The FSSP database: fold classification based on structure-structure alignment of proteins.

Abstract:

:The FSSP database presents a continuously updated classification of 3-D protein folds based on an all-against-all comparison of structures currently in the Protein Data Bank (PDB) [Bernstein et al. (1977) J. Mol. Biol., 112, 535- 542]. The database currently contains an extended structural family for each of 600 representative protein chains which have <25% mutual sequence identity. The results of the exhaustive pairwise structure comparisons are reported in the form of a fold tree generated by hierarchical clustering and as a series of structurally representative sets of folds at varying levels of uniqueness. For each query structure from the representative set, there is a database entry containing structure-structure alignments with its structural neighbours in the representative set and its sequence homologs in the PDB. All alignments are based purely on the 3-D co-ordinates of the proteins and are derived by an automatic structure comparison program (Dali). The FSSP database is accessible electronically on the World Wide Web and by anonymous ftp.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Holm L,Sander C

doi

10.1093/nar/24.1.206

subject

Has Abstract

pub_date

1996-01-01 00:00:00

pages

206-9

issue

1

eissn

0305-1048

issn

1362-4962

pii

5s1033

journal_volume

24

pub_type

杂志文章
  • BACH1 recruits NANOG and histone H3 lysine 4 methyltransferase MLL/SET1 complexes to regulate enhancer-promoter activity and maintains pluripotency.

    abstract::Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkab034

    authors: Niu C,Wang S,Guo J,Wei X,Jia M,Chen Z,Gong W,Qin Y,Wang X,Zhi X,Lu M,Chen S,Gu M,Zhang J,Han JJ,Lan F,Meng D

    更新日期:2021-01-27 00:00:00

  • NTDB: Thermodynamic Database for Nucleic Acids.

    abstract::A new thermodynamic database for normal and modified nucleic acids has been developed. This Thermodynamic Database for Nucleic Acids (NTDB) includes sequence, structure and thermodynamic information as well as experimental methods and conditions. In this release, there are 1851 sequences containing both normal and mod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.230

    authors: Chiu WL,Sze CN,Ip LN,Chan SK,Au-Yeung SC

    更新日期:2001-01-01 00:00:00

  • Antisense-induced ribosomal frameshifting.

    abstract::Programmed ribosomal frameshifting provides a mechanism to decode information located in two overlapping reading frames by diverting a proportion of translating ribosomes into a second open reading frame (ORF). The result is the production of two proteins: the product of standard translation from ORF1 and an ORF1-ORF2...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl531

    authors: Henderson CM,Anderson CB,Howard MT

    更新日期:2006-01-01 00:00:00

  • primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies.

    abstract::Primers4clades is an easy-to-use web server that implements a fully automatic PCR primer design pipeline for cross-species amplification of novel sequences from metagenomic DNA, or from uncharacterized organisms, belonging to user-specified phylogenetic clades or taxa. The server takes a set of non-aligned protein cod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp377

    authors: Contreras-Moreira B,Sachman-Ruiz B,Figueroa-Palacios I,Vinuesa P

    更新日期:2009-07-01 00:00:00

  • Malleable nature of mRNA-protein compositional complementarity and its functional significance.

    abstract::It has recently been demonstrated that nucleobase-density profiles of typical mRNA coding sequences exhibit a complementary relationship with nucleobase-interaction propensity profiles of their cognate protein sequences. This finding supports the idea that the genetic code developed in response to direct binding inter...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv166

    authors: Hlevnjak M,Zagrovic B

    更新日期:2015-03-31 00:00:00

  • Inversion of in situ synthesized oligonucleotides: improved reagents for hybridization and primer extension in DNA microarrays.

    abstract::Oligonucleotides synthesized in array format suffer from contamination by truncated species. We have developed a method to invert DNA molecules in situ after completed synthesis. Reactive functions at the 5'-ends of the oligonucleotides are permitted to react with functions on the support before the 3'-ends are releas...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.24.4710

    authors: Kwiatkowski M,Fredriksson S,Isaksson A,Nilsson M,Landegren U

    更新日期:1999-12-15 00:00:00

  • COMPASS server for remote homology inference.

