FastContact: rapid estimate of contact and binding free energies

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

[1]  C. Camacho,et al.  Modeling side‐chains using molecular dynamics improve recognition of binding region in CAPRI targets , 2005, Proteins.

[2]  Stephen R Comeau,et al.  Performance of the first protein docking server ClusPro in CAPRI rounds 3–5 , 2005, Proteins.

[3]  David Baker,et al.  Protein–protein docking predictions for the CAPRI experiment , 2003, Proteins.

[4]  R. Abagyan,et al.  ICM‐DISCO docking by global energy optimization with fully flexible side‐chains , 2003, Proteins.

[5]  Peter Willett,et al.  GAPDOCK: A genetic algorithm approach to protein docking in CAPRI round 1 , 2003, Proteins.

[6]  S. Wodak,et al.  Assessment of blind predictions of protein–protein interactions: Current status of docking methods , 2003, Proteins.

[7]  Ruth Nussinov,et al.  Taking geometry to its edge: Fast unbound rigid (and hinge‐bent) docking , 2003, Proteins.

[8]  Z. Weng,et al.  ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.

[9]  Ludwig Krippahl,et al.  Modeling protein complexes with BiGGER , 2003, Proteins.

[10]  Sandor Vajda,et al.  CAPRI: A Critical Assessment of PRedicted Interactions , 2003, Proteins.

[11]  Julie C Mitchell,et al.  Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information , 2003, Proteins.

[12]  Efrat Ben-Zeev,et al.  Prediction of the unknown: Inspiring experience with the CAPRI experiment , 2003, Proteins.

[13]  Michael J E Sternberg,et al.  Evaluation of the 3D‐Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial , 2003, Proteins.

[14]  Carlos J Camacho,et al.  Successful discrimination of protein interactions , 2003, Proteins.

[15]  S Vajda,et al.  Dynamical view of the positions of key side chains in protein-protein recognition. , 2001, Biophysical journal.

[16]  S. Vajda,et al.  Scoring docked conformations generated by rigid‐body protein‐protein docking , 2000, Proteins.

[17]  S Vajda,et al.  Free energy landscapes of encounter complexes in protein-protein association. , 1999, Biophysical journal.

[18]  Charles DeLisi,et al.  Protein‐protein recognition: exploring the energy funnels near the binding sites , 1999, Proteins.

[19]  Roland L. Dunbrack,et al.  Bayesian statistical analysis of protein side‐chain rotamer preferences , 1997, Protein science : a publication of the Protein Society.

[20]  J L Cornette,et al.  Consistency in structural energetics of protein folding and peptide recognition , 1997, Protein science : a publication of the Protein Society.

[21]  W. C. Still,et al.  The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii , 1997 .

[22]  C. DeLisi,et al.  Determination of atomic desolvation energies from the structures of crystallized proteins. , 1997, Journal of molecular biology.

[23]  K. Sharp,et al.  Finite difference Poisson‐Boltzmann electrostatic calculations: Increased accuracy achieved by harmonic dielectric smoothing and charge antialiasing , 1997 .

[24]  C DeLisi,et al.  Computational determination of side chain specificity for pockets in class I MHC molecules. , 1996, Molecular immunology.

[25]  M. Karplus,et al.  A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .

[26]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[27]  Peter A. Kollman,et al.  FREE ENERGY CALCULATIONS : APPLICATIONS TO CHEMICAL AND BIOCHEMICAL PHENOMENA , 1993 .

[28]  R W Pickersgill,et al.  A rapid method of calculating charge-charge interaction energies in proteins. , 1988, Protein engineering.

[29]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[30]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[31]  Sandor Vajda,et al.  ClusPro: an automated docking and discrimination method for the prediction of protein complexes , 2004, Bioinform..

[32]  D. Ritchie,et al.  Evaluation of Protein Docking Predictions Using Hex 3.1 in CAPRI Rounds 1{2 , 2002 .

[33]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..