Peptide binding site detection software tools | Protein interaction data analysis
Peptide–protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches.
Allows users to submit a protein sequence, and returns a probability estimate of each residue in the sequence being disordered. Predicted intrinsically disordered regions (IDRs) are annotated as protein binding through a novel SVM-based classifier, which uses profile data and additional sequence-derived features.
A fully automated command line tool for generating sequence alignments and superpositions of protein binding sites. It is geared to the alignment of alternative protein conformations and especially addresses the tasks of dealing with highly flexible backbone regions, detecting multiple occurrences of a binding site in oligomeric structures, and coping with arbitrary annotation inconsistencies and structural artifacts. Moreover, ASCONA is also able to deal with point mutations.
Enables analysis and visualization of high-throughput animal behavioral data. Rethomics is an R package, consisting of a collection of interconnected packages, designed to focus on analyzing data from the Ethoscope platform as well as TriKinetics' Drosophila Activity Monitor. The software permits users to import, store, manipulate and visualize large amounts of behavioral results. It was used for the analysis of behavioral rhythm in fruit flies.
Predicts ligand binding sites. MEDock incorporates a global search strategy that exploits the maximum entropy property of the Gaussian probability distribution in the context of information theory. It consistently converges to the correct binding modes with significantly smaller numbers of energy evaluations than the Lamarckian Genetic Algorithm (LGA) required. The tool is able to converge to the global minima within a short time scale.
Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). It is described in terms of a solution that brings together a number of protein analysis tools at a single web server. SMS is a very powerful tool which enables a quick estimate of the level of engagement for each amino acid within its own protein chain and functionally more importantly, in the mechanism of binding to substrate and/or inhibitor.
Calculates, visualizes, and understands specific interactions made in macromolecular binding sites. Arpeggio is a web server for calculating interatomic interactions of 15 subtypes based on atom type, distance and angle terms. It can be applied to protein–ligand, protein–protein, protein–nucleic acid, and nucleic acid–nucleic acid interactions. This application has also shed light on the role of mutations in genetic diseases and drug resistance.