    abstract::COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, CO...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm293

    authors: Sadreyev RI,Tang M,Kim BH,Grishin NV

    更新日期:2007-07-01 00:00:00

  • Decoding non-random mutational signatures at Cas9 targeted sites.

    abstract::The mutation patterns at Cas9 targeted sites contain unique information regarding the nuclease activity and repair mechanisms in mammalian cells. However, analytical framework for extracting such information are lacking. Here, we present a novel computational platform called Rational InDel Meta-Analysis (RIMA) that en...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky653

    authors: Taheri-Ghahfarokhi A,Taylor BJM,Nitsch R,Lundin A,Cavallo AL,Madeyski-Bengtson K,Karlsson F,Clausen M,Hicks R,Mayr LM,Bohlooly-Y M,Maresca M

    更新日期:2018-09-19 00:00:00

  • Synthesis and characterization of a ribavirin-3',5'-phosphate pentadecamer homoribopolymer bearing a 5'-amino tether group and a 3'-thymidine.

    abstract::The synthesis of a pentadecamer of the 5'-phosphate of the antiviral nucleoside ribavirin (1'-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide) has been achieved. This homoribopolymer is terminated at the 5'-position with an (6-aminohexyl)phosphate group to permit conjugation to a carrier and at the 3'-position by...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.5.1099

    authors: Dawson MI,Jina AN,Torkelson S,Rhee S,Moore M,Zarling DA,Hobbs PD

    更新日期:1990-03-11 00:00:00

  • Redox state of tumor suppressor p53 regulates its sequence-specific DNA binding in DNA-damaged cells by cysteine 277.

    abstract::Using a bio-oligo pull-down DNA-binding assay we investigated the binding capacity of endogenous, DNA damage-induced p53 in human diploid fibroblasts to several p53-responsive elements (REs) present in p53-regulated genes. During the course of p53 accumulation, we observed a decrease in p53 binding to the GADD45 but n...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/30.11.2340

    authors: Buzek J,Latonen L,Kurki S,Peltonen K,Laiho M

    更新日期:2002-06-01 00:00:00

  • Genomic organization and transcription of the alpha beta heat shock DNA in Drosophila melanogaster.

    abstract::Previous studies have shown that (i) several RNAs induced by heat shock of Drosophila melanogaster cells are homologous to tandemly repeated alpha beta units found in cloned segments of D. melanogaster DNA, and (ii) the alpha beta sequences are present both at a major heat shock locus, 87Cl, and the chromocenter of po...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.20.5297

    authors: Lis JT,Ish-Horowicz D,Pinchin SM

    更新日期:1981-10-24 00:00:00

  • Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element.

    abstract::Methylation of CpG motifs in DNA is involved in the control of gene expression and in several other epigenic effects. It suppresses also the immuno-stimulation properties of bacterial or viral DNAs that contain CPGS: However, effects of methylation on the DNA structure and dynamics are not clear. Here we carried out a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.11.2314

    authors: Derreumaux S,Chaoui M,Tevanian G,Fermandjian S

    更新日期:2001-06-01 00:00:00

  • Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae.

    abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky618

    authors: Iacovella MG,Bremang M,Basha O,Giacò L,Carotenuto W,Golfieri C,Szakal B,Dal Maschio M,Infantino V,Beznoussenko GV,Joseph CR,Visintin C,Mironov AA,Visintin R,Branzei D,Ferreira-Cerca S,Yeger-Lotem E,De Wulf P

    更新日期:2018-09-06 00:00:00

  • Using iodinated single-stranded M13 probes to facilitate rapid DNA sequence analysis--nucleotide sequence of a mouse lysine tRNA gene.

