.o grow.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_grow.o ga_grow.c
g++ main_grow.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o grow.o mutate.o score.o search.o ga_grow.o -o grow -lm

>sudo cp grow /usr/local/bin/grow

>cd ..
>cd link
g++ -c -o main_link.o main_link.c
g++ -c -o basic.o basic.c
g++ -c -o parameter.o parameter.c
g++ -c -o forcefield.o forcefield.c
g++ -c -o fraglib.o fraglib.c
g++ -c -o pocket.o pocket.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ -c -o ligand.o ligand.c
g++ -c -o logp.o logp.c
g++ -c -o link.o link.c
g++ -c -o mutate.o mutate.c
g++ -c -o score.o score.c
g++ -c -o search.o search.c
g++ -c -o ga_link.o ga_link.c
g++ main_link.o basic.o parameter.o forcefield.o fraglib.o pocket.o check.o misc.o ligand.o logp.o link.o mutate.o score.o search.o ga_link.o -o link -lm

>sudo cp link /usr/local/bin/link

>cd ..
>cd process
g++ -c -o main_process.o main_process.c
g++ -c -o parameter.o parameter.c
g++ -c -o basic.o basic.c
g++ -c -o ligand.o ligand.c
g++ -c -o population.o population.c
g++ -c -o check.o check.c
g++ -c -o misc.o misc.c
g++ main_process.o parameter.o basic.o ligand.o population.o check.o misc.o -o process -lm

>sudo cp process /usr/local/bin/process

LSD:- Logic for Structure Determination

Logic for Structure Determination (LSD) find all possible molecular structures of an organic compound that are compatible with its spectroscopic data.

Structure building relies on connectivity data found in 2D NMR spectra, without any reference to a chemical shift database. Molecular structures containing up to 50 non-hydrogen atoms were investigated by means of the LSD program.
The measurement protocol that is required by LSD includes the recording of 1D
1H and 13C as well as 2D COSY, HSQC and HMBC spectra. The status of each atom must be defined. It includes the atom symbol, the hybridization state (sp3, sp2 or sp), the number of attached hydrogen atoms, and the electric charge. This part of the data set is most often easily deduced by the user from elementary chemical shift knowledge. The status of the heteroatoms is deduced from the elemental molecular formula.
Carbon-carbon bonds are deduced from COSY and HSQC data while HMBC and HSQC data provide connectivity relationships through one or two bonds for non-hydrogen atom. The constraints imposed by atom status and 2D NMR data may be enforced by other atom neighborhood relationships. For example, it is possible to force a carbon atom to be bound only to carbon atoms. The user is responsible for such supplementary data. Contradictory constraints lead LSD to fail in the search of a solution structure.
The low resolution of HMBC and HSQC spectra in the C-13 chemical shift domain causes peak assignment ambiguities. It is possible to define groups of resonances and to assign a HMBC correlation peak to a group. This means that the correlation is caused by at least one member of the group.
The solutions may be selected using a substructure or a combination of substructures. Those violating Bredt's rule are also discarded.
The input to LSD is coded by the user as a text file, according to the instructions in the MANUAL_ENG.html document.

A program named OUTLSD reads the generated solutions and converts them into various formats: bonds lists, 2D coordinates, fancy 3D coordinates (fancy, due to the lack of stereochemical information), and SMILES chains. The 2D coordinates can be converted to Postscript drawings and to .mol (SDF) files.
Execution of the LSD program may be controlled by specific instructions for output formatting such as: single step execution, search of the biggest found fragment (for debgging purpose), report writing, verbosity level, substructure search.
Tens of structures were investigated by means of the LSD program, essentially in the field of natural product chemistry, and especially for terpenes and alkaloids.

Lumo:- Molecular Orbital Visualisation

Lumo accelerates the visualization of molecular orbitals from electronic structure calculations by harnessing the power of the graphics processing unit in modern macs. Lumo currently reads formatted checkpoint calculations from Gaussian03/09 calculations and there is preliminary support for Orca output files. Lumo was designed to speed up the slow part of looking at molecular orbitals and making molecular orbital diagrams. Lumo eliminates several steps along the process by reading in the output of programs like Gaussian, quickly visualizing the orbitals, and creating pictures of the essential orbitals in seconds.

