Geometry-based flexible and symmetric protein docking

Dina Schneidman-Duhovny; Yuval Inbar; Ruth Nussinov; Haim J. Wolfson

doi:10.1002/prot.20562

Geometry-based flexible and symmetric protein docking

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

182 Scopus citations

Abstract

We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3-5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying C _n symmetry for any n in a matter of minutes on a desktop PC.

Original language	American English
Pages (from-to)	224-231
Number of pages	8
Journal	Proteins: Structure, Function and Genetics
Volume	60
Issue number	2
DOIs	https://doi.org/10.1002/prot.20562
State	Published - 1 Aug 2005
Externally published	Yes

Keywords

CAPRI
FlexDock
Flexible docking
Patchdock
SymmDock
Symmetric docking
Unbound docking

Access to Document

10.1002/prot.20562

Cite this

@article{6c8ffeb138f841139bfb65fafdc4c7d6,

title = "Geometry-based flexible and symmetric protein docking",

abstract = "We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3-5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying C n symmetry for any n in a matter of minutes on a desktop PC.",

keywords = "CAPRI, FlexDock, Flexible docking, Patchdock, SymmDock, Symmetric docking, Unbound docking",

author = "Dina Schneidman-Duhovny and Yuval Inbar and Ruth Nussinov and Wolfson, {Haim J.}",

year = "2005",

month = aug,

day = "1",

doi = "10.1002/prot.20562",

language = "American English",

volume = "60",

pages = "224--231",

journal = "Proteins: Structure, Function and Genetics",

issn = "0887-3585",

publisher = "Wiley-Liss Inc.",

number = "2",

}

TY - JOUR

T1 - Geometry-based flexible and symmetric protein docking

AU - Schneidman-Duhovny, Dina

AU - Inbar, Yuval

AU - Nussinov, Ruth

AU - Wolfson, Haim J.

PY - 2005/8/1

Y1 - 2005/8/1

N2 - We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3-5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying C n symmetry for any n in a matter of minutes on a desktop PC.

AB - We present a set of geometric docking algorithms for rigid, flexible, and cyclic symmetry docking. The algorithms are highly efficient and have demonstrated very good performance in CAPRI Rounds 3-5. The flexible docking algorithm, FlexDock, is unique in its ability to handle any number of hinges in the flexible molecule, without degradation in run-time performance, as compared to rigid docking. The algorithm for reconstruction of cyclically symmetric complexes successfully assembles multimolecular complexes satisfying C n symmetry for any n in a matter of minutes on a desktop PC.

KW - CAPRI

KW - FlexDock

KW - Flexible docking

KW - Patchdock

KW - SymmDock

KW - Symmetric docking

KW - Unbound docking

UR - http://www.scopus.com/inward/record.url?scp=21644463278&partnerID=8YFLogxK

U2 - 10.1002/prot.20562

DO - 10.1002/prot.20562

M3 - Article

C2 - 15981269

AN - SCOPUS:21644463278

SN - 0887-3585

VL - 60

SP - 224

EP - 231

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

IS - 2

ER -

Geometry-based flexible and symmetric protein docking

Abstract

Keywords

Access to Document

Other files and links

Fingerprint

Cite this