New algorithm to model protein-protein recognition based on surface complementarity: Applications to antibody-antigen docking
PH Walls, MJE Sternberg - Journal of molecular biology, 1992 - Elsevier
A novel algorithm is presented which models protein-protein interactions using surface
complementarity. The method is applied to antibody-antigen docking. A steric scoring …
complementarity. The method is applied to antibody-antigen docking. A steric scoring …
Shape complementarity at protein–protein interfaces
R Norel, SL Lin, HJ Wolfson… - … : Original Research on …, 1994 - Wiley Online Library
A matching algorithm using surface complementarity between receptor and ligand protein
molecules is outlined. The molecular surfaces are represented by “critical points,” describing …
molecules is outlined. The molecular surfaces are represented by “critical points,” describing …
Protein docking for low-resolution structures
IA Vakser - Protein Engineering, Design and Selection, 1995 - academic.oup.com
A typical problem for a docking procedure is how to match two molecules with known 3-D
structure so as to predict the configuration of their complex. A very serious obstacle to …
structure so as to predict the configuration of their complex. A very serious obstacle to …
Protein‐protein recognition analyzed by docking simulation
J Cherfils, S Duquerroy, J Janin - Proteins: Structure, Function …, 1991 - Wiley Online Library
Antibody–lysozyme and protease–inhibitor complexes are reconstituted by docking
lysozyme as a rigid body onto the combining site of the antibodies and the inhibitors onto the …
lysozyme as a rigid body onto the combining site of the antibodies and the inhibitors onto the …
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
A comprehensive docking study was performed on 27 distinct protein‐protein complexes.
For 13 test systems, docking was performed with the unbound X‐ray structures of both the …
For 13 test systems, docking was performed with the unbound X‐ray structures of both the …
PUZZLE: a new method for automated protein docking based on surface shape complementarity
M Helmer-Citterich, A Tramontano - Journal of molecular biology, 1994 - Elsevier
We describe here a novel procedure for automated protein docking, based only on
geometric criteria. In our algorithm we project protein surfaces into bi-dimensional matrices; …
geometric criteria. In our algorithm we project protein surfaces into bi-dimensional matrices; …
Protein docking algorithms: simulating molecular recognition
J Cherfils, J Janin - Current Opinion in Structural Biology, 1993 - Elsevier
Docking algorithms simulate protein-protein association in molecular assemblies such as
protease-inhibitor or antigen-antibody complexes by reconstituting the complexes from their …
protease-inhibitor or antigen-antibody complexes by reconstituting the complexes from their …
Rapid refinement of protein interfaces incorporating solvation: application to the docking problem
RM Jackson, HA Gabb, MJE Sternberg - Journal of molecular biology, 1998 - Elsevier
A computationally tractable strategy has been developed to refine protein-protein interfaces
that models the effects of side-chain conformational change, solvation and limited rigid-body …
that models the effects of side-chain conformational change, solvation and limited rigid-body …
Molecular docking using surface complementarity
A method is described to dock a ligand into a binding site in a protein on the basis of the
complementarity of the inter‐molecular atomic contacts. Docking is performed by …
complementarity of the inter‐molecular atomic contacts. Docking is performed by …
Physicochemical and residue conservation calculations to improve the ranking of protein–protein docking solutions
Many protein–protein docking algorithms generate numerous possible complex structures
with only a few of them resembling the native structure. The major challenge is choosing the …
with only a few of them resembling the native structure. The major challenge is choosing the …