    abstract::From a recombinant lambda phage, we have determined a 387 bp sequence containing a mouse lysine tRNA gene. The putative lys tRNA (anticodon UUU) differs from rabbit liver lys tRNA at five positions. The flanking regions of the mouse gene are not generally homologous to published human and Drosophila lys tRNA genes. Ho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.7.2053

    authors: Han JH,Harding JD

    更新日期:1983-04-11 00:00:00

  • Independent parallel functions of p19 plant viral suppressor of RNA silencing required for effective suppressor activity.

    abstract::Plant viruses ubiquitously mediate the induction of miR168 trough the activities of viral suppressors of RNA silencing (VSRs) controlling the accumulation of ARGONAUTE1 (AGO1), one of the main components of RNA silencing based host defence system. Here we used a mutant Tombusvirus p19 VSR (p19-3M) disabled in its main...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt846

    authors: Várallyay É,Oláh E,Havelda Z

    更新日期:2014-01-01 00:00:00

  • MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis.

    abstract::Genomic meta-analysis to combine relevant and homogeneous studies has been widely applied, but the quality control (QC) and objective inclusion/exclusion criteria have been largely overlooked. Currently, the inclusion/exclusion criteria mostly depend on ad-hoc expert opinion or naïve threshold by sample size or platfo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr1071

    authors: Kang DD,Sibille E,Kaminski N,Tseng GC

    更新日期:2012-01-01 00:00:00

  • CEBS: a comprehensive annotated database of toxicological data.

    abstract::The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1077

    authors: Lea IA,Gong H,Paleja A,Rashid A,Fostel J

    更新日期:2017-01-04 00:00:00

  • High salt solution structure of a left-handed RNA double helix.

    abstract::Right-handed RNA duplexes of (CG)n sequence undergo salt-induced helicity reversal, forming left-handed RNA double helices (Z-RNA). In contrast to the thoroughly studied Z-DNA, no Z-RNA structure of natural origin is known. Here we report the NMR structure of a half-turn, left-handed RNA helix (CGCGCG)2 determined in ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh736

    authors: Popenda M,Milecki J,Adamiak RW

    更新日期:2004-08-03 00:00:00

  • Reverse genetics-based biochemical studies of the ribosomal exit tunnel constriction region in eukaryotic ribosome stalling: spatial allocation of the regulatory nascent peptide at the constriction.

    abstract::A number of regulatory nascent peptides have been shown to regulate gene expression by causing programmed ribosome stalling during translation. Nascent peptide emerges from the ribosome through the exit tunnel, and one-third of the way along which β-loop structures of ribosomal proteins uL4 and uL22 protrude into the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1190

    authors: Takamatsu S,Ohashi Y,Onoue N,Tajima Y,Imamichi T,Yonezawa S,Morimoto K,Onouchi H,Yamashita Y,Naito S

    更新日期:2020-02-28 00:00:00

  • DDBJ new system and service refactoring.

    abstract::The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1152

    authors: Ogasawara O,Mashima J,Kodama Y,Kaminuma E,Nakamura Y,Okubo K,Takagi T

    更新日期:2013-01-01 00:00:00

  • Structure of a Bacillus subtilis endo-beta-1,4-glucanase gene.

    abstract::The nucleotide sequence of the portion of a Bacillus subtilis (strain PAP115) 3 kb Pst I fragment which contains an endo-beta-1, 4-glucanase gene has been determined. This gene encodes a protein of 499 amino acid residues (Mr = 55,234) with a typical B. subtilis signal peptide. Escherichia coli which has been transfor...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.22.9159

    authors: MacKay RM,Lo A,Willick G,Zuker M,Baird S,Dove M,Moranelli F,Seligy V

    更新日期:1986-11-25 00:00:00

  • ComplexContact: a web server for inter-protein contact prediction using deep learning.

    abstract::ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky420

    authors: Zeng H,Wang S,Zhou T,Zhao F,Li X,Wu Q,Xu J

    更新日期:2018-07-02 00:00:00

  • High expression of functional adenovirus DNA polymerase and precursor terminal protein using recombinant vaccinia virus.

