FastContact: rapid estimate of contact and binding free energies

By Carlos J. Camacho. 2005

129 citations recorded by the source corpus.

UNLABELLED Interaction free energies are crucial for analyzing binding propensities in proteins. Although the problem of computing binding free energies remains open, approximate estimates have become very useful for filtering potential binding complexes. We report on the implementation of a fast computational estimate of the binding free energy based on a statistically determined desolvation contact potential and Coulomb electrostatics with a distance-dependent dielectric constant, and validated in the Critical Assessment of PRotein Interactions experiment. The application also reports residue contact free energies that rapidly highlight the hotspots of the interaction. AVAILABILITY The program was written in Fortran. The executable and full documentation is freely available at http://structure.pitt.edu/software/FastContact

Subfields: Materials Chemistry, Molecular Biology, Physical and Theoretical Chemistry, Computational Chemistry & Drug Discovery

How researchers see this paper

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

In Materials Chemistry

1. Glaucius Oliva
2. Adriano Defini Andricopulo
3. L. Ferreira
4. Ricardo N Dos Santos
5. Lidio M. C. Meireles
6. Alexander S. Dömling
7. Carlos J. Camacho

In Molecular Biology

1. Glaucius Oliva
2. L. Ferreira
3. Ricardo N Dos Santos
4. Adriano Defini Andricopulo
5. Lidio M. C. Meireles
6. Alexander S. Dömling
7. Carlos J. Camacho

In Physical and Theoretical Chemistry

1. Lidio M. C. Meireles
2. Alexander S. Dömling
3. Glaucius Oliva
4. Adriano Defini Andricopulo
5. L. Ferreira
6. Ricardo N Dos Santos

In Computational Chemistry & Drug Discovery

1. Lidio M. C. Meireles
2. Alexander S. Dömling
3. L. Ferreira
4. Glaucius Oliva
5. Ricardo N Dos Santos
6. Adriano Defini Andricopulo
7. Carlos J. Camacho
8. Giulio Rastelli

Citations in the corpus

• Molecular Docking and Structure-Based Drug Design Strategies (2015, methodology): “For a particular PPI interface, the method calculates the change in the solvent accessible surface area ( Δ SASA) upon binding, for each amino acid side-chain, as well as a measure of their contribution to the total interaction free energy [122].”
• ANCHOR: a web server and database for analysis of protein–protein interaction binding pockets for drug discovery (2010, methodology): “For a given protein–protein complex submitted by the user, ANCHOR calculates the change in solvent accessible surface area ( SASA) upon binding for each side-chain, along with an estimate of its contribution to the binding free energy (19,20).”