CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures.

Abstract:

:Classical simulations of protein flexibility remain computationally expensive, especially for large proteins. A few years ago, we developed a fast method for predicting protein structure fluctuations that uses a single protein model as the input. The method has been made available as the CABS-flex web server and applied in numerous studies of protein structure-function relationships. Here, we present a major update of the CABS-flex web server to version 2.0. The new features include: extension of the method to significantly larger and multimeric proteins, customizable distance restraints and simulation parameters, contact maps and a new, enhanced web server interface. CABS-flex 2.0 is freely available at http://biocomp.chem.uw.edu.pl/CABSflex2.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Kuriata A,Gierut AM,Oleniecki T,Ciemny MP,Kolinski A,Kurcinski M,Kmiecik S

doi

10.1093/nar/gky356

subject

Has Abstract

pub_date

2018-07-02 00:00:00

pages

W338-W343

issue

W1

eissn

0305-1048

issn

1362-4962

pii

4995689

journal_volume

46

pub_type

杂志文章
  • Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.

    abstract::The methyltransferase, M.EcoKI, recognizes the DNA sequence 5'-AACNNNNNNGTGC-3' and methylates adenine at the underlined positions. DNA methylation has been shown by crystallography to occur via a base flipping mechanism and is believed to be a general mechanism for all methyltransferases. If no structure is available...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh531

    authors: Su TJ,Connolly BA,Darlington C,Mallin R,Dryden DT

    更新日期:2004-04-23 00:00:00

  • MitoMiner v3.1, an update on the mitochondrial proteomics database.

    abstract::Mitochondrial proteins remain the subject of intense research interest due to their implication in an increasing number of different conditions including mitochondrial and metabolic disease, cancer, and neuromuscular degenerative and age-related disorders. However, the mitochondrial proteome has yet to be accurately a...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1001

    authors: Smith AC,Robinson AJ

    更新日期:2016-01-04 00:00:00

  • Nucleotide sequence of the putative recognition site for coat protein in the RNAs of alfalfa mosaic virus and tobacco streak virus.

    abstract::The sequence of the 3'-terminal 180 and 140 nucleotides of RNAs 2 and 3, respectively, of tobacco streak virus (TSV) was deduced by reverse transcription in the presence of a specific primer and chain terminators. Homology between the two RNAs was found to be restricted to a 3-terminal region of about 45 nucleotides. ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/8.15.3307

    authors: Koper-Zwarthoff EC,Bol JF

    更新日期:1980-08-11 00:00:00

  • PARP10 promotes cellular proliferation and tumorigenesis by alleviating replication stress.

    abstract::During carcinogenesis, cells are exposed to increased replication stress due to replication fork arrest at sites of DNA lesions and difficult to replicate genomic regions. Efficient fork restart and DNA repair are important for cancer cell proliferation. We previously showed that the ADP-ribosyltransferase PARP10 inte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky658

    authors: Schleicher EM,Galvan AM,Imamura-Kawasawa Y,Moldovan GL,Nicolae CM

    更新日期:2018-09-28 00:00:00

  • Pol5 is required for recycling of small subunit biogenesis factors and for formation of the peptide exit tunnel of the large ribosomal subunit.

    abstract::More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkz1079

    authors: Braun CM,Hackert P,Schmid CE,Bohnsack MT,Bohnsack KE,Perez-Fernandez J

    更新日期:2020-01-10 00:00:00

  • RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information.

    abstract::RNA-protein complexes are essential in mediating important fundamental cellular processes, such as transport and localization. In particular, ncRNA-protein interactions play an important role in post-transcriptional gene regulation like mRNA localization, mRNA stabilization, poly-adenylation, splicing and translation....

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv020

    authors: Suresh V,Liu L,Adjeroh D,Zhou X

    更新日期:2015-02-18 00:00:00

  • Mutation detection using immobilized mismatch binding protein (MutS).

    abstract::An accurate and highly sensitive mutation detection assay has been developed. The assay is based on the detection of mispaired and unpaired bases by immobilized mismatch binding protein (Escherichia coli MutS). The assay can detect most mismatches and all single base substitution mutations, as well as small addition o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.19.3944

    authors: Wagner R,Debbie P,Radman M

    更新日期:1995-10-11 00:00:00

  • Distinct regions of RPB11 are required for heterodimerization with RPB3 in human and yeast RNA polymerase II.

    abstract::In Saccharomyces cerevisiae, RNA polymerase II assembly is probably initiated by the formation of the RPB3-RPB11 heterodimer. RPB3 is encoded by a single copy gene in the yeast, mouse and human genomes. The RPB11 gene is also unique in yeast and mouse, but in humans a gene family has been identified that potentially e...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki672

    authors: Benga WJ,Grandemange S,Shpakovski GV,Shematorova EK,Kedinger C,Vigneron M

