A structure database for proteins and nuclear acids. Three-dimensional structure data of proteins and nuclear acids (atomic coordinates determined experimentally by X-ray crystal analysis, NMR, etc.) can be downloaded. The data reposited in PDB are in the public domain, and can be accessed by everyone freely.
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.
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 application for ab initio quantum chemical calculation. This application can calculate molecular structures, chemical reactivity, frequency analysis, electron spectrum, and NMR spectrum with high accuracy. It implements the density functional theory, the Hartree-Fock(HF) method as well as recently developed methods such as the post-HF correlation method. It also has GUI for molecular modeling and a tool for preparation of input files.
An open-source application for first-principles molecular dynamics based on a pseudopotential method using plane bases. This application can perform electronic-state calculation and molecular dynamics employing the Car-Parrinello method. It implements MPI parallelization, which enables us to perform efficient parallel computing in various environments including large-scale parallel computers. The program is written in C++, and is distributed in source form under the GPL license.
A collection of software tools for molecular dynamics calculations. Various interatomic potentials and tight binding models are implemented, and numerous external applications can be invoked. It also supports training and evaluation of GAP (Gaussian Approximation Potential), which is a form of machine learning potential.
A simple open-source application for visualization compatible to Protein Data Bank (PDB) format. This application also supports other formats such as Sybyl, Molden, Mopac, and CHARMM. It is a pioneering piece of software as an interactive PDB viewer.
An application for adding a function of the replica exchange method to the existing applications for molecular dynamics simulation such as MODYLAS, AMBER, and CHARMM. Without changing original programs of molecular dynamics, the replica exchange method can be implemented easily. This application also shows high performance in massive parallel computing by the K-computer.
This is a structure analysis program for solutes and solvents, based on the statistical mechanics theory of liquids. The program determines the solvent density distribution surrounding the solute, and calculates various physical values such as the solvation free energy, compressibility, and partial molar volume. The program implements a parallelized fast Fourier transform routine for large-scale parallel computing, and can analyze molecular functions such as the ligand binding affinity of proteins, that would be difficult using other methods.
An open-source application for the first-principles calculation based on the all-electron method with localized bases. By adopting the full-potential LMTO method, high-speed electronic state calculation can be performed with a less number of bases compared with the standard all-electron method. There is no restriction on symmetries as in the LMTO-ASA method, and spin polarization and spin-orbit interaction can also be treated.