Lumo requires Mac OS 10.6 or higher, 64-bit processor, and an OpenCL capable compute device. Lumo is routinely run on MacBook Pros and MacBook Airs. For analysis of larger systems, it is recommended to have at least 4GB of system RAM.

There is a movie of Lumo in action on the website

MacChess :-Crystallography

MacChess A Macromolecular crystallographic facility

MacMolPlt :-GAMESS viewer

MacMolPlt an excellent tool for viewing GAMESS results.
A modern graphics program for plotting 3-D molecular structures and normal modes (vibrations). Modern means: Mouse driven interface for real-time rotation and translation. Copy and paste functionality for interfacing to other programs such as word processors or other graphics programs (like ChemDraw). Simple printing to color or black and white printers (publication quality).

Macro MW:- iPhone app for calculating the molecular weight of your DNA/RNA or protein.

iPhone app for calculating the molecular weight of your DNA/RNA or protein.

Marvin :-Structure drawing/viewing

Marvin is a java application/applet recently updated, for displaying and editing chemical structures, it can be used to render different structure formats including SMILES/SMARTS and MOL files, it can also be used as a drawing package to generate a variety of file formats. There is a more detailed review here.


1. With the XpertDef module you define brand new polymer chemistries (what are the atoms, what are the monomers that make the polymer, what are the chemical modifications that you might need to simulate biological or synthetic chemical reactions, what are the different ways you might need to cut a polymer sequence into pieces (chemical or enzymatic), what are the different ways that a small oligomer might fragment in the mass spectrometer's gas phase, and so on...
2. With the XpertCalc module, you get a desktop calculator that understands your polymer chemistry definitions as defined in XpertDef. The calculator allows any kind of chemical reaction and is infinitely programmable. Any calculation is recorded in a logbook that is exportable to put in the lab-book;
3. With the XpertEdit module, you get a sophisticated polymer sequence editor and a chemical center where a huge amount of simulations might be performed. Anything mass-related is virtually feasible in XpertEdit.
4. With the XpertMiner module, you will get (it is being implemented) a data mining center. You'll be able to drag and drop data from the mass spectra (in the form of m/z lists) and data from the simulations performed in the XpertEdit module. Once there, all the data will be available for comparison, arbitrary calculations like, say : "this list of m/z values should be applied the following mass increase" or "this list of m/z values should be appplied this reaction: -H+Na". The possibilities should be infinite.

Mathematica :- Data analysis

Mathematica 11 Almost any area of science requires computational analysis and as Mathematica has evolved it has supported more and more areas of science. Chemistry is very well supported with detailed physical, chemical, and molecular properties of more than 34,000 compounds. Simulate your chemical processes with ready-to-deploy, fully interactive models using a combination of powerful computation, statistics and optimization, instant interactivity, and built-in chemical data. One system, one integrated workflow. A number of demonstrations and case studies are available.


MathMagic:- Equation editor

MathMagic is a WYSIWYG math editor with Graphic user interface, with support for MathML, LaTeX, MS Equation Editor, and more.

Maud:- Material Analysis Using Diffraction

MAUD stands for Material Analysis Using Diffraction. It is a general diffraction/reflectivity analysis program mainly based on the Rietveld method.

MayaChemTools:- CompChem Perl Scripts


MayaChemTools is a fabulous collection of Perl and Python scripts, modules, and classes to support a variety of day-to-day computational discovery needs.

