Homology modeling in a dynamical world
Sign Up to like & getrecommendations! Published in 2017 at "Protein Science"
DOI: 10.1002/pro.3274
Abstract: A key concept in template‐based modeling (TBM) is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at… read more here.
Keywords: structural divergence; diversity; correlation; conformational diversity ... See more keywords
Crystal structure and conformational diversity of fluorinated alkyl tosylates
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DOI: 10.1016/j.mencom.2020.01.034
Abstract: Crystal structures of fluorinated alkyl tosylates TsOCH2CF2CHFCF3 and TsOCH2(CF2)3CHF2 have been characterized by X-ray diffraction and quantum chemical calculations. The calculations have revealed the stabilization of head-to-tail conformation for TsOCH2CHFCF2CF3 due to intramolecular F・・・p and… read more here.
Keywords: crystal structure; alkyl tosylates; fluorinated alkyl; structure conformational ... See more keywords
Impact of protein conformational diversity on AlphaFold predictions
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac202
Abstract: MOTIVATION After the outstanding breakthrough of AlphaFold in predicting protein 3D models, new questions appeared and remain unanswered. The ensemble nature of proteins, for example, challenges the structural prediction methods because the models should represent… read more here.
Keywords: conformational diversity; impact protein; diversity; alphafold predictions ... See more keywords
An efficient use of X-ray information, homology modeling, molecular dynamics and knowledge-based docking techniques to predict protein–monosaccharide complexes
Sign Up to like & getrecommendations! Published in 2019 at "Glycobiology"
DOI: 10.1093/glycob/cwy102
Abstract: Unraveling the structure of lectin-carbohydrate complexes is vital for understanding key biological recognition processes and development of glycomimetic drugs. Molecular Docking application to predict them is challenging due to their low affinity, hydrophilic nature and… read more here.
Keywords: monosaccharide complexes; conformational diversity; molecular dynamics; receptor ... See more keywords
Large scale analysis of protein conformational transitions from aqueous to non-aqueous media
Sign Up to like & getrecommendations! Published in 2018 at "BMC Bioinformatics"
DOI: 10.1186/s12859-018-2044-2
Abstract: BackgroundBiocatalysis in organic solvents is nowadays a common practice with a large potential in Biotechnology. Several studies report that proteins which are co-crystallized or soaked in organic solvents preserve their fold integrity showing almost identical… read more here.
Keywords: large scale; non aqueous; aqueous media; conformational diversity ... See more keywords
Conformational diversity in purified prions produced in vitro
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Pathogens"
DOI: 10.1371/journal.ppat.1011083
Abstract: Prion diseases are caused by misfolding of either wild-type or mutant forms of the prion protein (PrP) into self-propagating, pathogenic conformers, collectively termed PrPSc. Both wild-type and mutant PrPSc molecules exhibit conformational diversity in vivo,… read more here.
Keywords: prpsc; conformational diversity; diversity; purified prions ... See more keywords