Enables biologists to solve structural biology problems by providing combinatorial, geometric and topological tools. SBL is a modular software library that offers end-user applications with state-of-the-art performances, as well as a C++/python toolbox, which involves core algorithms, biophysical models and modules, and fosters code re-usability and the development of complex applications.
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++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment.
Builds a structural/dynamics model that connects and rationalizes existing structural, single-molecule and mutagenesis data. bioStructureM is based on linear response theories and resolution-exchanged simulations. It can furnish a temporal and spatial description of programmed ribosomal frameshifting (PRF) with unprecedented mechanistic details. This tool is useful for the investigation of protein structures.
PyChimera is based on UCSF Chimera method and provides for users from UCSF Chimera to work by using python environment. UCSF Chimera is a visualization tool present in the computational chemistry and structural biology communities.
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 comes with a clean, well-documented API following good object-oriented engineering practice.
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 mathematics. BiopLib transparently handles PDBML (XML) format and standard PDB files. The core of the BiopLib library is a reliable PDB parser that handles alternate occupancies and deals with compressed PDB files and PDBML files automatically. The library is designed to be as flexible as possible, allowing users to handle PDB data as a simple list of atoms, or in a structured form using chains, residues and atoms.
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 command-line tools act as filters, taking a PDB (or PDBML) file as input and producing a PDB (or PDBML) file as output.
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 alignments and ab initio loop modeling.
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 molecules. Besides, it also extracts molecular surfaces and protruding atoms at custom fineness by non-random sampling, which can be used for shape estimation and molecular surface comparison for protein recognition and ligand design.
Integrates compound molecular substructures as information rich vectors. Mol2vec is an unsupervised machine learning approach that assimilates vector representations of molecular substructures. These substructures are obtained via the descriptors and molecular fingerprints (FP) based on Morgan algorithm. This software’s model was tested on all available chemical structures, yielding embeddings of molecules.
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 some additional functionalities. The tool allows high-quality large-scale automated alchemical free energy calculations due to amino acid mutations. It enables computational evaluation of the post-translational modification effects in terms of free energies.
Automates recognition of statistically significant patterns of amino acid enrichment or depletion. Composition Profiler aids in the discovery of statistically significant composition anomalies by color-coding and sorting residues according to their physico-chemical or structural properties. It permits to highlight bias in amino acid composition between two sets of protein sequences.
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 structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application development times but also helps in ensuring stability and correctness by avoiding the error-prone reimplementation of complex algorithms and replacing them with calls into the library that has been well-tested by a large number of developers.
Allows to calculate the center of mass of a protein. CALCOM can estimate the cartesian coordinates of the center of mass of a single chain, as well as complexed chains and ligands. It can be used to evaluate their distance in protein-protein and protein-small ligand complexes, and to measure the distance of selected amino acids and atoms to the center of mass. The tool was used to evaluate the distance between two subunits of the miraculin dimer during the molecular dynamics simulations performed at different pH conditions.
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 structures into VR programs using a combination of widely available software and custom-built codes. The use of VR allows changing of the level of details accessible to a researcher when analyzing protein-ligand interactions or conformational changes.
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 for assessing the generalization performance efficiently. It includes two efficient estimation methods for both no error rate and precision/recall. The algorithm proceeds by solving a sequence of optimization problems lower-bounding the solution using a form of local search. SVMlight has been used on a large range of problems, including text classification, image recognition tasks, bioinformatics and medical applications.
Implements probabilistic graphical models to biological applications. Biolearn reads observation data on the nodes of a Bayesian network. It can perform discretization on the data. This tool can retrieve an optimal network structure employing a search algorithm. It serves to run just one structure-learning search on the data, or to run any number of structure-learning searches using random samples of the data and perform model averaging.
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 the protein. This tool can create energetically favorable structures using over 10 different proteins from Portein Data Bank (PDB).
Provides functionalities for the modeling and the rendering of proteins alone and in complex with peptides and DNA. Structuropedia is an online application on which users have to upload a PDB file, PDBID or PDB URL for performing experiments.