GPCRM: a homology modeling web service with triple membrane-fitted quality assessment of GPCR models

By Przemyslaw Miszta, Pawel Pasznik, Jakub Jakowiecki, Agnieszka Sztyler, Dorota Latek, Slawomir Filipek. 2018

36 citations recorded by the source corpus.

Abstract Due to the involvement of G protein-coupled receptors (GPCRs) in most of the physiological and pathological processes in humans they have been attracting a lot of attention from pharmaceutical industry as well as from scientific community. Therefore, the need for new, high quality structures of GPCRs is enormous. The updated homology modeling service GPCRM (http://gpcrm.biomodellab.eu/) meets those expectations by greatly reducing the execution time of submissions (from days to hours/minutes) with nearly the same average quality of obtained models. Additionally, due to three different scoring functions (Rosetta, Rosetta-MP, BCL::Score) it is possible to select accurate models for the required purposes: the structure of the binding site, the transmembrane domain or the overall shape of the receptor. Currently, no other web service for GPCR modeling provides this possibility. GPCRM is continually upgraded in a semi-automatic way and the number of template structures has increased from 20 in 2013 to over 90 including structures the same receptor with different ligands which can influence the structure not only in the on/off manner. Two types of protein viewers can be used for visual inspection of obtained models. The extended sortable tables with available templates provide links to external databases and display ligand–receptor interactions in visual form.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

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In Computational Theory and Mathematics

1. Michael Feig
2. