4.2 Review

Analyzing Effects of Naturally Occurring Missense Mutations

Related references

Note: Only part of the references are listed.
Article Biochemical Research Methods

Predicting folding free energy changes upon single point mutations

Zhe Zhang et al.

BIOINFORMATICS (2012)

Article Biochemistry & Molecular Biology

SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants

Greet De Baets et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biochemistry & Molecular Biology

Phenylketonuria as a protein misfolding disease: The mutation pG46S in phenylalanine hydroxylase promotes self-association and fibril formation

Joao Leandro et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2011)

Article Biochemistry & Molecular Biology

Database resources of the National Center for Biotechnology Information

Eric W. Sayers et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemistry & Molecular Biology

A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics

Shawn Witham et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)

Article Biochemistry & Molecular Biology

Mutational hotspots in electron transfer flavoprotein underlie defective folding and function in multiple acyl-CoA dehydrogenase deficiency

Barbara J. Henriques et al.

BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE (2010)

Review Biochemistry & Molecular Biology

Predicting the Melting Point of Human C-Type Lysozyme Mutants

Deeptak Verma et al.

CURRENT PROTEIN & PEPTIDE SCIENCE (2010)

Article Genetics & Heredity

Computational Analysis of Missense Mutations Causing Snyder-Robinson Syndrome

Zhe Zhang et al.

HUMAN MUTATION (2010)

Article Genetics & Heredity

Performance of Protein Stability Predictors

Sofia Khan et al.

HUMAN MUTATION (2010)

Article Biochemical Research Methods

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

Sebastian Maurer-Stroh et al.

NATURE METHODS (2010)

Letter Biochemical Research Methods

A method and server for predicting damaging missense mutations

Ivan A. Adzhubei et al.

NATURE METHODS (2010)

Article Biochemistry & Molecular Biology

DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein-protein interactions

Dennis M. Krueger et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemistry & Molecular Biology

Testing computational prediction of missense mutation phenotypes: Functional characterization of 204 mutations of human cystathionine beta synthase

Qiong Wei et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)

Article Genetics & Heredity

A Missense Mutation, p.V132G, in the X-Linked Spermine Synthase Gene (SMS) Causes Snyder-Robinson Syndrome

L. E. Becerra-Solano et al.

AMERICAN JOURNAL OF MEDICAL GENETICS PART A (2009)

Review Biochemistry & Molecular Biology

Mammalian Polyamine Metabolism and Function

Anthony E. Pegg

IUBMB LIFE (2009)

Review Chemistry, Multidisciplinary

MCCE2: Improving Protein pKa Calculations with Extensive Side Chain Rotamer Sampling

Yifan Song et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Review Chemistry, Multidisciplinary

CHARMM: The Biomolecular Simulation Program

B. R. Brooks et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemical Research Methods

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

Prateek Kumar et al.

NATURE PROTOCOLS (2009)

Article Biochemical Research Methods

Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data

Joost Van Durme et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

A three-state prediction of single point mutations on protein stability changes

Emidio Capriotti et al.

BMC BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Crystal structure of human spermine synthase - Implications of substrate binding and catalytic mechanism

Hong Wu et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2008)

Article Biochemistry & Molecular Biology

COILCHECK: An Interactive Server for the Analysis of Interface Regions in Coiled Coils

R. Sowdhamini et al.

PROTEIN AND PEPTIDE LETTERS (2008)

Article Biochemistry & Molecular Biology

Specific interactions for ab initio folding of protein terminal regions with secondary structures

Yuedong Yang et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2008)

Article Biochemistry & Molecular Biology

Mutation of a single residue, beta-glutamate-20, alters protein-lipid interactions of light harvesting complex II

Lee Gyan Kwa et al.

MOLECULAR MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

Modeling backbone flexibility improves protein stability estimation

Shuangye Yin et al.

STRUCTURE (2007)

Article Biochemistry & Molecular Biology

Mutation at the polymerase active site of mouse DNA polymerase δ increases genomic instability and accelerates tumorigenesis

Ranga N. Venkatesan et al.

MOLECULAR AND CELLULAR BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Functional analysis of pancreatitis-associated missense mutations in the pancreatic secretory trypsin inhibitor (SPINK1) gene

Arnaud Boulling et al.

EUROPEAN JOURNAL OF HUMAN GENETICS (2007)

Article Biochemistry & Molecular Biology

The protein folding problem: when will it be solved?

Ken A. Dill et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Letter Biochemical Research Methods

Eris: an automated estimator of protein stability

Shuangye Yin et al.

NATURE METHODS (2007)

Article Biochemistry & Molecular Biology

Structural analysis and prediction of protein mutant stability using distance and torsion potentials: Role of secondary structure and solvent accessibility

Vijaya Parthiban et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2007)

Article Pharmacology & Pharmacy

Identification and functional analysis of common human flavin-containing monooxygenase 3 genetic variants

Sevasti B. Koukouritaki et al.

JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS (2007)

Article Biochemistry & Molecular Biology

FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: A large-scale thermodynamic analysis

Sagar D. Khare et al.

AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS (2006)

Article Medicine, Research & Experimental

Catalytic inactivation of human phospholipase D2 by a naturally occurring Gly901Asp mutation

Yoshiji Yamada et al.

ARCHIVES OF MEDICAL RESEARCH (2006)

Article Biochemistry & Molecular Biology

pKD:: re-designing protein pKa values

Barbara M. Tynan-Connolly et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

CUPSAT: prediction of protein stability upon point mutations

Vijaya Parthiban et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemical Research Methods

Emergence of protein fold families through rational design

Feng Ding et al.

