Journal ArticleDOI
Automated refinement of protein models.
Victor S. Lamzin,Keith S. Wilson +1 more
TLDR
An automated refinement procedure (ARP) for protein models is proposed, and its convergence properties discussed, which are comparable to the iterative least-squares minimization/difference Fourier synthesis approach for small molecules.Abstract:
An automated refinement procedure (ARP) for protein models is proposed, and its convergence properties discussed. It is comparable to the iterative least-squares minimization/difference Fourier synthesis approach for small molecules. ARP has been successfully applied to three proteins, and for two of them resulted in models very similar to those obtained by conventional least-squares refinement and rebuilding with FRODO. In real time ARP is about ten times faster than conventional refinement. In its present form ARP requires high (2.0 A or better) resolution data, which should be of high quality and a starting protein model having about 75% of the atoms in roughly the correct position. For the third protein at 2.4 A resolution, ARP was significantly less powerful but nevertheless gave definite improvement, in the density map at least.read more
Citations
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Journal ArticleDOI
Automated protein model building combined with iterative structure refinement.
TL;DR: Automatic pattern recognition (model building) combined with refinement, allows a structural model to be obtained reliably within a few CPU hours and is demonstrated with examples of a few recently solved structures.
Journal ArticleDOI
Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.
TL;DR: ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands; and finding ordered water molecules.
Journal ArticleDOI
Three-dimensional structure of the tyrosine kinase c-Src
TL;DR: The structure of a large fragment of the c-SRC tyrosine kinase, comprising the regulatory and kinase domains and the carboxy-terminal tail, has been determined and shows how appropriate cellular signals, or transforming mutations in v-Src, could break these interactions to produce an open, active kinase.
Journal ArticleDOI
Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.
TL;DR: The structure of the heterodimeric Fe-only hydrogenase from Desulfovibrio desulfuricans is reported - the first for this class of enzymes and it is suggested that it was imported from the inorganic world as an already functional unit.
Journal ArticleDOI
Crystal structures of c-Src reveal features of its autoinhibitory mechanism.
TL;DR: Four additional c-Src structures in which this segment adopts an ordered but inhibitory conformation are reported, in which the ordered activation loop forms an alpha helix that stabilizes the inactive conformation of the kinase domain, blocks the peptide substrate-binding site, and prevents Tyr-416 phosphorylation.
References
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Journal ArticleDOI
The CCP4 suite: programs for protein crystallography
TL;DR: The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography.