Coarse and Reliable Geometric Alignment for Protein Docking

We present an efficient algorithm for generating a small set of coarse alignments between interacting proteins using meaningful features on their surfaces. The proteins are treated as rigid bodies, but the results are more generally useful as the produced configurations can serve as input to local improvement algorithms that allow for protein flexibility. We apply our algorithm to a diverse set of protein complexes from the Protein Data Bank, demonstrating the effectivity of our algorithm, both for bound and for unbound protein docking problems.

[1]  Ruth Nussinov,et al.  A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility , 1998, J. Comput. Biol..

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

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

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

[5]  Herbert Edelsbrunner,et al.  Local Search Heuristic for Rigid Protein Docking , 2004, WABI.

[6]  R. Nussinov,et al.  A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.

[7]  Hans-Peter Lenhof.  An algorithm for the protein docking problem , 1995 .

[8]  M. Sternberg,et al.  Modelling protein docking using shape complementarity, electrostatics and biochemical information. , 1997, Journal of molecular biology.

[9]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[10]  H. Edelsbrunner,et al.  Accurate Protein Docking by Shape Complementarity Alone , 2022 .

[11]  M. L. Connolly.  Shape complementarity at the hemoglobin α1β1 subunit interface , 1986 .

[12]  M. Sternberg,et al.  Modelling Protein–Protein and Protein–DNA Docking , 2004 .

[13]  Zhiping Weng,et al.  A protein–protein docking benchmark , 2003, Proteins.

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

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

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

[17]  Herbert Edelsbrunner,et al.  Extreme Elevation on a 2-Manifold , 2004, SCG '04.

[18]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[19]  Brian B. Goldman,et al.  QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock) , 2000, Proteins.

[20]  I. Vakser.  Protein docking for low-resolution structures. , 1995, Protein engineering.

[21]  Ho-Lun Cheng,et al.  Dynamic Skin Triangulation , 2001, SODA '01.