Abstract:
:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Jendele L,Krivak R,Skoda P,Novotny M,Hoksza Ddoi
10.1093/nar/gkz424subject
Has Abstractpub_date
2019-07-02 00:00:00pages
W345-W349issue
W1eissn
0305-1048issn
1362-4962pii
5494740journal_volume
47pub_type
杂志文章abstract::The binding of anti poly(I). poly (C) Fab fragments to double or triple stranded polynucletides has been studied by fluorescence. Association constants were deduced from competition experiments. The comparison of the association constants leads to the conclusion that several atoms of the base residues do not interact ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.12.3337
更新日期:1976-12-01 00:00:00
abstract::Gramene (http://www.gramene.org) is a knowledgebase for comparative functional analysis in major crops and model plant species. The current release, #54, includes over 1.7 million genes from 44 reference genomes, most of which were organized into 62,367 gene families through orthologous and paralogous gene classificat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1111
更新日期:2018-01-04 00:00:00
abstract::The DNA sequences at and around the junctions between viral and cellular DNA in the polyoma virus transformed mouse cell line, TS-A-3T3, have been determined. No common sequence specificity or structural features at the joins have been observed. The sequence indicates that the 94K truncated large T antigen found in TS...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.15.4515
更新日期:1982-08-11 00:00:00
abstract::We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.17.8603
更新日期:1988-09-12 00:00:00
abstract::Translational repression (TR) plays an important role in post-transcriptional regulation of gene expression and embryonic development in metazoans. TR also regulates the expression of a subset of the cytoplasmic mRNA population during development of fertilized female gametes of the unicellular malaria parasite, Plasmo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1142
更新日期:2008-03-01 00:00:00
abstract::The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11-Rad50-Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Ra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1203
更新日期:2020-03-18 00:00:00
abstract::microRNAs (miRNAs) are small endogenous RNA molecules that are implicated in many biological processes through post-transcriptional regulation of gene expression. The DIANA-microT Web server provides a user-friendly interface for comprehensive computational analysis of miRNA targets in human and mouse. The server has ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr294
更新日期:2011-07-01 00:00:00
abstract::The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of 17,929 in release 32.0. New additions have been coupled with efforts to improve existing families, including refinement of domain boundaries, their classification into Pfa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky995
更新日期:2019-01-08 00:00:00
abstract::During the splicing process, spliceosomal snRNAs undergo numerous conformational rearrangements that appear to be catalyzed by proteins belonging to the DEAD/H-box superfamily of RNA helicases. We have cloned a new RNA helicase gene, designated DBP2 (DEAH-boxprotein), homologous to the Schizosaccaromyces pombe cdc28(+...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.9.2063
更新日期:1998-05-01 00:00:00
abstract::Transcriptional co-activator LEDGF/p75 is the major cellular interactor of HIV-1 integrase (IN), critical to efficient viral replication. In this work, a series of INs from the Betaretrovirus, Gammaretrovirus, Deltaretrovirus, Spumavirus and Lentivirus retroviral genera were tested for interaction with the host factor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl885
更新日期:2007-01-01 00:00:00
abstract::Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindere...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp248
更新日期:2009-06-01 00:00:00
abstract::Mitochondrial aprataxin (APTX) protects the mitochondrial genome from the consequence of ligase failure by removing the abortive ligation product, i.e. the 5'-adenylate (5'-AMP) group, during DNA replication and repair. In the absence of APTX activity, blocked base excision repair (BER) intermediates containing the 5'...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx654
更新日期:2017-09-29 00:00:00
abstract::The R-Coffee web server produces highly accurate multiple alignments of noncoding RNA (ncRNA) sequences, taking into account predicted secondary structures. R-Coffee uses a novel algorithm recently incorporated in the T-Coffee package. R-Coffee works along the same lines as T-Coffee: it uses pairwise or multiple seque...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn278
更新日期:2008-07-01 00:00:00
abstract::A problem in EST clustering is the presence of repeat sequences. To avoid false matches, repeats have to be masked. This can be a time-consuming process, and it depends on available repeat libraries. We present a fast and effective method that aims to eliminate the problems repeats cause in the process of clustering. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki511
更新日期:2005-04-14 00:00:00
abstract::To investigate the mechanisms by which oligonucleotides hybridize to target molecules, the binding of two oligodeoxynucleotide probes to RNA targets was measured over a broad range of temperatures. Mutations were then scanned across each DNA/RNA hybrid to map, at single base resolution, sequences important for hybridi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn134
更新日期:2008-05-01 00:00:00
abstract::The Pk-rec gene, encoding a RecA/RAD51 homologue from the hyperthermophilic archaeon Pyrococcussp. KOD1, was expressed in Escherichia coli. The recombinant Pk-REC was purified to homogeneity and was shown to be in a dimeric form. A striking property of the purified recombinant Pk-REC was the unusual DNase activity on ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.719
更新日期:1997-02-15 00:00:00
abstract::Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.92
更新日期:1996-01-01 00:00:00
abstract::As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.3233
更新日期:1992-06-25 00:00:00
abstract::Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1146
更新日期:2018-01-25 00:00:00
abstract::We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4960
更新日期:1998-11-01 00:00:00
abstract::MLL, the trithorax ortholog, is a well-characterized histone 3 lysine 4 methyltransferase that is crucial for proper regulation of the Hox genes during embryonic development. Chromosomal translocations, disrupting the Mll gene, lead to aggressive leukemia with poor prognosis. However, the functions of MLL in cellular ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku458
更新日期:2014-07-01 00:00:00
abstract::The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm800
更新日期:2008-01-01 00:00:00
abstract::Regulation of mRNA translation is an important mechanism determining the level of expression of proteins in eukaryotic cells. Translation is most commonly initiated by cap-dependent scanning, but many eukaryotic mRNAs contain internal ribosome entry segments (IRESs), providing an alternative means of initiation capabl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp623
更新日期:2009-09-01 00:00:00
abstract::The high-mobility-group A2 protein (HMGA2) plays important functional roles in transcriptional regulation, DNA replication and chromatin structure. In this study, the effect of histone deacetylase inhibition on the transcriptional activity of the Hmga2 gene was investigated in vivo both at the endogenous gene level an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg403
更新日期:2003-06-15 00:00:00
abstract::Using two primers corresponding to helix 1 and helix 3 regions in the homeodomain, we subjected genomic DNA from Caenorhabditis elegans to amplification by the polymerase chain reaction. Sequence analysis of the amplified products revealed a new homeobox-containing gene, designated ceh-19. This gene was located betwee...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.2967
更新日期:1992-06-25 00:00:00
abstract::Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to creat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky255
更新日期:2018-07-27 00:00:00
abstract::The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq834
更新日期:2011-01-01 00:00:00
abstract::In order to study the effects of DNA structure on cellular processes such as transcription, we have made a series of plasmids that locate several different kinds of DNA structure (stiff, flexible or curved) near the sites of cleavage by commonly-used restriction enzymes. One can use these plasmids to place any DNA reg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.22.9447
更新日期:1989-11-25 00:00:00
abstract::Controller (C) proteins regulate the timing of the expression of restriction and modification (R-M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn448
更新日期:2008-08-01 00:00:00
abstract::At the DNA/RNA level, biological signals are defined by a combination of spatial structures and sequence motifs. Until now, few attempts had been made in writing general purpose search programs that take into account both sequence and structure criteria. Indeed, the most successful structure scanning programs are usua...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.8.1395
更新日期:1996-04-15 00:00:00