Abstract：
:Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon static structures. Here we present DynaMut, a web server implementing two distinct, well established normal mode approaches, which can be used to analyze and visualize protein dynamics by sampling conformations and assess the impact of mutations on protein dynamics and stability resulting from vibrational entropy changes. DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability. We demonstrate our approach outperforms alternative approaches to predict the effects of mutations on protein stability and flexibility (P-value < 0.001), achieving a correlation of up to 0.70 on blind tests. DynaMut also provides a comprehensive suite for protein motion and flexibility analysis and visualization via a freely available, user friendly web server at http://biosig.unimelb.edu.au/dynamut/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rodrigues CH,Pires DE,Ascher DBdoi
10.1093/nar/gky300subject
Has Abstractpub_date
2018-07-02 00:00:00pages
W350-W355issue
W1eissn
0305-1048issn
1362-4962pii
4990022journal_volume
46pub_type
杂志文章abstract：:Computational modelling has become increasingly common in life science research. To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (https://www.ebi.ac.uk/biomodels/), a repository for mathematical models, was established in 2005. The current BioModels platform ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1055
更新日期：2020-01-08 00:00:00
abstract：:Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr600
更新日期：2011-10-01 00:00:00
abstract：:The high mobility group protein (HMG)-box is a DNA-binding domain found in many proteins that bind preferentially to DNA of irregular structures in a sequence-independent manner and can bend the DNA. We show here that GST-fusion proteins of HMG domains from HMG1 and HMG2 promote a triple-stranded complex formation bet...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.23.4733
更新日期：1996-12-01 00:00:00
abstract：:Nitrated polycyclic aromatic hydrocarbons are common environmental pollutants, of which many are mutagenic and carcinogenic. 1-Nitropyrene is the most abundant nitrated polycyclic aromatic hydrocarbon, which causes DNA damage and is carcinogenic in experimental animals. Error-prone translesion synthesis of 1-nitropyre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1296
更新日期：2013-02-01 00:00:00
abstract：:MODPROPEP is a web server for knowledge-based modeling of protein-peptide complexes, specifically peptides in complex with major histocompatibility complex (MHC) proteins and kinases. The available crystal structures of protein-peptide complexes in PDB are used as templates for modeling peptides of desired sequence in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm266
更新日期：2007-07-01 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 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm022
更新日期：2007-01-01 00:00:00
abstract：:Non-homologous DNA end joining (NHEJ) is considered the major pathway of double-strand break (DSB) repair in mammalian cells and depends, among other things, on the DNA end-binding Ku70/80 hetero-dimer. To investigate the function of Ku in NHEJ we have compared the ability of cell-free extracts from wild-type CHO-K1 c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.13.2585
更新日期：2000-07-01 00:00:00
abstract：:Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks004
更新日期：2012-05-01 00:00:00
abstract：:Variable regions within ribosomal RNAs frequently vary in length as a result of incorporating products of slippage. This makes constructing secondary structure models problematic because base homology is difficult or impossible to establish between species. Here, we model such a region by comparing the results of the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1689
更新日期：1998-04-01 00:00:00
abstract：:The chemical shifts of the well-resolved ring nitrogen protons of uracil and a series of substituted uracils, including pseudouridine (5-ribosyl-uracil) and uridine (1-ribosyl-uracil) were determined using nuclear magnetic resonance (NMR). The observed chemical shifts suggest the existence of an atypical syn conformat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.8.2747
更新日期：1977-08-01 00:00:00
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
更新日期：1995-10-11 00:00:00
abstract：:The 338.5 kb of the Escherichia coli genome described here together with previously described segments bring the total of contiguous finished sequence of this genome to > 1 Mb. Of 319 open reading frames (ORFs) found in this 338.5 kb segment, 147 (46%) are potential new genes. The positions of several genes which had ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.12.2105
更新日期：1995-06-25 00:00:00
