Allosteric site detection software tools | Protein structure data analysis
Allostery is a fundamental process that regulates a protein’s functional activity through the induction of changes in its conformation and dynamics in response to the perturbation of an effector at a site distinct from the active site, also termed the allosteric site. Structure-based allosteric site prediction tools analyze protein structure to identify potential effector binding sites and allosteric communication between sites.
Predicts allosteric pockets on proteins, was developed. AlloPred uses perturbation of normal modes alongside pocket descriptors in a machine learning approach that ranks the pockets on a protein. AlloPred ranked an allosteric pocket top for 23 out of 40 known allosteric proteins, showing comparable and complementary performance to two existing methods. The AlloPred web server allows visualisation and analysis of predictions.
A modular and scalable modelling methodology that alleviates the regulatory as well as the combinatorial complexity of biochemical networks. ANC can provide a basis for scalable, modular and executable modelling of biochemical networks in systems and synthetic biology.
Allows users to analyze allosteric signaling in proteins. AlloSigMA is a web platform supplying an estimate of the allosteric free energy thanks to a structure-based statistical mechanical model. The program can be used for investigating various proteins including small monomeric structures or even large protein complexes. Besides, it also can be employed for searching latent regulatory exosites or analyzing of clinical high-throughput data on mutations.
A server for the prediction of allosteric and regulatory sites on protein structures. PARS queries protein dynamics and structural conservation to identify pockets that may exert a regulatory effect upon binding of a small-molecule ligand.
Provides an effective tool for the prediction of key residues that mediate the allosteric communication in an ensemble of pathways and functionally plausible residues. The centrality parameters also provided by the MCPath server labels the plausible functional regions of the structure, such as active sites or catalytic sites and also the regions with a role in allosteric communication.
Provides a user-friendly interface to predict the binding affinities of allosteric ligand-protein interactions. Furthermore, critical energy contributions that contribute to allosteric binding are offered. Alloscore exhibits prominent performance in describing allosteric binding and could be useful in allosteric virtual screening and the structural optimization of allosteric agonists/antagonists.
A computational method that predicts a pathway of residues that mediate protein allosteric communication. The pathway is predicted using only a combination of distance constraints between contiguous residues and evolutionary data. AlloPathFinder provides a simple, computationally efficient means of predicting a set of residues that mediate allosteric communication.