The core set of command line Perl scripts available in the current release of MayaChemTools has no external dependencies and provide functionality for the following tasks:

  • Manipulation and analysis of data in SD, CSV/TSV, sequence/alignments, and PDB files
  • Listing information about data in SD, CSV/TSV, Sequence/Alignments, PDB, and fingerprints files
  • Calculation of a key set of physicochemical properties, such as molecular weight, hydrogen bond donors and acceptors, logP, and topological polar surface area
  • Generation of 2D fingerprints corresponding to atom neighborhoods, atom types, E-state indices, extended connectivity, MACCS keys, path lengths, topological atom pairs, topological atom triplets, topological atom torsions, topological pharmacophore atom pairs, and topological pharmacophore atom triplets
  • Generation of 2D fingerprints with atom types corresponding to atomic invariants, DREIDING, E-state, functional class, MMFF94, SLogP, SYBYL, TPSA and UFF
  • Similarity searching and calculation of similarity matrices using available 2D fingerprints
  • Listing properties of elements in the periodic table, amino acids, and nucleic acids
  • Exporting data from relational database tables into text files

The command line Python scripts based on RDKit provide functionality for the following tasks:

  • Calculation of molecular descriptors
  • Comparison 3D molecules based on RMSD and shape
  • Conversion between different molecular file formats
  • Enumeration of compound libraries and stereoisomers
  • Filtering molecules using SMARTS, PAINS, and names of functional groups
  • Generation of graph and atomic molecular frameworks
  • Generation of images for molecules
  • Performing structure minimization and conformation generation based on distance geometry and forcefields
  • Picking and clustering molecules based on 2D fingerprints and various clustering methodologies
  • Removal of duplicate molecules

These invaluable scripts can be used in other applications, I've written a Vortex Script that uses them.

McQSAR:- QSAR equations using the genetic function approximation paradigm


McQSAR:  A Multiconformational Quantitative Structure−Activity Relationship Engine Driven by Genetic Algorithms

McQSAR, an extension to the traditional GA approach to derive QSARs. McQSAR is able to use descriptors for multiple representations per compound, such as different conformers, tautomers, or protonation forms. Test runs show that the algorithm converges to a set of representations that describe the binding mode of the set of input molecules to a reasonable resolution provided that suitable descriptors based on the three-dimensional structure are used.

Mikko J. Vainio and Mark S. Johnson (2005) McQSAR: A Multiconformational Quantitative Structure-Activity Relationship Engine Driven by Genetic Algorithms. J. Chem. Inf. Model. 45, 1953-1961 DOI

Mercury :- Crystal structure viewer

Mercury updated to version 2.0 (Jan 2008) is now available for MacOSX from CCDC. Mercury offers a comprehensive range of tools for structure visualisation and the exploration of crystal packing.
Its features include:
Input of hit-lists from ConQuest, or other format files such as CIF, PDB, MOL2 and MOLfile. A full range of structure display styles, including displacement ellipsoids (please note that displacement ellipsoids can be displayed for CIFs or SHELX res files which contain Uequiv or Uij values only). The ability to measure and display distances, angles and torsion angles involving atoms, centroids and planes. The ability to create and display centroids, least-squares mean planes and Miller planes. The ability to display unit cell axes, the contents of any number of unit cells in any direction, or a slice through a crystal in any direction. Location and display of intermolecular and/or intramolecular hydrogen bonds, short nonbonded contacts, and user-specified types of contacts. The ability to build and visualise a network of intermolecular contacts. The ability to show extra information about the structure on display, such as the chemical diagram (if available) and the atomic coordinates. The ability to calculate, display and save the powder diffraction pattern for the structure on view. The ability to save displays

MestReNova NMR processing software

MestReNova is the natural evolution of the popular application MestReC. In addition to all the functionality available in MestReC, MestReNova incorporates a wealth of additional features:
  • Full WYSIWYG with different Zoom in/out levels
  • Powerful Undo/Redo mechanism
  • Powerful drawing tools with advanced text editing capabilities.
  • Anti-aliasing for improved drawing quality
  • Cutting tool to exclude non-interesting regions from the spectrum
  • Automatic processing capabilities
  • Powerful scripting engine
  • Molecular viewer
  • Peak to atom assignment module
  • Prediction of 1H and 13C NMR from chemical structure
  • Simulation of spin systems with any number of spin particles
  • Automatic fitting of experimental to predicted spectrum

Millsian:- Molecular Modeling

Millsian a new approach to molecular modeling

According to Millsian theory, atoms and bonds are made up of discrete surfaces of negative charge, not probability-density clouds. This gives Millsian the ability to calculate and render the exact charge distribution profiles for molecules of any size and complexity.