abstract：:One of the obstacles hindering a better understanding of cancer is its heterogeneity. However, computational approaches to model cancer heterogeneity have lagged behind. To bridge this gap, we have developed a new probabilistic approach that models individual cancer cases as mixtures of subtypes. Our approach can be s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt577
更新日期：2013-09-01 00:00:00
abstract：:DEAD-box helicases catalyze the non-processive unwinding of double-stranded RNA (dsRNA) at the expense of adenosine triphosphate (ATP) hydrolysis. Nucleotide and RNA binding and unwinding are mediated by the RecA domains of the helicase core, but their cooperation in these processes remains poorly understood. We there...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku747
更新日期：2014-01-01 00:00:00
abstract：:Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1236
更新日期：2016-01-04 00:00:00
abstract：:African trypanosomes are extracellular protozoan parasites that are transmitted from one mammalian host to the next by tsetse flies. Bloodstream forms express variant surface glycoprotein (VSG); the tsetse fly (procyclic) forms express instead the procyclic acidic repetitive protein (PARP). PARP mRNA is abundant in pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.7.1202
更新日期：1996-04-01 00:00:00
abstract：:The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here P...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky466
更新日期：2018-07-02 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：:We have isolated the 5'-end of the gene for the rat and human link protein by screening genomic libraries with oligonucleotides corresponding to the 5'-cDNA sequence. Several overlapping clones were isolated for the human link protein gene, while only one clone was obtained for the rat. All the clones contained a sing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.8.1933
更新日期：1991-04-25 00:00:00
abstract：:TATA-binding protein (TBP) is central to the regulation of eukaryotic transcription initiation. Recruitment of TBP to target genes can be positively regulated by one of two basal transcription factor complexes: SAGA or TFIID. Negative regulation of TBP promoter association can be performed by Mot1p or the NC2 complex....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr784
更新日期：2012-02-01 00:00:00
abstract：:Nuclei isolated from cultured mouse and rat cell lines initiated pre-rRNA chains at the correct site and with the correct nucleotide specificity (A for mouse, G for rat). Nucleic acid filter hybridization and S1 nuclease mapping were used to analyze the RNA products initiated with nucleoside (beta-S)triphosphates. Ini...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.21.8115
更新日期：1984-11-12 00:00:00
abstract：:Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw475
更新日期：2016-08-19 00:00:00
abstract：:More than one-third of the RAG1 protein can be truncated from the N-terminus with only subtle effects on the products of V(D)J recombination in vitro or in a mouse. What, then, is the function of the N-terminal domain? We believe it to be regulatory. We determined, several years ago, that an included RING motif could ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp192
更新日期：2009-06-01 00:00:00
abstract：:In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing envir...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr555
更新日期：2011-10-01 00:00:00
abstract：:We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.7.2387
更新日期：1982-04-10 00:00:00
abstract：:Spliced leader (SL) trans-splicing is a critical element of gene expression in a number of eukaryotic groups. This process is arguably best understood in nematodes, where biochemical and molecular studies in Caenorhabditis elegans and Ascaris suum have identified key steps and factors involved. Despite this, the preci...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx500
更新日期：2017-08-21 00:00:00
abstract：:Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and transla...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg161
更新日期：2003-01-15 00:00:00
abstract：:Metabolite-responsive RNA pseudoknots derived from prokaryotic riboswitches have been shown to stimulate -1 programmed ribosomal frameshifting (PRF), suggesting -1 PRF as a promising gene expression platform to extend riboswitch applications in higher eukaryotes. However, its general application has been hampered by d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw718
更新日期：2016-10-14 00:00:00
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
更新日期：1983-07-11 00:00:00
abstract：:The human thrombopoietin (TPO) gene, which codes for the principal cytokine involved in platelet maturation, shows a peculiar alternative splicing of its last exon, where an intra-exonic 116 nt alternative intron is spliced out in a fraction of its mRNA. To characterize the molecular mechanism underlying this alternat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.4.886
更新日期：2001-02-15 00:00:00
