Guided docking: First step to locate potential binding sites

The long‐range electrostatic forces of the targets in round 2 of the Critical Assessment of PRediction of Interactions (CAPRI) experiment were examined and a simple guided docking method, based on these forces, was applied. The method described consists of calculating an initial rigid body trajectory and an optional final, fully flexible refinement stage. Although only limited success was found in predicting the final complexes, some interesting information was discovered. In particular, the long‐range forces seem to give some insight into the unusual binding mode of target 4 while raising some questions about target 7, which warrant further investigation. Proteins 2003;52:28–32. © 2003 Wiley‐Liss, Inc.

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

[2]  A. Llera,et al.  Structure‐function studies of T‐cell receptor‐superantigen interactions , 1998, Immunological reviews.

[3]  S Vajda,et al.  Kinetics of desolvation-mediated protein-protein binding. , 2000, Biophysical journal.

[4]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[5]  Hongmin Li,et al.  Crystal structure of a T-cell receptor β-chain complexed with a superantigen , 1996, Nature.

[6]  R. Abagyan,et al.  Soft protein–protein docking in internal coordinates , 2002, Protein science : a publication of the Protein Society.

[7]  Lode Wyns,et al.  Three Camelid VHH Domains in Complex with Porcine Pancreatic α-Amylase , 2002, The Journal of Biological Chemistry.

[8]  Marc A. Martí-Renom,et al.  EVA: continuous automatic evaluation of protein structure prediction servers , 2001, Bioinform..

[9]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[10]  Rebecca C Wade,et al.  Biomolecular diffusional association. , 2002, Current opinion in structural biology.

[11]  Sandor Vajda,et al.  Protein-protein association kinetics and protein docking. , 2002, Current Opinion in Structural Biology.

[12]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[13]  R. Mariuzza,et al.  Crystal structure of the beta chain of a T cell antigen receptor. , 1995, Science.

[14]  M. Sternberg,et al.  Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.

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

[16]  Hongmin Li,et al.  Structures of two streptococcal superantigens bound to TCR beta chains reveal diversity in the architecture of T cell signaling complexes. , 2002, Structure.

[17]  S. Vajda,et al.  Protein docking along smooth association pathways , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[18]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[19]  K. Acharya,et al.  Structural basis for the recognition of superantigen streptococcal pyrogenic exotoxin A (SpeA1) by MHC class II molecules and T‐cell receptors , 1999, The EMBO journal.

[20]  L. Wyns,et al.  Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology. , 2002, The Journal of biological chemistry.

[21]  R. Huber,et al.  Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics. , 1996, Journal of molecular biology.

[22]  M J Sternberg,et al.  Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM , 2001, Proteins.

[23]  B. A. Fields,et al.  Crystal structure of a T-cell receptor beta-chain complexed with a superantigen. , 1996, Nature.