Further, electrons are localized in molecules to specific regions, i.e. functional groups which act as building blocks, or independent units, in larger structures. Using two basic equations, Millsian has solved the important functional groups of chemistry, allowing molecules of arbitrary size and complexity to be modeled trivially and almost instantly on a personal computer.
To learn about how Millsian translates the underlying theory into a molecular modeling product, please consult the papers:

Millsian 2.0: A Molecular Modeling Software for Structures, Charge Distributions and Energetics of Biomolecules, W. Xie, R.L. Mills, W. Good, A. Makwana, B. Holverstott, N. Hogle - 08/18/09
Total Bond Energies of Exact Classical Solutions of Molecules Generated by Millsian 1.0 Compared to Those Computed Using Modern 3-21G and 6-31G* Basis Sets - R.L. Mills, B. Holverstott, W. Good, N. Hogle, A. Makwana - 07/23/09
The Nature of the Chemical Bond Revisited and an Alternative Maxwellian Approach - R.L. Mills, Physics Essays, Vol. 17, No. 3, September (2004), pp. 342-389. View accompanying spreadsheets.

mMass :- Open Source Mass Spectrometry Tool

mMass is an open source and multi-platfrom package of many tools for mass spectrometric data analysis, mainly in proteomics.

Mnova:- Spectroscopic and analytical software

Mnova is a multipage, multivendor, multitechnique and multiplatform analytical chemistry software suite designed as a container for our NMR & MS plugins.

MOE :-Molecular modelling

Chemical Computing Group have released MOE for MacOSX. The Molecular Operating Enviroment is a comprehensive piece of software providing extensible tools for molecualr modelling, bioinformatics, computer aided molecular design all built using Scientific Vector Language (SVL). This programming language allows the rapid construction of novel tools many examples of which are available via SVL exchange.
Read a review of MOE I wrote for MacResearch

MODELLER :-Protein modelling

MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints and can perform many additional tasks, including de novo modeling of oligopeptides, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

ModelFree:- A program for optimizing "Lipari-Szabo model

ModelFree A program for optimizing "Lipari-Szabo model free" parameters to heteronuclear relaxation data

MoFa :-Chemoinformatics

MoFa is a program for finding frequent, discriminative molecular substructures in a set of molecules. The name MoFa is an acronym for Molecular Fragment Miner

MOLCAS :-Quantum chemistry

MOLCAS is a quantum chemistry software developed by scientists to be used by scientists. It is not primarily a commercial product and it is not sold in order to produce a fortune for its owner (the Lund University). The authors have tried in MOLCAS to assemble their collected experience and knowledge in computational quantum chemistry. MOLCAS is a research product and it is used as a platform by the Lund quantum chemistry group in their work to develop new and better computational tools in quantum chemistry

Molconn :-QSAR

Molconn is the standard program for generation of Molecular Connectivity, Shape, and Information Indices for Quantitative Structure Activity Relationship (QSAR) Analyses.

MOLDEN :-Molecular density display

MOLDEN is a package for displaying molecular density.  It is tuned to the Ab Initio packages GAMESS* and GAUSSIAN.
Instructions for installing molden are

Molecula Numerica:- Molecular Dynamics

Molecula Numerica is a software categorized in Molecular Dynamics Simulator. The software is produced to give priority to the visualization of the atoms/molecules. You can see what happened in the atomic world in a REAL-TIME sense. Of course the actual time scale of the phenomena in atomic world is pretty small, we mean you can see the computation results in REAL-TIME.
The software simulates not only translating motions but also rotational motions of atoms/molecules. Multi-atom molecules are dealt as a rigid body. So the software has a limitation coming from which High frequency vibration of the bonding is neglected. But the time integration is effectively fast by the simple model. To solve the rotational motion the simulator adopts
quaternion based rotational equation. As for the scheme for time stepping, a Leap-Frog is adopted.

