scholarly article | Q13442814 |
P8978 | DBLP publication ID | journals/bioinformatics/ZhangWGZZA12 |
P356 | DOI | 10.1093/BIOINFORMATICS/BTS005 |
P932 | PMC publication ID | 3289912 |
P698 | PubMed publication ID | 22238268 |
P5875 | ResearchGate publication ID | 221741435 |
P2093 | author name string | Yang Gao | |
Lin Wang | |||
Jie Zhang | |||
Zhe Zhang | |||
Emil Alexov | |||
Maxim Zhenirovskyy | |||
P2860 | cites work | The Protein Data Bank | Q24515306 |
The FoldX web server: an online force field | Q24530376 | ||
The RCSB PDB information portal for structural genomics | Q24538661 | ||
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions | Q24643464 | ||
Native protein sequences are close to optimal for their structures | Q24656322 | ||
CHARMM: the biomolecular simulation program | Q24658108 | ||
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure | Q24812223 | ||
Experimental verification of the 'stability profile of mutant protein' (SPMP) data using mutant human lysozymes | Q27619558 | ||
Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase | Q27645128 | ||
The crystal structure of staphylococcal nuclease refined at 1.7 A resolution | Q27652694 | ||
Crystal structure analysis of oxidized Pseudomonas aeruginosa azurin at pH 5.5 and pH 9.0. A pH-induced conformational transition involves a peptide bond flip | Q27655390 | ||
Crystal structural analysis of mutations in the hydrophobic cores of barnase | Q27731488 | ||
Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor | Q27744237 | ||
The Amber biomolecular simulation programs | Q27860745 | ||
ProTherm, version 4.0: thermodynamic database for proteins and mutants | Q28234996 | ||
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution | Q28286232 | ||
Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect | Q28292427 | ||
In silico and in vitro investigations of the mutability of disease-causing missense mutation sites in spermine synthase | Q28744180 | ||
Human non-synonymous SNPs: server and survey | Q29547603 | ||
Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations | Q29615143 | ||
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models | Q29616389 | ||
Direct test of the Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins | Q30164892 | ||
SNPs, protein structure, and disease. | Q30328103 | ||
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. | Q30350543 | ||
SNPs3D: candidate gene and SNP selection for association studies. | Q30353456 | ||
Modeling backbone flexibility improves protein stability estimation. | Q30366423 | ||
Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis. | Q30370720 | ||
Computational modeling of structurally conserved cancer mutations in the RET and MET kinases: the impact on protein structure, dynamics, and stability. | Q30374663 | ||
Performance of protein stability predictors. | Q30386719 | ||
Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation | Q30389098 | ||
Knowledge-based potential defined for a rotamer library to design protein sequences | Q30726969 | ||
Extending the accuracy limits of prediction for side-chain conformations | Q30998288 | ||
Emergence of protein fold families through rational design | Q33250082 | ||
A Gaussian-chain model for treating residual charge-charge interactions in the unfolded state of proteins | Q34019157 | ||
Computational analysis of missense mutations causing Snyder-Robinson syndrome | Q34101193 | ||
Gut-enriched Kruppel-like factor represses ornithine decarboxylase gene expression and functions as checkpoint regulator in colonic cancer cells | Q34151428 | ||
Tumor suppressor von Hippel-Lindau (VHL) stabilization of Jade-1 protein occurs through plant homeodomains and is VHL mutation dependent. | Q34299645 | ||
A missense mutation in CLIC2 associated with intellectual disability is predicted by in silico modeling to affect protein stability and dynamics | Q35093751 | ||
Single nucleotide polymorphisms that cause structural changes in the cyclic AMP receptor protein transcriptional regulator of the tuberculosis vaccine strain Mycobacterium bovis BCG alter global gene expression without attenuating growth | Q36593916 | ||
Hot spots--a review of the protein-protein interface determinant amino-acid residues | Q36839286 | ||
Prediction of protein stability upon point mutations | Q37010344 | ||
Approaches and resources for prediction of the effects of non-synonymous single nucleotide polymorphism on protein function and interactions | Q37130832 | ||
SNPs: impact on gene function and phenotype | Q37600710 | ||
Contribution of the hydrophobic effect to protein stability: analysis based on simulations of the Ile-96----Ala mutation in barnase | Q37637250 | ||
Conformational ensembles, signal transduction and residue hot spots: application to drug discovery. | Q37784746 | ||
Modeling of denatured state for calculation of the electrostatic contribution to protein stability | Q38270088 | ||
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction | Q38270534 | ||
Free energy via molecular simulation: applications to chemical and biomolecular systems | Q38648060 | ||
Missense polymorphism in the human carboxypeptidase E gene alters enzymatic activity. | Q40791331 | ||
Prediction of the stability of protein mutants based on structural environment-dependent amino acid substitution and propensity tables | Q40914387 | ||
On the electrostatic component of protein-protein binding free energy | Q41825118 | ||
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking | Q41921801 | ||
The response of T4 lysozyme to large-to-small substitutions within the core and its relation to the hydrophobic effect. | Q42126112 | ||
Electrostatic contributions to the stability of halophilic proteins | Q43025485 | ||
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential | Q43057880 | ||
Large-scale prediction of protein geometry and stability changes for arbitrary single point mutations | Q44491602 | ||
Molecular dynamics simulations of the unfolding of beta(2)-microglobulin and its variants | Q44580868 | ||
Numerical calculations of the pH of maximal protein stability. The effect of the sequence composition and three-dimensional structure | Q44700318 | ||
Thermodynamic database for proteins: features and applications. | Q45934587 | ||
