Application of the AMPLE Cluster-and-truncate Approach to NMR Structures for Molecular Replacement

Overview

Journal Acta Crystallogr D Biol Crystallogr

Specialty Chemistry

Date 2013 Nov 6

PMID 24189230

Citations 8

Authors

Jaclyn Bibby

Ronan M Keegan

Olga Mayans

Martyn D Winn

Daniel J Rigden

Affiliations

Soon will be listed here.

Abstract

AMPLE is a program developed for clustering and truncating ab initio protein structure predictions into search models for molecular replacement. Here, it is shown that its core cluster-and-truncate methods also work well for processing NMR ensembles into search models. Rosetta remodelling helps to extend success to NMR structures bearing low sequence identity or high structural divergence from the target protein. Potential future routes to improved performance are considered and practical, general guidelines on using AMPLE are provided.

Citing Articles

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Simpkin A, Caballero I, McNicholas S, Stevenson K, Jimenez E, Sanchez Rodriguez F Acta Crystallogr D Struct Biol. 2023; 79(Pt 9):806-819.

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Redeployment of automated MrBUMP search-model identification for map fitting in cryo-EM.

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Factors influencing estimates of coordinate error for molecular replacement.

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Fragon: rapid high-resolution structure determination from ideal protein fragments.

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ARCIMBOLDO on coiled coils.

Caballero I, Sammito M, Millan C, Lebedev A, Soler N, Uson I Acta Crystallogr D Struct Biol. 2018; 74(Pt 3):194-204.

PMID: 29533227 PMC: 5947760. DOI: 10.1107/S2059798317017582.

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