Protein Data Bank (PDB)

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.

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PARATEC

  • Level of openness 0 ☆☆☆
  • Document quality 0 ☆☆☆

PARATEC is a parallel DFT program package based on plane-wave basis and norm-conserving pseudopotential.

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PolyParGen

  • Level of openness 0 ☆☆☆
  • Document quality 2 ★★☆

PolyParGen is a free web application that automatically generates OPLS force field for molecular dynamics calculations. It is possible to create OPLS-AA parameters of macromolecules such as fullerenes with complex crosslinking structures, graphene and cyclic molecules. The generated OPLS-AA force field parameter file in Gromacs format is automatically sent to users.

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PAICS

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

PAICS is a program of quantum chemical calculation. In this program, fragment molecular orbital (FMO) method is adopted, by which large molecules including biomolecular systems can be treated with several quantum chemical approaches including HF and MP2 methods. At the same time, PaicsView has been developed, which is a supporting program for making input files and analyzing calculation results.

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pymatgen

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

A python library for materials analysis. Flexible classes for representation of materials are prepared, and data for crystal structures and various material properties can be handled efficiently. This application can performs analysis of phase diagrams, Pourbaix diagrams, diffusion analyses etc. as well as electronic structure analyses such as density of states and band structures. This software is being actively developed keeping close relation with Materials Project.

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PyMOL

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

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.

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ParaView

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open-source application for analysis and visualization of two- and three-dimensional data. The function of this application can be used not only by interactive operation with three-dimensional display, but also by batch processing. This application supports various environments such as Windows, Mac, and Linux from a desktop PC to a supercomputer performing large scale parallel computation.

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PLUMED

  • Level of openness 3 ★★★
  • Document quality 3 ★★★

An open source library to calculate free energy in molecular dynamics simulation. It supports several famous molecular dynamics software packages such as Amber and Lammps.

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Parsec

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

Parsec is a DFT program package based on real space basis and norm-conserving pseudopotential.

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PFAPACK

  • Level of openness 3 ★★★
  • Document quality 2 ★★☆

Library for calculating Pfaffian (square root of determinant), which is defined for skew-symmetric matrices. Algorithms are implemented in several languages (Fortran, Python, Matlab, Mathematica) and users can choose favorite one. Interfaces for C are also provided.

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