Abstract:
:The structural description of peptide ligands bound to G protein-coupled receptors (GPCRs) is important for the discovery of new drugs and deeper understanding of the molecular mechanisms of life. Here we describe a three-stage protocol for the molecular docking of peptides to GPCRs using a set of different programs: (1) CABS-dock for docking fully flexible peptides; (2) PD2 method for the reconstruction of atomistic structures from C-alpha traces provided by CABS-dock and (3) Rosetta FlexPepDock for the refinement of protein-peptide complex structures and model scoring. We evaluated the proposed protocol on the set of seven different GPCR-peptide complexes (including one containing a cyclic peptide), for which crystallographic structures are available. We show that CABS-dock produces high resolution models in the sets of top-scored models. These sets of models, after reconstruction to all-atom representation, can be further improved by Rosetta high-resolution refinement and/or minimization, leading in most of the cases to sub-Angstrom accuracy in terms of interface root-mean-square-deviation measure.
journal_name
Brief Bioinformjournal_title
Briefings in bioinformaticsauthors
Badaczewska-Dawid AE,Kmiecik S,Koliński Mdoi
10.1093/bib/bbaa109subject
Has Abstractpub_date
2020-06-10 00:00:00eissn
1467-5463issn
1477-4054pii
5855394pub_type
杂志文章abstract::Recent development of high-throughput technology has accelerated interest in the development of molecular biomarker classifiers for safety assessment, disease diagnostics and prognostics, and prediction of response for patient assignment. This article reviews and evaluates some important aspects and key issues in the ...
journal_title:Briefings in bioinformatics
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更新日期:2021-01-18 00:00:00
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更新日期:2020-07-31 00:00:00
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更新日期:2019-05-21 00:00:00
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更新日期:2014-07-01 00:00:00
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abstract::Integrative analyses of genomic, epigenomic and transcriptomic features for human and various model organisms have revealed that many such features are nonrandomly distributed in the genome. Significant enrichment (or depletion) of genomic features is anticipated to be biologically important. Detection of genomic regi...
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journal_title:Briefings in bioinformatics
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abstract:MOTIVATION:Over the past decade, the field of next-generation sequencing (NGS) has seen dramatic advances in methods and a decrease in costs. Consequently, a large expansion of data has been generated by NGS, most of which have originated from RNA-sequencing (RNA-seq) experiments. Because mitochondrial genes are expres...
journal_title:Briefings in bioinformatics
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pub_type: 杂志文章
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更新日期:2016-09-01 00:00:00
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