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Structure manipulation software tools | Protein data analysis

Handling PDB files is central to almost all research in structural bioinformatics and structural biology.

BiopLib
Desktop

BiopLib

A mature C programming library for manipulating protein structure. The library…

A mature C programming library for manipulating protein structure. The library also provides a small number of functions for handling protein sequence as well as general purpose programming and…

Pmx
Desktop

Pmx

Enables automated hybrid amino acid structure and topology generation for all…

Enables automated hybrid amino acid structure and topology generation for all common biomolecular force fields. pmx (formerly pymacs) is a versatile bio-molecular structure manipulation package with…

BiopTools
Desktop

BiopTools

A set of command-line tools which exploit BiopLib. BiopTools provides…

A set of command-line tools which exploit BiopLib. BiopTools provides facilities ranging from renumbering atoms and residues, to calculation of solvent accessibility. Many of the BiopTools…

Victor
Desktop

Victor VIrtual Constrution TOol for pRoteins

An open-source project dedicated to providing tools for analyzing and…

An open-source project dedicated to providing tools for analyzing and manipulating protein structures. The provided application examples cover statistical energy potentials, profile-profile sequence…

OpenStructure
Desktop

OpenStructure

A modular open source platform to provide a powerful, yet flexible general…

A modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++…

Layers
Web

Layers

An algorithm to peel the atoms of proteins as layers from periphery to center.…

An algorithm to peel the atoms of proteins as layers from periphery to center. Layers identifies residue transition pattern, which may be used for the comparison of folding pattern between two…

CSB
Desktop

CSB Computational Structural Biology Toolbox

A cross-platform Python class library for reading, storing and analyzing…

A cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and…

BALL
Desktop

BALL Biochemical Algorithms Library

A comprehensive rapid application development framework for structural…

A comprehensive rapid application development framework for structural bioinformatics. BALL provides an extensive C++ class library of data structures and algorithms for molecular modeling and…

SCOPE
Desktop

SCOPE Semi Classical Open Source Protein Energy

Allows users to recreate structures and explore the calculated non-bonded…

Allows users to recreate structures and explore the calculated non-bonded energy. SCOPE is a program utilizing the topology information to calculate Van der Waals energy and electrostatic energy of…

RatameroEtAl201…
Desktop

RatameroEtAl2017

Allows users to visualize and interact with both static structure and dynamics…

Allows users to visualize and interact with both static structure and dynamics of proteins by using virtual reality (VR). The software pipeline enables nonexpert researchers to embed protein…

SVMlight
Desktop

SVMlight

An implementation of support vector machine (SVM) for the problem of pattern…

An implementation of support vector machine (SVM) for the problem of pattern recognition, for the problem of regression, and for the problem of learning a ranking function. SVMlight provides methods…

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