ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation

Acta Crystallographica. Section D, Structural Biology
Ana MedinaMassimo Sammito

Abstract

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structur...Continue Reading

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Citations

Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Rafael Junqueira BorgesIsabel Usón
Aug 4, 2020·Acta Crystallographica. Section D, Structural Biology·Logan S RichardsJose A Rodriguez
Oct 7, 2020·Acta Crystallographica. Section D, Structural Biology·Filomeno Sánchez RodríguezDaniel J Rigden
Oct 8, 2020·Nature Communications·Harriet Crawley-SnowdonDavid J Owen
Feb 10, 2021·Acta Crystallographica. Section D, Structural Biology·Iracema CaballeroAirlie J McCoy

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Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

ARCIMBOLDO
PDBeFold
PyMOL
BORGES
CaBLAM
ALEPH
_ BORGES
Conda
Pyside2
PyPI

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