SDM--a server for predicting effects of mutations on protein stability and malfunction (Q30402863)

7 November 2017

SDM--a server for predicting effects of mutations on protein stability and malfunction (English)

1 reference

7 November 2017

Robert Preissner

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Tom Blundell

series ordinal

object named as

Tom L Blundell

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7 November 2017

Catherine Louise Worth

series ordinal

object named as

Catherine L Worth

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7 November 2017

language of work or name

English

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publication date

18 May 2011

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full work available at URL

7 November 2017

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125769

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published in

Nucleic Acids Research

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7 November 2017

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7 November 2017

Web Server issue

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7 November 2017

W215-22

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Creative Commons Attribution-NonCommercial 3.0 Unported

7 November 2017

start time

14 November 2016

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April 2022 Public Data File from Crossref

copyrighted

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cites work

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Missense mutations in dystrophin that trigger muscular dystrophy decrease protein stability and lead to cross-beta aggregates

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Mixed lineage kinase 3 gene mutations in mismatch repair deficient gastrointestinal tumours

20 June 2018

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Tumor risks and genotype-phenotype-proteotype analysis in 358 patients with germline mutations in SDHB and SDHD.

20 June 2018

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Stability effects of mutations and protein evolvability

20 June 2018

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A TIR domain variant of MyD88 adapter-like (Mal)/TIRAP results in loss of MyD88 binding and reduced TLR2/TLR4 signaling

20 June 2018

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Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains.

20 June 2018

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Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis.

20 June 2018

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Stabilizing mutation of CTNNB1/beta-catenin and protein accumulation analyzed in a large series of parathyroid tumors of Swedish patients.

20 June 2018

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The complete genome of an individual by massively parallel DNA sequencing

20 June 2018

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Modeling backbone flexibility improves protein stability estimation.

20 June 2018

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A second generation human haplotype map of over 3.1 million SNPs

20 June 2018

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Genome bioinformatic analysis of nonsynonymous SNPs

20 June 2018

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Inference of macromolecular assemblies from crystalline state

20 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Andante: reducing side-chain rotamer search space during comparative modeling using environment-specific substitution probabilities

20 June 2018

1 reference

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20 June 2018

Whole-genome genotyping

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CUPSAT: prediction of protein stability upon point mutations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Very fast empirical prediction and rationalization of protein pKa values

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

A protein domain interaction interface database: InterPare

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Missense meanderings in sequence space: a biophysical view of protein evolution

20 June 2018

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Systematically perturbed folding patterns of amyotrophic lateral sclerosis (ALS)-associated SOD1 mutants

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Prediction of the mutation-induced change in thermodynamic stabilities of membrane proteins from free energy simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

SIFT: Predicting amino acid changes that affect protein function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Structural bases of stability-function tradeoffs in enzymes

20 June 2018

1 reference

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Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

20 June 2018

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SNPs, protein structure, and disease.

20 June 2018

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The Sequence of the Human Genome

20 June 2018

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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

20 June 2018

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20 June 2018

The Protein Data Bank

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HOMSTRAD: a database of protein structure alignments for homologous families

20 June 2018

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Partial characterization and three-dimensional-structural localization of eight mutations in exon 7 of the human phenylalanine hydroxylase gene associated with phenylketonuria.

20 June 2018

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Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

20 June 2018

Proteins and temperature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

The interpretation of protein structures: Estimation of static accessibility

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Dependence of conformational stability on hydrophobicity of the amino acid residue in a series of variant proteins substituted at a unique position of tryptophan synthase alpha subunit

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Protein stability and molecular adaptation to extreme conditions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3125769

How can free energy component analysis explain the difference in protein stability caused by amino acid substitutions? Effect of three hydrophobic mutations at the 56th residue on the stability of human lysozyme

20 June 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Predicting protein stability changes from sequences using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

A neural-network-based method for predicting protein stability changes upon single point mutations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Prediction of protein stability changes for single-site mutations using support vector machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

A structural bioinformatics approach to the analysis of nonsynonymous single nucleotide polymorphisms (nsSNPs) and their relation to disease.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Investigating the effects of mutations on protein aggregation in the cell.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Correlation of levels of folded recombinant p53 in escherichia coli with thermodynamic stability in vitro

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Using model proteins to quantify the effects of pathogenic mutations in Ig-like proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

The Parkinson disease-associated A30P mutation stabilizes alpha-synuclein against proteasomal degradation triggered by heme oxygenase-1 over-expression in human neuroblastoma cells.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Thermodynamic database for proteins: features and applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Distinguishing structural and functional restraints in evolution in order to identify interaction sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Structural bioinformatics mutation analysis reveals genotype-phenotype correlations in von Hippel-Lindau disease and suggests molecular mechanisms of tumorigenesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Novel TSHR mutations in consanguineous families with congenital nongoitrous hypothyroidism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

AIRE's CARD revealed, a new structure for central tolerance provokes transcriptional plasticity

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Robust prediction of mutation-induced protein stability change by property encoding of amino acids

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

A Hyperthermophilic Protein Acquires Function at the Cost of Stability†

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKR363

Average assignment method for predicting the stability of protein mutants

21 January 2018

1 reference

12 December 2020

Free energy calculations by computer simulation

1 reference

12 December 2020

Effect of active site residues in barnase on activity and stability

1 reference

12 December 2020

Can the stability of protein mutants be predicted by free energy calculations?

1 reference

12 December 2020

Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKR363

1 reference

7 November 2017

journals/nar/WorthPB11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

7 November 2017

PubMed publication ID

21593128

1 reference