Abstract:
:Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schneidman-Duhovny D,Inbar Y,Nussinov R,Wolfson HJdoi
10.1093/nar/gki481keywords:
subject
Has Abstractpub_date
2005-07-01 00:00:00pages
W363-7issue
Web Server issueeissn
0305-1048issn
1362-4962pii
33/suppl_2/W363journal_volume
33pub_type
杂志文章abstract::Alternative splicing expands the coding capacity of metazoan genes, and it was largely genetic studies in the fruit-fly Drosophila melanogaster that established the principle that regulated alternative splicing results in tissue- and stage-specific protein isoforms with different functions in development. Alternative ...
journal_title:Nucleic acids research
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更新日期:2012-01-01 00:00:00
abstract::We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...
journal_title:Nucleic acids research
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doi:10.1093/nar/gki129
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abstract::The androgen receptor (AR) is a member of the nuclear hormone receptor family of transcription factors that plays a critical role in regulating expression of genes involved in prostate development and transformation. Upon hormone binding, the AR associates with numerous co-regulator proteins that regulate the activati...
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更新日期:2020-09-25 00:00:00
abstract::Accurate T-cell epitope prediction is a principal objective of computational vaccinology. As a service to the immunology and vaccinology communities at large, we have implemented, as a server on the World Wide Web, a partial least squares-based multivariate statistical approach to the quantitative prediction of peptid...
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abstract::Two factors are mainly responsible for the stability of the DNA double helix: base pairing between complementary strands and stacking between adjacent bases. By studying DNA molecules with solitary nicks and gaps we measure temperature and salt dependence of the stacking free energy of the DNA double helix. For the fi...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2006-01-31 00:00:00
abstract::DNA supercoiling is an important regulator of gene activity. The transmission of transcription-generated supercoiling wave along a DNA helix provides a way for a gene being transcribed to communicate with and regulate its neighboring genes. Currently, the dynamic behavior of supercoiling transmission remains unclear o...
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journal_title:Nucleic acids research
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更新日期:1994-10-11 00:00:00
abstract::The early DNa products of reverse transcription have been analyzed from reconstructed reactions containing avian myeloblastosis virus 35S RNA . tRNAtrp complex and highly purified reverse transcriptase. We describe conditions for the synthesis of genome-length complementary DNA and two discrete species of plus strand ...
journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt401
更新日期:2013-07-01 00:00:00
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journal_title:Nucleic acids research
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更新日期:1995-10-25 00:00:00
abstract::The DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) has been providing public data services for thirty years (since 1987). We are collecting nucleotide sequence data from researchers as a member of the International Nucleotide Sequence Database Collaboration (INSDC, http://www.insdc.org), in collaboration wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1001
更新日期:2017-01-04 00:00:00
abstract::7SK snRNA, an abundant RNA discovered in human nucleus, regulates transcription by RNA polymerase II (RNAPII). It sequesters and inhibits the transcription elongation factor P-TEFb which, by phosphorylation of RNAPII, switches transcription from initiation to processive elongation and relieves pauses of transcription....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq660
更新日期:2010-11-01 00:00:00
abstract::During culture, a chicken B cell line DT40 spontaneously mutates immunoglobulin (Ig) genes by gene conversion, which involves activation-induced cytidine deaminase (AID)-dependent homologous recombination of the variable (V) region gene with upstream pseudo-V genes. To explore whether this mutation mechanism can targe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj013
更新日期:2006-01-18 00:00:00
abstract::Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRN...
journal_title:Nucleic acids research
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doi:10.1093/nar/gky802
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abstract::Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ri...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkv566
更新日期:2015-07-13 00:00:00
abstract::A simple, reproducible affinity chromatography method has been adapted for separation of high molecular weight supercoiled circular molecules from mammalian cells. Electron microscopic analysis of EB viral DNA obtained by this method, from the non-producer Burkitt's lymphoma line Raji, revealed monomer-sized viral mol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.24.10345
更新日期:1987-12-23 00:00:00
abstract::The sequence requirements for specific and efficient transcription from the 16S/23S rRNA promoter of Sulfolobus shibatae were analysed by point mutations and by cassette mutations using an in vitro transcription system. The examination of the box A-containing distal promoter element (DPE) showed the great importance o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.20.5423
更新日期:1992-10-25 00:00:00
abstract::In Escherichia coli, the MnmEG complex modifies transfer RNAs (tRNAs) decoding NNA/NNG codons. MnmEG catalyzes two different modification reactions, which add an aminomethyl (nm) or carboxymethylaminomethyl (cmnm) group to position 5 of the anticodon wobble uridine using ammonium or glycine, respectively. In tRNA(cmnm...
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abstract::The sxy (tfoX) gene product is the central regulator of DNA uptake by naturally competent gamma-proteobacteria such as Haemophilus influenzae, Vibrio cholerae and probably Escherichia coli. However, the mechanisms regulating sxy gene expression are not understood despite being key to understanding the physiological ro...
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更新日期:1994-03-25 00:00:00
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更新日期:2018-09-28 00:00:00
abstract::DNA primer sets, labeled with two fluorescent dyes to exploit fluorescence energy transfer (ET), can be efficiently excited with a single laser line and emit strong fluorescence at distinctive wavelengths. Such ET primers are superior to single fluorophore-labeled primers for DNA sequencing and other multiple color-ba...
journal_title:Nucleic acids research
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更新日期:1996-03-15 00:00:00
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更新日期:2010-10-01 00:00:00
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更新日期:2019-09-05 00:00:00
abstract::Human thymine-DNA glycosylase (TDG) is well known to excise thymine and uracil from G.T and G.U mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. In this study, we characterized ...
journal_title:Nucleic acids research
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更新日期:2003-05-01 00:00:00
abstract::The environmental carcinogen benzo[a]pyrene (BP) is metabolized to reactive diol epoxides that bind to cellular DNA by predominantly forming N2-guanine adducts (G*). Mutation hotspots for these adducts are frequently found in 5'- ... GG ... dinucleotide sequences, but their origins are poorly understood. Here we used ...
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