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• W2444229884 startingPage "259" @default.
• W2444229884 abstract "For many protein families, the deluge of new sequence information together with new statistical protocols now allow the accurate prediction of contacting residues from sequence information alone. This offers the possibility of more accurate ab initio (non-homology-based) structure prediction. Such models can be used in structure solution by molecular replacement (MR) where the target fold is novel or is only distantly related to known structures. Here, AMPLE, an MR pipeline that assembles search-model ensembles from ab initio structure predictions ('decoys'), is employed to assess the value of contact-assisted ab initio models to the crystallographer. It is demonstrated that evolutionary covariance-derived residue-residue contact predictions improve the quality of ab initio models and, consequently, the success rate of MR using search models derived from them. For targets containing β-structure, decoy quality and MR performance were further improved by the use of a β-strand contact-filtering protocol. Such contact-guided decoys achieved 14 structure solutions from 21 attempted protein targets, compared with nine for simple Rosetta decoys. Previously encountered limitations were superseded in two key respects. Firstly, much larger targets of up to 221 residues in length were solved, which is far larger than the previously benchmarked threshold of 120 residues. Secondly, contact-guided decoys significantly improved success with β-sheet-rich proteins. Overall, the improved performance of contact-guided decoys suggests that MR is now applicable to a significantly wider range of protein targets than were previously tractable, and points to a direct benefit to structural biology from the recent remarkable advances in sequencing." @default.
• W2444229884 created "2016-06-24" @default.
• W2444229884 creator A5009636964 @default.
• W2444229884 creator A5020751117 @default.
• W2444229884 creator A5037456386 @default.
• W2444229884 creator A5061781296 @default.
• W2444229884 creator A5072809208 @default.
• W2444229884 creator A5082040267 @default.
• W2444229884 date "2016-06-15" @default.
• W2444229884 modified "2023-10-14" @default.
• W2444229884 title "Residue contacts predicted by evolutionary covariance extend the application of<i>ab initio</i>molecular replacement to larger and more challenging protein folds" @default.
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• W2444229884 doi "https://doi.org/10.1107/s2052252516008113" @default.
• W2444229884 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/4937781" @default.
• W2444229884 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/27437113" @default.

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