Molecule :- Molecular editor

  • Molecule for Macintosh. Molecule is a program for generating, editing and displaying molecular structures
  • A native Mac OSX version is underway

Molegro Data Modeller :- Chemoinformatics data analysis

Molegro Data Modeller offers a high-quality modelling tool based on state-of-the-art data mining techniques.
Highlights of Molegro Data Modeller: - Regression: Multiple Linear Regression, Support Vector Machines, and Neural Networks - Feature selection and cross-validation is simple to set up and use (using the built-in wizards) - Principal Component Analysis (PCA) - Visualization: Histograms, 2D scatter plots, and 3D plots - Clustering: K-means clustering and density-based clustering - Built-in algebraic data transformation tool - Outlier Detection - Sophisticated subset creation: create diverse subsets by sampling from n-dimensional grids

Molegro Viewer:- Molecule Viewer

Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and Molegro Virtual Docker results.
Features at a glance
• Free!
• Cross-platform: Windows, Linux, and Mac OS X is supported.
• Share and view results from Molegro Virtual Docker docking runs.
• Imports and exports PDB, SDF, Mol2, and MVDML files.
• Built-in raytracer for high-quality images.
• Automatic preparation of molecules.
• Molecular surface and backbone visualization.
• Labels, sequence viewer and biomolecule generator.
• Cropping of molecules and clipping planes.
• Structural protein alignment.
• Support for KNIME workflows.

Molegro Virtual Docker :- Protein ligand docking

Molegro Virtual Docker is an integrated platform for predicting protein - ligand interactions. Molegro Virtual Docker handles all aspects of the docking process from preparation of the molecules to determination of the potential binding sites of the target protein, and prediction of the binding modes of the ligands.

New features in version 5.5:

* A new 'Energy Maps' tool provides volumetric visualization of protein force fields. This makes it possible to understand why a compound interacts with a given receptor, and may provide insights on how to improve the binding.

* We also added a new execution mode in the Docking Wizard: 'Run Docking in Multiple Processes'. This makes it possible to run medium sized jobs on a local machine, while utilizing multiple CPU cores and even multiple GPU graphics cards. For large jobs on multiple machines, Molegro Virtual Grid should still be used.

* The ray-tracer has been improved to more closely match the live 3D view output. This makes it possible to create high resolution renderings of the 3D view.

Molegro Virtual Grid :- Grid controller for docking

Molegro Virtual Grid creates an infrastructure for distributing docking runs on multiple machines.
By simply installing the MVG agent on a computer, its resources can be used transparently by the grid controller. Virtual Grid support is built into Molegro Virtual Docker: for instance, to dock a library of compounds against a receptor, simply setup a compound data source, and select 'start job on Virtual Grid' in the Docking Wizard.
Molegro Virtual Grid is multi-core aware and can be installed on any platform: Linux, Windows, and Mac. The machines in the grid do not need to run the same operating system.

Molecules:- A molecular viewer for the iPhone and iPod Touch

Molecules is an application from Sunset Lake Software for the iPhone and iPod Touch that allows you to view three-dimensional renderings of molecules and manipulate them using your fingers. The molecules can be downloaded from the Protein Data Bank ( You can rotate the molecules by moving your finger across the display, zoom in or out by using two-finger pinch gestures, or pan the molecule by moving two fingers across the screen at once. Molecules is free and its source code is available under the BSD license.

Molekel :- Molecular visualiser

Molekel is a multiplatform molecular visualization program being developed at the Swiss National Supercomputing Centre (CSCS).

Molekel was developed at the University of Geneva and CSCS/ETH Zurich in the early nineties, and is currently being rewritten under an open source GPL license.

Current version is available

Molinspiration :-Chemoinformatics

Molinspiration Molinspiration specializes in the development of cheminformatics software in Java. Molinspiration tools are therefore platform independent and may be run on any PC, Mac, UNIX or LINUX machine. The software is distributed in a form of toolkits, which may be used as stand-alone computational engines, used to power web-based tools, or easily incorporated into larger in-house Java applications

MOLMOL :-Molecule viewer

MOLMOL A molecule viewer ported to Darwin

Moloc :- Molecular Design Software Suite

Moloc a Molecular Design Software Suite, includes

Small Molecule Modeling
Matching Utilities
Conformational analysis
Peptide and Protein Modeling
Pharmacophore Modeling
Similarity Concepts and Database Mining
Diversity Analysis and Similarity Models
Dynamics: trajectory generation and evaluation
X-ray Facilities
Display Features