    更新日期:2005-06-24 00:00:00

  • Human transcription factor IIIC contains a polypeptide of 55 kDa specifically binding to Pol III genes.

    abstract::Human transcription factor IIIC contains a 55 kDa polypeptide which specifically interacts with the Adenovirus 2 VAI gene promoter and which mimics most of the DNA binding properties of the entire factor. The specificity and affinity of this protein:DNA interaction was demonstrated by: (i) Separation of purified fract...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/18.16.4743

    authors: Schneider HR,Waldschmidt R,Seifart KH

    更新日期:1990-08-25 00:00:00

  • During negative regulation of the human papillomavirus-16 E6 promoter, the viral E2 protein can displace Sp1 from a proximal promoter element.

    abstract::The principal early promoter of human papillomaviruses (HPVs), designated P97 in the case of HPV-16, contains four characteristically aligned cis-responsive elements, namely one binding site for Sp1, two for the viral E2 proteins, and the TATA box. The Sp1 binding site is needed to mediate activation of P97 by the rem...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.2.251

    authors: Tan SH,Gloss B,Bernard HU

    更新日期:1992-01-25 00:00:00

  • The separation between the 5'-3' ends in long RNA molecules is short and nearly constant.

    abstract::RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. De...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1249

    authors: Leija-Martínez N,Casas-Flores S,Cadena-Nava RD,Roca JA,Mendez-Cabañas JA,Gomez E,Ruiz-Garcia J

    更新日期:2014-12-16 00:00:00

  • Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

    abstract::A-tracts are functionally important DNA sequences which induce helix bending and have peculiar structural properties. While A-tract structure has been qualitatively well characterized, their mechanical properties remain controversial. A-tracts appear structurally rigid and resist nucleosome formation, but seem flexibl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku338

    authors: Dršata T,Špačková N,Jurečka P,Zgarbová M,Šponer J,Lankaš F

    更新日期:2014-06-01 00:00:00

  • COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    abstract::An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the map...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw026

    authors: Yamagata K,Yamanishi A,Kokubu C,Takeda J,Sese J

    更新日期:2016-05-05 00:00:00

  • Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes.

    abstract::Toxin-antitoxin systems are widespread in bacteria and archaea. They perform diverse functional roles, including the generation of persistence, maintenance of genetic loci and resistance to bacteriophages through abortive infection. Toxin-antitoxin systems have been divided into three types, depending on the nature of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks231

    authors: Blower TR,Short FL,Rao F,Mizuguchi K,Pei XY,Fineran PC,Luisi BF,Salmond GP

    更新日期:2012-07-01 00:00:00

  • PALI-a database of Phylogeny and ALIgnment of homologous protein structures.

    abstract::PALI (release 1.2) contains three-dimensional (3-D) structure-dependent sequence alignments as well as structure-based phylogenetic trees of homologous protein domains in various families. The data set of homologous protein structures has been derived by consulting the SCOP database (release 1.50) and the data set com...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/29.1.61

    authors: Balaji S,Sujatha S,Kumar SS,Srinivasan N

    更新日期:2001-01-01 00:00:00

  • Regulated functional alternative splicing in Drosophila.

    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

    pub_type: 杂志文章,评审

    doi:10.1093/nar/gkr648

    authors: Venables JP,Tazi J,Juge F

    更新日期:2012-01-01 00:00:00

  • Dynamic topology of double-stranded telomeric DNA studied by single-molecule manipulation in vitro.

    abstract::The dynamic topological structure of telomeric DNA is closely related to its biological function; however, no such structural information on full-length telomeric DNA has been reported due to difficulties synthesizing long double-stranded telomeric DNA. Herein, we developed an EM-PCR and TA cloning-based approach to s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa479

    authors: Zhang X,Zhang Y,Zhang W

    更新日期:2020-07-09 00:00:00

  • BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

    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

    authors: Paz I,Kligun E,Bengad B,Mandel-Gutfreund Y

    更新日期:2016-07-08 00:00:00

  • Structural dynamics of propeller loop: towards folding of RNA G-quadruplex.

    abstract::We have carried out an extended set of standard and enhanced-sampling MD simulations (for a cumulative simulation time of 620 μs) with the aim to study folding landscapes of the rGGGUUAGGG and rGGGAGGG parallel G-hairpins (PH) with propeller loop. We identify folding and unfolding pathways of the PH, which is bridged ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky712

    authors: Havrila M,Stadlbauer P,Kührová P,Banáš P,Mergny JL,Otyepka M,Šponer J

    更新日期:2018-09-28 00:00:00

  • ARGONAUTE2 cooperates with SWI/SNF complex to determine nucleosome occupancy at human Transcription Start Sites.

