ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

Bioinformatics (Oxford, England) - Tập 30 Số 12 - Trang 1771-1773 - 2014
Brian G. Pierce1, Kevin Wiehe1, Bong‐Hyun Kim1, Thom Vreven1, Zhiping Weng1
11 Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605 and 2Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA 02215 USA

Tóm tắt

Abstract Summary: Protein–protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein–protein complexes and symmetric multimers. With a goal of providing an accessible and intuitive interface, we provide options for users to guide the scoring and the selection of output models, in addition to dynamic visualization of input structures and output docking models. This server enables the research community to easily and quickly produce structural models of protein–protein complexes and symmetric multimers for their own analysis. Availability: The ZDOCK server is freely available to all academic and non-profit users at: http://zdock.umassmed.edu. No registration is required. Contact:  [email protected] or [email protected]

Từ khóa


Tài liệu tham khảo

Chen, 2002, Docking unbound proteins using shape complementarity, desolvation, and electrostatics, Proteins, 47, 281, 10.1002/prot.10092

Comeau, 2004, ClusPro: a fully automated algorithm for protein-protein docking, Nucleic Acids Res., 32, W96, 10.1093/nar/gkh354

Hwang, 2010, Performance of ZDOCK and ZRANK in CAPRI rounds 13-19, Proteins, 78, 3104, 10.1002/prot.22764

Hwang, 2010, Protein-protein docking benchmark version 4.0, Proteins, 78, 3111, 10.1002/prot.22830

Lyskov, 2008, The RosettaDock server for local protein-protein docking, Nucleic Acids Res., 36, W233, 10.1093/nar/gkn216

Mashiach, 2010, FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking, Nucleic Acids Res., 38, W457, 10.1093/nar/gkq373

Pierce, 2005, M-ZDOCK: a grid-based approach for Cn symmetric multimer docking, Bioinformatics, 21, 1472, 10.1093/bioinformatics/bti229

Pierce, 2011, Accelerating protein docking in ZDOCK using an advanced 3D convolution library, PLoS One, 6, e24657, 10.1371/journal.pone.0024657

Ritchie, 2010, Ultra-fast FFT protein docking on graphics processors, Bioinformatics, 26, 2398, 10.1093/bioinformatics/btq444

Rose, 2011, The RCSB Protein Data Bank: redesigned web site and web services, Nucleic Acids Res., 39, D392, 10.1093/nar/gkq1021

Schneidman-Duhovny, 2005, PatchDock and SymmDock: servers for rigid and symmetric docking, Nucleic Acids Res., 33, W363, 10.1093/nar/gki481

Torchala, 2013, SwarmDock: a server for flexible protein-protein docking, Bioinformatics, 29, 807, 10.1093/bioinformatics/btt038

Tovchigrechko, 2006, GRAMM-X public web server for protein-protein docking, Nucleic Acids Res., 34, W310, 10.1093/nar/gkl206

Vreven, 2013, Performance of ZDOCK in CAPRI rounds 20-26, Proteins, 81, 2175, 10.1002/prot.24432

Wiehe, 2005, ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5, Proteins, 60, 207, 10.1002/prot.20559

Wiehe, 2007, The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI, Proteins, 69, 719, 10.1002/prot.21747

Thông tin
Thông tin xuất bản

Bioinformatics (Oxford, England)

Tập 30 Số 12

1771-1773

Thông tin tác giả