Commercially-available free software for Computer-Aided Drug Development. It includes programs for compound database, protein-compound docking, structure-based drug screening, ligand-based drug screening, protein-ligand binding site prediction, molecular editor, physical property prediction, synthetic accessibility prediction, thermodynamic calculation including multi-canonical dynamics, and molecular dynamics simulations with and without acceleration using GPUs and MPI parallelization.
Open-source package for molecular dynamics simulation designed for biological macromolecules. This package can perform molecular dynamics simulation of biological macromolecules such as proteins, lipids, and nuclear acids as well as solutions by controlling temperature and pressure. This package can treat long-range interaction and free energy, and is designed for parallel computing.
Payware for quantum chemical calculation based on the density functional theory. This application supports relativistic effects needed in treatment of transition-metal complexes and heavy elements, and can also treat effect of solvents with the method of COSMO and 3D-RISM. In addition to ordinal optical spectra, it can evaluate various spectra data such as NMR, atomic vibration, electron spin resonance, and nuclear quadrupole resonance (NQR).
An open-source first-principles calculation library for pseudopotential and all-electron calculations. One of or a mixture of Gaussian and plane wave basis sets can be used. A lot of the development focuses on massively parallel calculations and linear scaling. The user can choose various calculation methods including density functional theory and Hartree-Fock.
An application for visualization of biopolymers. This application can visualize biopolymers by using its original command line and graphical user interface, more than 600 settings for visualization, and more than 20 visualization schemes. This application also supports more than 30 file formats such as PDB and multi-SDF, and can utilize sophisticated visualization methods such as the ray tracing.
An open-source application for visualization of atoms and molecules developed for molecular dynamics. This application supports a number of input file formats for molecular configration, and can perform visualization of three-dimensional atom configration as well as creation of a animation. The main feature of this application is that various useful analysis tools can be used by intuitive control of a graphical user interface (GUI).
ChemSpider is a free chemical structure database that provides fast access to over 100 million structures, properties, and related information, and is operated by the Royal Society of Chemistry.
By integrating and linking compounds from hundreds of high-quality data sources, ChemSpider makes it easy to find chemical data from diverse data sources that are freely available for online searching. Users can also add and manage data in a wikipedia-like fashion. Meanwhile, manual curation by the Royal Society of Chemistry continuously improves data quality.
An open-source application for quantum chemical calculation. This application can perform quantum chemical calculation based on the Hartree-Fock method and the density functional method. The code is developed on the emphasis of readability and flexibility, and can be called from Python scripts. Quantum chemical calculation based on two-electron wave functions (geminals) is also possible.
An open-source application for first-principles calculation based on pseudopotential and wavelet basis. Electronic state calculation of massive systems is performed with high accuracy and high efficiency by using adaptive mesh. Parallel computing by MPI, OpenMP, and GPU is also supported.
An open-source application for quantum chemical calculation. This package implements various methods for quantum chemical calculation such as Hartree-Fock approximation, density functional theory, coupled-cluster method, and CI (configuration interaction) method. The package is written in C++, and provides API for Python, by which users can perform for preparation of setting and execution of calculation.