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ASAD ASAD is a software package developed for creating and integrating chemistry schemes in atmospheric models without the need to write any FORTRAN code to solve the chemical rate equations. BIGMAC BIGMAC is a general-purpose parallel CBMC code. Configurational Bias Monte Carlo (CBMC) is a recent technique to compute thermodynamic properties of flexible molecules. BOSS (commercial) performs (a) Monte Carlo (MC) statistical mechanics simulations for solutes in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase, and (b) standard energy minimizations, normal mode analysis, and conformational searching CAMEO (commercial) Computer Assisted Mechanistic Evaluation of Organic reactions (CAMEO) is an expert system that predicts the outcome of organic reactions given starting materials, reagents and reaction conditions. ChemApp ChemApp provides the powerful calculation capabilities of ChemSage in the form of a programmer's library. It consists of a rich set of subroutines which provides all the necessary tools for the calculation of complex multicomponent, multiphase chemical equilibria and the determination of the associated energy balances. ChemCalc ChemCalc is a calculator that is more oriented towards chemistry. Although starting out as a console app, it is a hope that an X11 interface will be designed at a later time. Chemiehelfer Chemiehelfer is a German console program for chemical calculations. CP-Optimizer CP-Optimizer is an automatic procedure to perform geometry optimisation and harmonic frequency calculations using GAUSSIAN package. DBWatcher DBWatcher is a program handling periodic BLAST searches to find similarities to your own sequences. It keeps track of the previous searches and only performs new ones when necessary. Dirac DIRAC is a FORTRAN (and a bit of C) code for relativistic molecular calculations based on the Dirac-Coulomb Hamiltonian. It has support for uncontracted and contracted basis sets. DOCK DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. DYNAMO DYNAMO is a structure calculation and analysis system built as an extension of our TCL/TK interpreter NMRWish, so that analysis schemes and annealing protocols are TCL scripts, and therefore relatively short, easy, and flexible. EChem++ EChem++ is a software system based on an object oriented approach to electrochemical experimentation, simulation, and data analysis. Currently, development emphasis lies on the modelling and simulation as well as the analysis modules. FlexS FlexS is a computer program for predicting ligand superpositions. For a given pair of ligands, FlexS predicts the conformation and orientation of one of the ligands relative to the other one. In FlexS the reference-ligand is assumed to be rigid, thus, it should be given in a conformation which is similar to the bound state. FlexX FlexX is an extremely fast, robust, and highly configurable (FlexX-able) computer program for predicting protein-ligand interactions. frowns Frowns is a chemoinformatics toolkit geared toward rapid development of chemistry related algorithms. It is written in almost 100% Python with a small portion written in C++. Frowns is loosely based on the PyDaylight API that Andrew Dalke wrote to wrap the daylight C API. In some cases programs written using PyDaylight will also work under Frowns with a few minor changes. Gabedit Gabedit is a graphical interface to Molpro and Gaussian computational chemistry packages running locally or on a remote server. It includes a 3D molecule editor and viewer. GaussSum GaussSum is a collection of scripts which parse the output of Gaussian 03, Gaussian 98 or GAMESS calculation to extract useful information. This includes the progress of the SCF cycles, geometry optimisation, UV-Vis/IR/Raman spectra, MO levels, MO contributions and more. GenChemLab GenChemLab is an OpenGL-based application intended to simulate several common general chemistry exercises. It is meant to be used to help students prepare for actual lab experience. It could also be used in cases where laboratory facilites are not accessible, for instance in K-12 schools or home schooling. Supported experiments include titration, calorimetry, freezing point depression, vapor pressure, and spectrophotometry. GENSPECT GENSPECT is a line-by-line radiative transfer toolbox to calculate gas absorption and emissivity, emission and transmission for a wide range of atmospheric gases. Given information including gas types, gas amounts, temperature, pressure, path length and frequency range for an atmosphere or laboratory cell, the GENSPECT toolbox computes the spectral characteristics of the gas mixture. Ghemical Ghemical is a computational chemistry software package released under the GNU GPL. It has a graphical user interface (which is based on GTK2), and it supports both quantum-mechanics (semi-empirical and ab initio) models and molecular mechanics models (there is an experimental Tripos 5.2-like force field for organic molecules). Also a tool for reduced protein models is included. Ghemical-GMS The Ghemical-GMS project has implemented a set of features/additions to the Ghemical codebase which provide the ability to generate GAMESS input files and submit these files to a graphical GAMESS queue system (GTK-Gamess). Gibbs Gibbs perfoms Gibbs-ensemble simulations to determine the densities of coexisting liquid and vapor phases in equilibrium with each other. The particle exchange step can be performed with the cavity-biased method of Mezei. GULP GULP is a program for performing a variety of types of simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material. In particular GULP is designed to handle both molecular solids and ionic materials through the use of the shell model. One difference between GULP and other similar programs is that symmetry is used for solids to accelerate the calculations and to simplify the input. Isotopic Pattern Calculator IPC is a program that calculates the isotopic distribution of a given chemical formula. It gives the rel. intensities and the propability of the masses belonging to a molecule ion, fragment or whatever is represented by the given chemical formula. Furthernmore it can use GNUPlot to