    abstract::Argonaute (AGO) proteins have a well-established role in post-transcriptional regulation of gene expression as key component of the RNA silencing pathways. Recent evidence involves AGO proteins in mammalian nuclear processes such as transcription and splicing, though the mechanistic aspects of AGO nuclear functions re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1387

    authors: Carissimi C,Laudadio I,Cipolletta E,Gioiosa S,Mihailovich M,Bonaldi T,Macino G,Fulci V

    更新日期:2015-02-18 00:00:00

  • The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).

    abstract::The NHGRI-EBI GWAS Catalog has provided data from published genome-wide association studies since 2008. In 2015, the database was redesigned and relocated to EMBL-EBI. The new infrastructure includes a new graphical user interface (www.ebi.ac.uk/gwas/), ontology supported search functionality and an improved curation ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw1133

    authors: MacArthur J,Bowler E,Cerezo M,Gil L,Hall P,Hastings E,Junkins H,McMahon A,Milano A,Morales J,Pendlington ZM,Welter D,Burdett T,Hindorff L,Flicek P,Cunningham F,Parkinson H

    更新日期:2017-01-04 00:00:00

  • Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells.

    abstract::The nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼ 30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt1179

    authors: Choi JH,Gaddameedhi S,Kim SY,Hu J,Kemp MG,Sancar A

    更新日期:2014-02-01 00:00:00

  • Synthesis, thermal stability and resistance to enzymatic hydrolysis of the oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridines.

    abstract::The synthesis of oligonucleotides (ODNs) containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine (D) is described, and thermal stability and resistance to enzymatic hydrolysis of the ODNs are compared with ODNs containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine (H). The ODNs containing D and the complementary RNA de...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg374

    authors: Ito T,Ueno Y,Komatsu Y,Matsuda A

    更新日期:2003-05-15 00:00:00

  • TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.

    abstract::This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx815

    authors: Tan Z,Fu Y,Sharma G,Mathews DH

    更新日期:2017-11-16 00:00:00

  • Non-canonical translation initiation of the spliced mRNA encoding the human T-cell leukemia virus type 1 basic leucine zipper protein.

    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

    pub_type: 杂志文章

    doi:10.1093/nar/gky802

    authors: Cáceres CJ,Angulo J,Lowy F,Contreras N,Walters B,Olivares E,Allouche D,Merviel A,Pino K,Sargueil B,Thompson SR,López-Lastra M

    更新日期:2018-11-16 00:00:00

  • Spectroscopic studies of (m5dC-dG)3: thermal stability of B- and Z-forms.

    abstract::The hexanucleoside pentaphosphate d(m5CpGpm5CpGpm5CpG) has been studied in solution by ultra-violet absorption, circular dichroism and 31P nuclear magnetic resonance under various experimental conditions. In 0.2 M NaClO4 at low temperature, an hexamer duplex is formed which has a B or B-like conformation. As the salt ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.13.4453

    authors: Hartmann B,Thuong NT,Pouyet J,Ptak M,Leng M

    更新日期:1983-07-11 00:00:00

  • Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development.

    abstract::Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkt030

    authors: Sanges R,Hadzhiev Y,Gueroult-Bellone M,Roure A,Ferg M,Meola N,Amore G,Basu S,Brown ER,De Simone M,Petrera F,Licastro D,Strähle U,Banfi S,Lemaire P,Birney E,Müller F,Stupka E

    更新日期:2013-04-01 00:00:00

  • Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform.

    abstract::With read lengths of currently up to 2 × 300 bp, high throughput and low sequencing costs Illumina's MiSeq is becoming one of the most utilized sequencing platforms worldwide. The platform is manageable and affordable even for smaller labs. This enables quick turnaround on a broad range of applications such as targete...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku1341

    authors: Schirmer M,Ijaz UZ,D'Amore R,Hall N,Sloan WT,Quince C

    更新日期:2015-03-31 00:00:00

  • Isolation of developmentally regulated genes by differential display screening of cDNA libraries.

    abstract::mRNA differential display RT-PCR has been extensively used for the isolation of genes differentially expressed between RNA populations. We have assessed its utility for the identification of developmentally regulated genes in plasmid cDNA libraries derived from individual tissues dissected from early mouse embryos. Us...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.19.4538

    authors: Gupta R,Thomas P,Beddington RS,Rigby PW

    更新日期:1998-10-01 00:00:00

  • 5' flanking sequence and genomic structure of Egr-1, a murine mitogen inducible zinc finger encoding gene.

    abstract::Egr-1 is a murine zinc finger encoding cDNA whose expression is modulated by a variety of ligand-receptor interactions and is often coregulated with c-fos (1). This study reports the isolation of a mouse Egr-1 genomic clone, its intron-exon structure, and 935 bp of 5' flanking sequence. The gene spans about 3.8 kb and...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.18.8835

    authors: Tsai-Morris CH,Cao XM,Sukhatme VP

    更新日期:1988-09-26 00:00:00