    abstract::Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.6.2431

    authors: Stunnenberg HG,Lange H,Philipson L,van Miltenburg RT,van der Vliet PC

    更新日期:1988-03-25 00:00:00

  • Crystal structure of a tick-borne flavivirus RNA-dependent RNA polymerase suggests a host adaptation hotspot in RNA viruses.

    abstract::The RNA-dependent RNA polymerases (RdRPs) encoded by RNA viruses represent a unique class of nucleic acid polymerases. RdRPs are essential in virus life cycle due to their central role in viral genome replication/transcription processes. However, their contribution in host adaption has not been well documented. By sol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa1250

    authors: Yang J,Jing X,Yi W,Li XD,Yao C,Zhang B,Zheng Z,Wang H,Gong P

    更新日期:2021-01-06 00:00:00

  • A directed evolution design of a GCG-specific DNA hemimethylase.

    abstract::DNA cytosine-5 methyltransferases (C5-MTases) are valuable models to study sequence-specific modification of DNA and are becoming increasingly important tools for biotechnology. Here we describe a structure-guided rational protein design combined with random mutagenesis and selection to change the specificity of the H...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp772

    authors: Gerasimaite R,Vilkaitis G,Klimasauskas S

    更新日期:2009-11-01 00:00:00

  • Metabolism of dITP in HeLa cell extracts, incorporation into DNA by isolated nuclei and release of hypoxanthine from DNA by a hypoxanthine-DNA glycosylase activity.

    abstract::dITP may be generated from dATP by a slow, nonenzymatic hydrolysis. While [3H]dITP was degraded rapidly to [3H]deoxyinosine by HeLa cell nuclear extracts, no net degradation of [3H]dITP was observed in the presence of physiological concentrations of ATP, apparently because the extract contained deoxynucleoside diphosp...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.12.3693

    authors: Myrnes B,Guddal PH,Krokan H

    更新日期:1982-06-25 00:00:00

  • Selected base sequence outside the target binding site of zinc finger protein Sp1.

    abstract::Human transcription factor Sp1 contains three contiguous repeats of the C2H2-type zinc finger motif and binds to the decanucleotide sequence 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3' (GC box). In order to determine whether the three-zinc finger peptide Sp1(530-623) has selectivity for sequence outside the GC box, we used a sel...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.24.4920

    authors: Nagaoka M,Shiraishi Y,Sugiura Y

    更新日期:2001-12-15 00:00:00

  • Improved thrombin binding aptamer by incorporation of a single unlocked nucleic acid monomer.

    abstract::A 15-mer DNA aptamer (named TBA) adopts a G-quadruplex structure that strongly inhibits fibrin-clot formation by binding to thrombin. We have performed thermodynamic analysis, binding affinity and biological activity studies of TBA variants modified by unlocked nucleic acid (UNA) monomers. UNA-U placed in position U3,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq823

    authors: Pasternak A,Hernandez FJ,Rasmussen LM,Vester B,Wengel J

    更新日期:2011-02-01 00:00:00

  • Enzyme-free optical DNA mapping of the human genome using competitive binding.

    abstract::Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM tradi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz489

    authors: Müller V,Dvirnas A,Andersson J,Singh V,Kk S,Johansson P,Ebenstein Y,Ambjörnsson T,Westerlund F

    更新日期:2019-09-05 00:00:00

  • Structural basis for uracil DNA glycosylase interaction with uracil: NMR study.

    abstract::Two dimensional (2D) NMR and molecular dynamics simulations have been used to determine the three dimensional (3D) structure of a hairpin DNA, d-CTA-GAGGATCC-TUTT-GGATCCT (22mer; abbreviated as U2-hairpin), which has uracil at the second position from the 5' end of the tetraloop. The(1)H resonances of this hairpin hav...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.9.1906

    authors: Ghosh M,Vinay Kumar N,Varshney U,Chary KV

    更新日期:2000-05-01 00:00:00