Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking

Raquel Norel, Shuo L. Lin, Haim J. Wolfson, Ruth Nussinov*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Rigid-body docking of two molecules involves matching of their surfaces. A successful docking methodology considers two key issues: molecular surface representation, and matching. While approaches to the problem differ, they all employ certain surface geometric features. While surface normals are routinely created with molecular surfaces, their employment has surprisingly been almost completely overlooked. Here we show how the normals to the surface, at specific, well placed points, can play a critical role in molecular docking. If the points for which the normals are calculated represent faithfully and accurately the molecular surfaces, the normals can substantially ameliorate the efficiency of the docking in a number of ways. The normals can drastically reduce the combinatorial complexity of the receptor-ligand docking. Furthermore, they can serve as a powerful filter in screening for quality docked conformations. Below we show how deploying such a straight forward device, which is easy to calculate, large protein-protein molecules are docked with unparalleled short times and with a manageable number of potential solutions. Considering the facts that here we dock (1) two large protein molecules, including several large immunoglobulin-lysozyme complexes; (2) that we use the entire molecular surfaces, without a predefinition of the active sites, or of the epitopes, of neither the ligand nor the receptor; that (3) the docking is completely automated, without any labelling, or pre-specification, of the input structural database, and (4) with a single set of parameters, without any further tuning whatsoever, such results are highly desirable. This approach is specifically geared towards matching of the surfaces of large protein molecules and is not applicable to small molecule drugs.

Original languageEnglish
Pages (from-to)263-273
Number of pages11
JournalJournal of Molecular Biology
Issue number2
StatePublished - 15 Sep 1995


FundersFunder number
U.S. Israel Binational Science Foundation
U.S. Department of Health and Human Services1-CO-74102, 91-00219
National Cancer Institute
United States-Israel Binational Science Foundation
Israel Academy of Sciences and Humanities
Israel Science Foundation


    • Docking
    • Molecular surface complementarity
    • Protein-protein recognition
    • Rigid-body matching
    • Surface normals


    Dive into the research topics of 'Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking'. Together they form a unique fingerprint.

    Cite this