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.
A database of structures and properties for various materials including polymers and inorganic substances. This database is maintained by National Institute of Materials Science (NIMS), and provides crystal structures, various physical properties, and phase diagrams for material science via a user interface based on web browsers. This database also provides calculation results of phase diagrams and electronic structures. This database can be used without charge after registration.
A results database of first-principle calculation for material science. This database provides numerical data of crystal structures, band structures, thermodynamic quantities, phase diagrams, magnetic moments, and so on. This site is maintained by a research group of MIT, and has extensive data of materials related to lithium battery. In addition to a user interface based on web browsers, an http-based API is also provided to enable user-defined material screening. This database can be used without charge after registration.
A results database of first-principle calculation for material science. This database provides numerical data of crystal structures, band structures, thermodynamic quantities, phase diagrams, magnetic moments, and so on. This site is maintained by a research group of Duke University, and in particular, has extensive data of Heusler alloys. In addition to a user interface based on web browsers, an http-based API is also provided to enable user-defined material screening. This database can be used without charge after registration.
An application for modeling and visualization of molecules for quantum chemical calculation. This application implements a construction of
molecular structures with classical molecular dynamics simulation and structure optimization by simple generic force fields, and a preparation of input files for applications of quantum chemical calculation such as Gaussian. A binary package for Windows XP is available, and informal packages for Windows 7, iPad, and Linux exist.
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.
An open-source application for molecular dynamics. This application can perform molecular dynamics simulation of biopolymers and solvents consisting of a number of molecules/atoms. It implements a number of force field sets and algorithms, and supports parallel computing based on OpenMP. Java graphical user interface (GUI) is also included.
MODYLAS is a highly parallelized general-purpose molecular dynamics (MD) simulation program appropriate for very large physical, chemical, and biological systems. It is equipped most standard MD techniques including free energy calculations based on thermodynamic integration method. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT) in order to realize excellent scalability. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers. It works on ordinary linux machines, too.
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.
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.