PLOS COMPUTATIONAL BIOLOGY (2006)

Article Biochemical Research Methods

SNPs3D: Candidate gene and SNP selection for association studies

P Yue et al.

BMC BIOINFORMATICS (2006)

Article Biochemistry & Molecular Biology

Identification and analysis of deleterious human SNPs

P Yue et al.

JOURNAL OF MOLECULAR BIOLOGY (2006)

Article Biochemistry & Molecular Biology

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

JL Cheng et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Review Biochemistry & Molecular Biology

Aminopropyltransferases: Function, structure and genetics

Y Ikeguchi et al.

JOURNAL OF BIOCHEMISTRY (2006)

Review Chemistry, Multidisciplinary

GROMACS: Fast, flexible, and free

D Van der Spoel et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2005)

Article Biochemical Research Methods

Predicting protein stability changes from sequences using support vector machines

E Capriotti et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

The FoldX web server: an online force field

J Schymkowitz et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

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

E Capriotti et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Multidisciplinary Sciences

Molecular dynamics and protein function

M Karplus et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Biochemistry & Molecular Biology

Mutation of active site residues of insulin-degrading enzyme alters allosteric interactions

ES Song et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2005)

Article Biochemistry & Molecular Biology

Neural network-based prediction of mutation-induced protein stability changes in staphylococcal nuclease at 20 residue positions

CM Frenz

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Biochemical Research Methods

Mapping SNPs to protein sequence and structure data

A Cavallo et al.

BIOINFORMATICS (2005)

Article Biochemical Research Methods

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

S Mooney

BRIEFINGS IN BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Noonan syndrome type I with PTPN11 3 bp deletion: structure-function implications

WH Lee et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2005)

Article Hematology

A critical role for Gly25 in the B chain of human thrombin

S Akhavan et al.

JOURNAL OF THROMBOSIS AND HAEMOSTASIS (2005)

Review Oncology

Polyamines and cancer: Old molecules, new understanding

EW Gerner et al.

NATURE REVIEWS CANCER (2004)

Article Biotechnology & Applied Microbiology

Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins

AM Fernandez-Escamilla et al.

NATURE BIOTECHNOLOGY (2004)

Article Biochemistry & Molecular Biology

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

V Chelliah et al.

JOURNAL OF MOLECULAR BIOLOGY (2004)

Article Biochemical Research Methods

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

Emidio Capriotti et al.

BIOINFORMATICS (2004)

Review Biochemistry & Molecular Biology

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

AJ Bordner et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2004)

Article Biochemistry & Molecular Biology

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

CT Porter et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Biochemistry & Molecular Biology

HGVbase: a curated resource describing human DNA variation and phenotype relationships

D Fredman et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Multidisciplinary Sciences

Automated prediction of protein function and detection of functional sites from structure

F Pazos et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)

Review Multidisciplinary Sciences

Protein folding and misfolding

CM Dobson

NATURE (2003)

Article Biochemistry & Molecular Biology

X-linked spermine synthase gene (SMS) defect: the first polyamine deficiency syndrome

AL Cason et al.

EUROPEAN JOURNAL OF HUMAN GENETICS (2003)

Article Biochemistry & Molecular Biology

Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor VP domain

Z Wang et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)

Article Biochemistry & Molecular Biology

SIFT: predicting amino acid changes that affect protein function

PC Ng et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

Structural location of disease-associated single-nucleotide polymorphisms

NO Stitziel et al.

JOURNAL OF MOLECULAR BIOLOGY (2003)

Article Biochemistry & Molecular Biology

Evaluation of structural and evolutionary contributions to deleterious mutation prediction

CT Saunders et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Human non-synonymous SNPs: server and survey

V Ramensky et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

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

R Guerois et al.

JOURNAL OF MOLECULAR BIOLOGY (2002)

Review Biochemistry & Molecular Biology

Evolutionary predictions of binding surfaces and interactions

O Lichtarge et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2002)

Article Biochemistry & Molecular Biology

Effect of single active-site cleft mutation on product specificity in a thermostable bacterial cellulase

TR Rignall et al.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY (2002)

Article Biochemistry & Molecular Biology

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

A Hamosh et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

Extending the accuracy limits of prediction for side-chain conformations

ZX Xiang et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Knowledge-based potential defined for a rotamer library to design protein sequences

M Ota et al.

PROTEIN ENGINEERING (2001)

Article Biochemistry & Molecular Biology

Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins

R Landgraf et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Prediction of deleterious human alleles

S Sunyaev et al.

HUMAN MOLECULAR GENETICS (2001)

Article Genetics & Heredity

SNPs, protein structure, and disease

Z Wang et al.

HUMAN MUTATION (2001)

Article Biochemistry & Molecular Biology

dbSNP: the NCBI database of genetic variation

ST Sherry et al.

NUCLEIC ACIDS RESEARCH (2001)

Article Biotechnology & Applied Microbiology

Improving the refolding yield of interleukin-4 through the optimization of local interactions

H Domingues et al.

JOURNAL OF BIOTECHNOLOGY (2000)

Review Chemistry, Multidisciplinary

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

PA Kollman et al.

ACCOUNTS OF CHEMICAL RESEARCH (2000)

Article Biochemistry & Molecular Biology

PoPMuSiC, an algorithm for predicting protein mutant stability changes. Application to prion proteins

D Gilis et al.

PROTEIN ENGINEERING (2000)

Article Multidisciplinary Sciences

Native protein sequences are close to optimal for their structures

B Kuhlman et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

dbSNP: a database of single nucleotide polymorphisms

EM Smigielski et al.

NUCLEIC ACIDS RESEARCH (2000)

Article Biochemistry & Molecular Biology

The Protein Data Bank

HM Berman et al.

NUCLEIC ACIDS RESEARCH (2000)