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DaReUS-Loop: a web server to model multiple loops in homology models.

ABSTRACT: Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.

SUBMITTER: Karami Y

PROVIDER: S-EPMC6602439 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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DaReUS-Loop: a web server to model multiple loops in homology models.

Karami Yasaman Y Rey Julien J Postic Guillaume G Murail Samuel S Tufféry Pierre P de Vries Sjoerd J SJ

Nucleic acids research 20190701 W1

Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform f ...[more]

PMID: 31114872

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