Abstract：
:Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yan Y,Zhang D,Zhou P,Li B,Huang SYdoi
10.1093/nar/gkx407subject
Has Abstractpub_date
2017-07-03 00:00:00pages
W365-W373issue
W1eissn
0305-1048issn
1362-4962pii
3829194journal_volume
45pub_type
杂志文章abstract：:The aminoacylation kinetics of T7 transcripts representing defined regions of Escherichia coli serine tRNAs were determined using purified E.coli seryl-tRNA synthetase (SerRS) and the kinetic values were used to estimate the relative contribution of various tRNA(Ser) domains to recognition by SerRS. The analysis revea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.19.4467
更新日期：1993-09-25 00:00:00
abstract：:Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purifie...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.4.787
更新日期：1997-02-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1088
更新日期：2015-01-01 00:00:00
abstract：:The human lymphoid cell lines Walker and Daudi constitute a particularly suitable system for studies on the chromatin structure of K light chain genes (see preceding paper). The rearranged and non-rearranged alleles of Walker cells were found to be about equally sensitive towards digestion with DNAase I. A DNAase I hy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.18.7007
更新日期：1984-09-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.15.6091
更新日期：1987-08-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky010
更新日期：2018-02-28 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.8.1516
更新日期：1997-04-15 00:00:00
abstract：:Superhelical PM2 DNA can be photochemically modified by u.v. irradiation. The variation of S20,w with dose shows the following characteristics. There is a linear increase from 28 to 31s produced by a low dose of u.v. irradiation (4,000 ergs/mm2). A plateau in S20,w occurs between 4,000 and 10,000 ergs/mm2. The S20,w t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1243
更新日期：1977-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw447
更新日期：2016-08-19 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni143
更新日期：2005-10-06 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9527
更新日期：1988-10-25 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm088
更新日期：2007-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.2.318
更新日期：1997-01-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz246
更新日期：2019-05-21 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2015-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.11.4037
更新日期：1977-11-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1214
更新日期：2013-02-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2018-09-06 00:00:00
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journal_title：Nucleic acids research
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更新日期：2009-09-01 00:00:00
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journal_title：Nucleic acids research
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doi：10.1093/nar/gkh400
更新日期：2004-07-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2005-10-27 00:00:00
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pub_type： 杂志文章
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更新日期：2019-01-10 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2017-05-19 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg510
更新日期：2003-07-01 00:00:00
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journal_title：Nucleic acids research
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更新日期：2008-01-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
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更新日期：2020-11-04 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.22.5067
更新日期：1993-11-11 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.12.2511
更新日期：1999-06-15 00:00:00
