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How far are we from automatic crystal structure solution via molecular‐replacement techniques?
Author(s) -
Burla Maria Cristina,
Carrozzini Benedetta,
Cascarano Giovanni Luca,
Giacovazzo Carmelo,
Polidori Giampiero
Publication year - 2020
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798319015468
Subject(s) - translation (biology) , rotation (mathematics) , computer science , molecular replacement , algorithm , pipeline (software) , orientation (vector space) , conditional probability , probabilistic logic , conditional probability distribution , point (geometry) , joint probability distribution , probability distribution , probability density function , statistical physics , theoretical computer science , artificial intelligence , mathematics , physics , molecule , geometry , chemistry , programming language , statistics , messenger rna , gene , biochemistry , quantum mechanics
Although the success of molecular‐replacement techniques requires the solution of a six‐dimensional problem, this is often subdivided into two three‐dimensional problems. REMO 09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non‐oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO 09 are used as a starting point for a pipeline which in its first step extends and refines the molecular‐replacement phases, and in its second step creates the final electron‐density map which is automatically interpreted by CAB , an automatic model‐building program for proteins and DNA/RNA structures.