Identification and analysis of deleterious human SNPs. | Q45966155 | ||
A neural-network-based method for predicting protein stability changes upon single point mutations. | Q45966727 | ||
Statistical potentials extracted from protein structures: how accurate are they? | Q46096070 | ||
Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides | Q46149002 | ||
Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala98-->Val mutants of T4 lysozyme | Q46200928 | ||
Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core | Q46497654 | ||
The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin | Q47682341 | ||
Neural network-based prediction of mutation-induced protein stability changes in Staphylococcal nuclease at 20 residue positions. | Q51538130 | ||
Eris: an automated estimator of protein stability. | Q51913485 | ||
PoPMuSiC, an algorithm for predicting protein mutant stability changes: application to prion proteins. | Q52067226 | ||
ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. | Q52213861 | ||
Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. | Q52267131 | ||
Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. | Q52306639 | ||
Stabilization of proteins by rational design of alpha-helix stability using helix/coil transition theory. | Q52315122 | ||
Predicting free energy contributions to the conformational stability of folded proteins from the residue sequence with radial basis function networks | Q52361537 | ||
Simulation analysis of the stability mutant R96H of T4 lysozyme. | Q52451866 | ||
Model for calculation of electrostatic interactions in unfolded proteins. | Q53675127 | ||
FALS mutations in Cu, Zn superoxide dismutase destabilize the dimer and increase dimer dissociation propensity: a large-scale thermodynamic analysis. | Q53877582 | ||
Modeling and analyzing three-dimensional structures of human disease proteins | Q56978786 | ||
Improving the refolding yield of interleukin-4 through the optimization of local interactions | Q57902378 | ||
Three-dimensional structural location and molecular functional effects of missense SNPs in the T cell receptor V? domain | Q57972072 | ||
Free energy calculations by computer simulation | Q69004087 | ||
Protein stability for single substitution mutants and the extent of local compactness in the denatured state | Q72543389 | ||
Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence | Q73702777 | ||
Predicting free energy changes using structural ensembles | Q83130634 | ||
P433 | issue | 5 | |
P407 | language of work or name | English | Q1860 |
P1104 | number of pages | 8 | |
P304 | page(s) | 664-671 | |
P577 | publication date | 2012-01-11 | |
P1433 | published in | Bioinformatics | Q4914910 |
P1476 | title | Predicting folding free energy changes upon single point mutations | |
P478 | volume | 28 |
Q42563242 | A Y328C missense mutation in spermine synthase causes a mild form of Snyder-Robinson syndrome |
Q47757226 | A component analysis of the free energies of folding of 35 proteins: A consensus view on the thermodynamics of folding at the molecular level |
Q115574415 | A guide to machine learning for biologists |
Q37406440 | A mutation in a ganglioside biosynthetic enzyme, ST3GAL5, results in salt & pepper syndrome, a neurocutaneous disorder with altered glycolipid and glycoprotein glycosylation |
Q39360964 | A novel p.Leu(381)Phe mutation in presenilin 1 is associated with very early onset and unusually fast progressing dementia as well as lysosomal inclusions typically seen in Kufs disease |
Q46037815 | A pH-dependent computational approach to the effect of mutations on protein stability. |
Q42250997 | A rational free energy-based approach to understanding and targeting disease-causing missense mutations |
Q21284966 | Analyzing effects of naturally occurring missense mutations |
Q38966406 | Annotating Mutational Effects on Proteins and Protein Interactions: Designing Novel and Revisiting Existing Protocols |
Q36353615 | Assessing predictors of changes in protein stability upon mutation using self-consistency |
Q47265199 | Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains |
Q28397104 | Chronic Beryllium Disease: revealing the role of beryllium ion and small peptides binding to HLA-DP2 |
Q90419543 | Computational Approaches to Prioritize Cancer Driver Missense Mutations |
Q97643241 | Computational analysis of androgen receptor (AR) variants to decipher the relationship between protein stability and related-diseases |
Q33907569 | Computational and experimental approaches to reveal the effects of single nucleotide polymorphisms with respect to disease diagnostics |
Q41876505 | Electrostatic effects on the folding stability of FKBP12. |
Q34611078 | Enhancing human spermine synthase activity by engineered mutations |
Q90479878 | In silico mutational analysis and identification of stability centers in human interleukin-4 |
Q38673851 | Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine |
Q42409589 | Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding |
Q42358723 | Localized structural frustration for evaluating the impact of sequence variants |
Q27021940 | Molecular mechanisms of disease-causing missense mutations |
Q37182110 | MutaBind estimates and interprets the effects of sequence variants on protein-protein interactions |
Q36324695 | Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease |
Q39951577 | On human disease-causing amino acid variants: statistical study of sequence and structural patterns |
Q40475532 | On the physics of thermal-stability changes upon mutations of a protein. |
Q34323807 | Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases |
Q35164244 | Predicting the Impact of Missense Mutations on Protein-Protein Binding Affinity. |
Q34503059 | Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling |
Q39857355 | SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach |
Q64273189 | Structural Perspective on Revealing and Altering Molecular Functions of Genetic Variants Linked with Diseases |
Q26865027 | Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins |
Q89521806 | Variation benchmark datasets: update, criteria, quality and applications |
Q30660227 | ZC4H2, an XLID gene, is required for the generation of a specific subset of CNS interneurons. |
Search more.