Abstract：
:The webPDBinder (http://pdbinder.bio.uniroma2.it/PDBinder) is a web server for the identification of small ligand-binding sites in a protein structure. webPDBinder searches a protein structure against a library of known binding sites and a collection of control non-binding pockets. The number of similarities identified with the residues in the two sets is then used to derive a propensity value for each residue of the query protein associated to the likelihood that the residue is part of a ligand binding site. The predicted binding residues can be further refined using conservation scores derived from the multiple alignment of the PFAM protein family. webPDBinder correctly identifies residues belonging to the binding site in 77% of the cases and is able to identify binding pockets starting from holo or apo structures with comparable performances. This is important for all the real world cases where the query protein has been crystallized without a ligand and is also difficult to obtain clear similarities with bound pockets from holo pocket libraries. The input is either a PDB code or a user-submitted structure. The output is a list of predicted binding pocket residues with propensity and conservation values both in text and graphical format.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bianchi V,Mangone I,Ferrè F,Helmer-Citterich M,Ausiello Gdoi
10.1093/nar/gkt457subject
Has Abstractpub_date
2013-07-01 00:00:00pages
W308-13issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkt457journal_volume
41pub_type
杂志文章abstract：:Sae2 cooperates with the Mre11-Rad50-Xrs2 (MRX) complex to initiate resection of DNA double-strand breaks (DSBs) and to maintain the DSB ends in close proximity to allow their repair. How these diverse MRX-Sae2 functions contribute to DNA damage resistance is not known. Here, we describe mre11 alleles that suppress th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky086
更新日期：2018-04-06 00:00:00
abstract：:Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.20.9631
更新日期：1988-10-25 00:00:00
abstract：:Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky386
更新日期：2018-06-20 00:00:00
abstract：:Overexpression of the flap endonuclease FEN1 has been observed in a variety of cancer types and is a marker for poor prognosis. To better understand the cellular consequences of FEN1 overexpression we utilized a model of its Saccharomyces cerevisiae homolog, RAD27. In this system, we discovered that flap endonuclease ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky313
更新日期：2018-06-20 00:00:00
abstract：:In plant organelles, RNA editing alters specific cytidine residues to uridine in transcripts. All of the site-specificity factors of RNA editing identified so far are pentatricopeptide repeat (PPR) proteins. A defect in a specific PPR protein often impairs RNA editing at multiple sites, at which the cis-acting element...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks164
更新日期：2012-06-01 00:00:00
abstract：:Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1171
更新日期：2019-02-20 00:00:00
abstract：:Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and acces...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1358
更新日期：2017-05-19 00:00:00
abstract：:Most type II restriction-modification (R-M) systems produce separate endonuclease (REase) and methyltransferase (MTase) proteins. After R-M genes enter a new cell, MTase activity must appear before REase or the host chromosome will be cleaved. Temporal control of these genes thus has life-or-death consequences. PvuII ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1010
更新日期：2009-02-01 00:00:00
abstract：:DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz837
更新日期：2019-12-02 00:00:00
abstract：:In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm697
更新日期：2008-01-01 00:00:00
abstract：:Large-scale cooperative helix opening has been previously observed in A + T rich sequences contained in supercoiled DNA molecules at elevated temperatures. Since it is well known that helix melting of linear DNA is suppressed by addition of salt, we have investigated the effects of added salts on opening transitions i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.11.2042
更新日期：1994-06-11 00:00:00
abstract：:Tomato golden mosaic geminivirus has a genome of two single-stranded (ss) DNA components, A and B. An almost identical 'common' region in DNA A and DNA B is thought to contain sequence elements controlling replication and transcription. Hence investigation of sequences important for DNA replication by in vitro mutagen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.24.10213
更新日期：1989-12-25 00:00:00
abstract：:MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.1.242
更新日期：1996-01-01 00:00:00
abstract：:Thermophilic viruses represent a novel source of genetic material and enzymes with great potential for use in biotechnology. We have isolated a number of thermophilic viruses from geothermal areas in Iceland, and by combining high throughput genome sequencing and state of the art bioinformatics we have identified a nu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg914
更新日期：2003-12-15 00:00:00
abstract：:The majority of genome-wide association study (GWAS) risk variants reside in non-coding DNA sequences. Understanding how these sequence modifications lead to transcriptional alterations and cell-to-cell variability can help unraveling genotype-phenotype relationships. Here, we describe a computational method, dubbed C...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1263
更新日期：2017-03-17 00:00:00
abstract：:The cDNA of human DNA polymerase delta was cloned. The cDNA had a length of 3.5 kb and encoded a protein of 1107 amino acid residues with a calculated molecular mass of 124 kDa. Northern blot analysis showed that the cDNA hybridized to a mRNA of 3.4 kb. Monoclonal and polyclonal antibodies to the C-terminal 20 residue...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.4.735
更新日期：1992-02-25 00:00:00
abstract：:Properties of a mutant bacteriophage T2 DNA [N:(6)-adenine] methyltransferase (T2 Dam MTase) have been investigated for its potential utilization in RecA-assisted restriction endonuclease (RARE) cleavage. Steady-state kinetic analyses with oligonucleotide duplexes revealed that, compared to wild-type T4 Dam, both wild...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.7.1484
更新日期：2001-04-01 00:00:00
abstract：:The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1178
更新日期：2012-01-01 00:00:00
abstract：:Aberrant CpG methylation changes occurring during tumour progression include the loss (hypomethylation) and gain (hypermethylation) of methyl groups. Techniques currently available for examining such changes either require selection of a region, then examination of methylation changes, or utilise methylation-sensitive...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.24.e123
更新日期：2001-12-15 00:00:00
abstract：:The side chains of the 20 types of amino acids, owing to a large extent to their different physical properties, have characteristic distributions in interior/surface regions of individual proteins and in interface/non-interface portions of protein surfaces that bind proteins or nucleic acids. These distributions have ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm231
更新日期：2007-07-01 00:00:00
abstract：:The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr914
更新日期：2012-01-01 00:00:00
abstract：:Tetrahymena thermophila mitochondrial DNA is a linear molecule with two tRNAs, large subunit beta (LSU beta) rRNA (21S rRNA) and LSU alpha rRNA (5.8S-like RNA) encoded near each terminus. The DNA sequence of approximately 550 bp of this region was determined in six species of Tetrahymena. In three species the LSU beta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.1.327
更新日期：1988-01-11 00:00:00
abstract：:We have developed an improved and rapid genomic engineering procedure for the construction of custom-designed microorganisms. This method, which can be performed in 2 days, permits restructuring of the Escherichia coli genome via markerless deletion of selected genomic regions. The deletion process was mediated by a s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn359
更新日期：2008-08-01 00:00:00
abstract：:The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.2.555
更新日期：1988-01-25 00:00:00
abstract：:The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1316
更新日期：2013-02-01 00:00:00
abstract：:The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.3.459
更新日期：1990-02-11 00:00:00
abstract：:Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm854
更新日期：2008-01-01 00:00:00
abstract：:Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw454
更新日期：2016-07-08 00:00:00
abstract：:A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3813
更新日期：1990-07-11 00:00:00
abstract：:Histone post-translational modifications regulate chromatin structure and function largely through interactions with effector proteins that often contain multiple histone-binding domains. PHF1 [plant homeodomain (PHD) finger protein 1], which contains two kinds of histone reader modules, a Tudor domain and two PHD fin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky461
更新日期：2018-07-27 00:00:00