visualize the result. Kemistry Kemistry is a collection of chemistry-related applications written for the KDE Desktop Environment. It includes KMolCalc, a molecular weight and elemental composition calculator, and KemBabel, a file conversion program based on Open Babel. KMovisto KMovisto allows you to open GAUSSIAN files directly without conversions and you see the results of your optimizations. MCCCS Towhee Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. MCPRO MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Version 1.68 does not include conformational search, quantum mechanics, or normal mode calculations. The MC simulations can be performed in a periodic solvent box, in a solvent cluster, or in a dielectric continuum including the gas phase. MetaSite MetaSite is a computational procedure specially designed to predict the site of metabolism for xenobiotics starting from the 3D structure of a compound. The site of metabolism can be described by a probability function Psm that is correlated to, and can be considered, the free energy of the Cyp-substrate recognition and reactivity process. MMC MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change). Molaris Molaris includes Enzymix: a macromolecular simulation program designed to study the functions of proteins ranging from ligand binding to free energy profiles of enzymatic reactions using the Empirical Valence Bond (EVB) approach and the Free Energy Perturbation (FEP) method and Polaris: a fast converging computational software based on the Protein Dipoles-Langevin Dipoles (PDLD) approach. Open Babel Open Babel is a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry. ORAC ORAC is a program for running classical simulations of biomolecules. Simulations can be carried out in the NVE, NPT, NHP, and NVT thermodynamic ensembles. The integration of the equations of motion in any ensemble can be carried out with the r-RESPA multiple time step integrator and electrostatic interactions can be handled with the Smooth Particle Mesh Ewald method. PhosphoFind PhosphoFind locates and quantifies phosphorylated peptides and proteins from a set of four MALDI mass spectra run in linear positive (Lin+), linear negative (Lin-), reflectron positive (Refl+), and reflectron negative (Refl-) modes. PWscf Plane-Wave Self-Consistent Field: a set of programs for electronic structure calculations within Density-Functional Theory and Density-Functional Perturbation Theory, using a Plane-Wave basis set and pseudopotentials PyMOlyze PyMOlyze is a program to analyze the results of quantum chemistry (DFT) calculations. Gaussian 98/03, ADF, GAMESS (US), GAMESS (UK), and PC-GAMESS files are supported. The following analyses are available for user-defined molecular fragments: Mulliken Population Analysis (MPA), C-squared Population Analysis (SCPA), Overlap Population Analysis (OPA), Mayer's Bond Orders, Charge Decomposition Analysis (CDA), and Fragment Analysis. SCORE An empirical method for estimating the binding affinity of a protein-ligand complex with known 3D structure. SCORE uses a linear equation to describe the binding energy changes upon the binding process, which includes terms accounting for hydrogen-bonding, hydrophobic effect, and deformation effect. SimSoup SimSoup is a graphical Artificial Chemistry simulator for Linux and Windows. The program enables a Chemistry to be defined in terms of Molecule Types and the possible Interactions between them. A simulation run involves setting up a number of Molecules of various Molecule Types in a Reactor, and then allowing Interactions to take place over a period of time. Interactions taking place in the Reactor are shown on a graphical display. Sparkle/AM1 Sparkle/AM1 is a computational chemistry model which exploits the lanthanide series characteristics to accurately predict geometries of the coordination polyhedra of complexes of ions of the rare earth metals. It is distributed as an external file for MOPAC 93r2, and as the default model for a modified version of the public domain MOPAC 6. SPASM SPatial Arrangements of Side chains and Main chains SPROUT (commercial) SPROUT is the sixth generation of the successful, mature de novo ligand design system. Through its use at various academic, government and industrial molecular modeling research centers, the software has proven to be successful for the generation of novel active ligand molecules. Turbomole (commercial) Turbomole is for standard quantum chemical applications (HF, DFT, MP2). Unlike many other programs, the main focus in the development of Turbomole has not been to implement all new methods and functionals, but to provide a fast and stable code which is able to treat molecules of industrial relevance at reasonable time and memory requirements. VOIDOO VOIDOO is for detection of cavities in macromolecular structures. It uses an algorithm that makes it possible to detect even certain types of cavities that are connected to "the outside world". Three different types of cavity can be handled by VOIDOO: Vanderwaals cavities (the complement of the molecular Vanderwaals surface), probe-accessible cavities (the cavity volume that can be occupied by the centres of probe atoms) and MS-like probe-occupied cavities (the volume that can be occupied by probe atoms, i.e. including their radii). XMakemol XMakemol is a mouse-based program, written using the LessTif widget set, for viewing and manipulating atomic and other chemical systems. It reads XYZ input and renders atoms, bonds and hydrogen bonds. XMolCalc XMolCalc is a small utility that allows you to calculate a molecular weight. Xykron Xykron is the front end of the Chemical Resource Kit. Of the components, Xykron is the most feature-filled and provides the most diverse range of functions. xyz2rgb xyz2rgb is a tool for animating molecules. xyz2rgb makes pretty pictures and movies of molecules. It expects input in the form of an XYZ file, one of the file formats frequently used by computational chemists. As output, it produces one or more line-interlaced RGB files. YAeHMOP Yet Another extended Huckel Molecular Orbital Package: intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions. ZORTEP ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.
