Permits users to predict and validate macromolecular structures, including ligand docking and highly accurate force fields with knowledge-based potentials. YASARA Structure can perform twisted structural alignments. This application includes a knowledge-based loop modeler with a compressed index of the PDB, allowing peptide segments spanning selected anchor residues to be located.
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.
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 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.
Enables phylogenetic inference. QmmRAxML is a program that implements a simple class frequency (cF) mixture model for modelling site-specific distributions for phylogenetic inference. This software can be useful for exploring model fit in protein evolution and reconstructing accurate phylogenies. It can also be used to model any mixture of amino acid substitution matrices, such as those based on protein secondary structures and solvent accessibilities at sites.
Provides support for molecular simulations. YASARA Dynamics includes force fields such as NOVA and YAMBER. Users can employ other molecular dynamics (MD) force fields like AMBER, and run all-atom MD simulations in aqueous solution with Particle Mesh Ewald long-range electrostatics. This application permits researchers to manipulate a simulation interactively and includes features to: (i) pull atoms or entire molecules around, (ii) fix and free atoms, (iii) add restraints, and (iv) toggle force field terms.
Allows users to upload a PDB structure to be modified by single or multiple non-canonical amino acids and/or simultaneously mutated. FFNCAA is a web application that permits user to download the forcefield parameters calculated and derived for FF_NCAA. With a user submission, the interface performs the requested modifications and minimizes the structure to remove any clashes that have been formed by introducing the non-canonical amino acid to the nearest local minimum.