ANCHOR: a web server and database for analysis of protein–protein interaction binding pockets for drug discovery

By Lidio M. C. Meireles, Alexander S. Dömling, Carlos J. Camacho. 2010

111 citations recorded by the source corpus.

ANCHOR is a web-based tool whose aim is to facilitate the analysis of protein–protein interfaces with regard to its suitability for small molecule drug design. To this end, ANCHOR exploits the so-called anchor residues, i.e. amino acid side-chains deeply buried at protein–protein interfaces, to indicate possible druggable pockets to be targeted by small molecules. For a given protein–protein complex submitted by the user, ANCHOR calculates the change in solvent accessible surface area (ΔSASA) upon binding for each side-chain, along with an estimate of its contribution to the binding free energy. A Jmol-based tool allows the user to interactively visualize selected anchor residues in their pockets as well as the stereochemical properties of the surrounding region such as hydrogen bonding. ANCHOR includes a Protein Data Bank (PDB) wide database of pre-computed anchor residues from more than 30 000 PDB entries with at least two protein chains. The user can query according to amino acids, buried area (SASA), energy or keywords related to indication areas, e.g. oncogene or diabetes. This database provides a resource to rapidly assess protein–protein interactions for the suitability of small molecules or fragments with bioisostere anchor analogues as possible compounds for pharmaceutical intervention. ANCHOR web server and database are freely available at http://structure.pitt.edu/anchor.

Subfields: Computational Theory and Mathematics, Computer Vision and Pattern Recognition, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Glaucius Oliva
2. L. Ferreira
3. Ricardo N Dos Santos
4. Adriano Defini Andricopulo
5. Luca Pinzi
6. Giulio Rastelli

In Computer Vision and Pattern Recognition

1. Glaucius Oliva
2. Adriano Defini Andricopulo
3. L. Ferreira
4. Ricardo N Dos Santos

In Materials Chemistry

1. Glaucius Oliva
2. Adriano Defini Andricopulo
3. L. Ferreira
4. Ricardo N Dos Santos

In Molecular Biology

1. Glaucius Oliva
2. L. Ferreira
3. Ricardo N Dos Santos
4. Adriano Defini Andricopulo

Citations in the corpus

• Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “Strategies for detection of such binding sites and evaluation of their drugability have been implemented in several computational methodologies, among which one can highlight the freely available web-based tools Q-SiteFinder [120] and ANCHOR [121].”