MolPro:- Ab initio calculations

Molpro is a complete system of ab initio programs for molecular electronic structure calculations, designed and maintained by H.-J. Werner and P. J. Knowles, and containing contributions from a number of other authors. As distinct from other commonly used quantum chemistry packages, the emphasis is on highly accurate computations, with extensive treatment of the electron correlation problem through the multiconfiguration-reference CI, coupled cluster and associated methods. The recently developed explicitly correlated coupled-cluster methods yield CCSD(T) results with near basis set limit accuracy already with double-ζ or triple-ζ basis sets, thus reducing the computational effort for calculations of this quality by two orders of magnitude. Using local electron correlation methods, which significantly reduce the increase of the computational cost with molecular size, accurate ab initio calculations can be performed for much larger molecules than with most other programs.

molSeeker:- Find molecular structures from identifier/name


A simple app that uses a couple of web services to get molecular structures, SMILES and inChiKeys from a query name/identfier

More about molSeeker here


MolView X :- Molecule viewer

MolView X is the OSX version of MolView

MolWeight:- iPhone for calculation of the molecular weight

MolWeight is a simple tool for scientists and students that allows calculation of the molecular weight and other key properties of peptides and oligonucleotides from their sequence. In addition, a calculator is provided for determining the molecular weight of any substance from its chemical formula

MolWorks :-Chemoinformatics

MOLWORKS a platform for chemical information software written in Java

Mona:- Small molecule visualiser


Mona is an interactive tool that can be used to prepare and visualize large small-molecule datasets. A set centric workflow allows to intuitively handle hundred thousands of molecules. Building upon the robust framework Naomi common cheminformatics tasks such as analysis, filtering and converting of molecular files can be performed with high efficiency.

MOPAC:- Semi-empirical quantum chemistry

MOPAC12 A practical quantum chemistry tool for modeling biological systems and co-crystals. MOPAC2012™ brings major improvements in the prediction of intermolecular interactions and hydrogen-bonding. This significantly improves geometries and energies of proteins, crystals, co-crystals, metal clusters, inorganics and other condensed phase systems

Moscito:- simulation software for molecular dynamics (MD) simulation.

Moscito simulation software for molecular dynamics (MD) simulation.
Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT or NPT using the weak coupling scheme. (Smooth Particle Mesh) Ewald summation is used for long range electrostatic interactions.

Moscito is quite fast on Intel/AMD architectures since some essential code has been written in assembler.
A parallel version (MPI) of the MD code is part of the distribution.
The distribution comes with a number of tools for setting up and analysing MD simulation runs.

MOSFLM :- CCD analysis

MOSFLM for processing image plate and CCD data. An excellent description of how to install is available here

Motofit:- refining X-ray data


Motofit co-refines Neutron and X-ray reflectometry data, using the Abeles matrix / Parratt recursion and least squares fitting (Genetic algorithm or Levenberg Marquardt). It works in the IGOR Pro environment (TM Wavemetrics).

MPQC :-Parallel quantum chemistry

MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrödinger equation. It runs on a wide range of architectures ranging from individual workstations to symmetric multiprocessors to massively parallel computers. Its design is object oriented, using the C++ programming language and has been ported to G5/MacOSX.

MultiSEq 2.0:- A unified bioinformatics analysis environment

MultiSeq is a unified bioinformatics analysis environment that allows one to organize, display, and analyze both sequence and structure data for proteins and nucleic acids. Special emphasis is placed on analyzing the data within the framework of evolutionary biology. MultiSeq is included with VMD

  • A paper describing MutiSeq has been published ; (Elijah Roberts, John Eargle, Dan Wright, and Zaida Luthey Schulten. MultiSeq: Unifying sequence and structure data for evolutionary analysis. BMC Bioinformatics, 2006, 7:382.)

Multiwfn:- Waveform analysis

Multiwfn is capable of plotting curve map, plot plane map, generate grid data and display isosurface, perform topology analysis and basin analysis for ELF (electron localization function) (as well as ELF-pi, ELF-sigma and localized orbital locator (LOL)).