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Cited by 1,571 publications
(1,802 citation statements)
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References 90 publications
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“…In order to identify the interacting region of two peptides studied in this work (DEEFLIKIAAIDN from human phosphatidylinositol 4-kinase and FTVYGLLDKAQDLF from human melanotransferrin), the peptides were divided into nine amino acids length fragments. Using the FoldX [43][44][45] software, the core positions of the CLIP peptide were mutated to reproduce every one of these nine amino acid sequences. FoldX generated 10 different models considering different putative residues rotamers for each of the nine amino acid sequence.…”
Section: Modeling Of Hla-dr8 With Peptidementioning
confidence: 99%
“…In order to identify the interacting region of two peptides studied in this work (DEEFLIKIAAIDN from human phosphatidylinositol 4-kinase and FTVYGLLDKAQDLF from human melanotransferrin), the peptides were divided into nine amino acids length fragments. Using the FoldX [43][44][45] software, the core positions of the CLIP peptide were mutated to reproduce every one of these nine amino acid sequences. FoldX generated 10 different models considering different putative residues rotamers for each of the nine amino acid sequence.…”
Section: Modeling Of Hla-dr8 With Peptidementioning
confidence: 99%
“…25 The influence of the residues on the structural stability was studied by computational alanine scanning using the Foldx4 software. 26 The structural stability of the wild-type protein was computed and compared with that of the alanine mutants. The stability is estimated as a difference between the free energy of the unfolded and folded states of the protein.…”
Section: Molecular Modeling Analysismentioning
confidence: 99%
“…Guerois et al [104] developed the FOLD-X energy function to study the stabilities of 1088 mutants. They used a comprehensive set of parameters to describe the van der Waals, solvation, hydrogen-bonding, electrostatic and entropic contribution to the protein stability, and obtained a correlation of 0.64 for the blind test set after training their parameters on 339 mutants [104]. Khatun et al [105] utilized contact potentials to predict ΔΔG of three sets of 303, 658 and 1356 mutants and their prediction correlations varied between 0.45 to 0.78.…”
Section: Protein Stabilitymentioning
confidence: 99%
“…To our knowledge, protein dynamics and flexibility have not been explicitly modeled in previous methods. Ignoring protein flexibility prohibits the application of current prediction methods to a wide range of mutations [100,104].…”
Section: Protein Stabilitymentioning
confidence: 99%
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