(commercial) ATK is a first principles electronic structure program capable of modelling electrical properties of nanostructured systems coupled to semi-infinite electrodes. The two electrodes, for instance, could be a nanotube and a metal, and the nanostructure could be the interface region between the two systems. Other typical systems include molecules between metal surfaces and interfaces between materials.
The Chemical Structures project aims to provide a complete set of 3D molecular structures in CML format. As CML format permits structural data and many properties to be included, each file also contains additional information, like molecular weight, boiling point, melting point, or InChI code. Data can be explored with a CML-aware software, like Jmol, or by using a Web browser.
Chemical2vmd lets you use the Babel interface of VMD to load various molecular coordinate files via the .mailcap interface used by web clients like Mosaic or Netscape.
COPASI is a software application for modeling and simulation of biochemical networks. The software package has a GUI that lets users define biochemical network models by entering chemical reactions and kinetic equations. A powerful simulation engine can then perform simulations of the dynamics of the networks and carry out many different computational analyses. COPASI can simulate dynamics using either an ODE approach or a stochastic chemical kinetics approach (Gillespie-type algorithms).
(commercial) CRYSTAL computes the electronic structure of periodic systems within Hartree Fock, density functional or various hybrid approximations.
Dockres reads the log file of docking runs performed by Autodock and extracts the top scoring poses subject to various filters.
eHiTS (Electronic High Throughput Screening) is a program for flexible docking of ligands to proteins. It is fast, fully automated, and comprehensively covers the searc space.
FlipDCD is a small utility for reversing the endianism of binary DCD trajectory files from Charmm, and NAMD. This can be useful when running simulations on one architecture and visualizing or analyzing the results on another.
(commercial) Glide offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level.
Ionize is a threaded program for placing counterions near a biological molecule in preparation for molecular dynamics simulations.
LaTeX Chemistry Packages
Chemistry packages for using with the document typesetting system LaTeX.
Lennard-Jones Gas Simulation
Lennard-Jones Gas Simulator does a molecular simulation of noble gases.
MCTDH stands for Multi Configuration Time Dependent Hartree. MCTDH is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces.
The purpose of the MDAPI (molecular dynamics applications programming interface) is to provide a high performance C programming interface for the separation of code for molecular dynamics (MD) simulations into a front end and a computational engine.
MDEnergy is a program to calculate energies from DCD or PDB-files.
Molegro Virtual Docker
(commercial) 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.
MOPAC7 is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions.
(commercial) MULTIMODE does Vibrational Self Consistent Field (VSCF) and several types of "CI" calculations for the rovibrational energies and wavefunctions of polyatomic molecules, transition states, clusters, etc.
Mychem is an extension that provides a set of functions that permit you to handle chemical data within a MySQL database.
OSET (Organic Synthesis Exploration Tool) is a computer-assisted organic synthesis (CAOS) program for the retrosynthetic analysis of target molecules. Intended for educational use, as a tool for learning chemical synthetic design at undergraduate organic chemistry courses.
POLYRATE is a computer program for the calculation of chemical reaction rates of polyatomic species
(commercial) Shop is a guide to .the Scaffold Hopping procedure during the Drug Discovery process. Scaffold Hopping is the methodology that substitutes one part of a molecule with another one, retaining their pharmacophoric interaction points.
Symmetry is a set of C codes for automatic molecular symmetry recognition.
Triton is graphical tool for modelling protein mutants and assessment of their activities. Protein mutants are modelled based on the wild type structure by homology modelling using the external program MODELLER.
(commercial) VAMP is a semi-empirical molecular orbital package for molecular organic and inorganic systems. It is capable of calculating many physical and chemical molecular properties very rapidly. Its speed, stability, and reliability make it ideally suited to use for high-throughput screening in areas such as computational drug discovery.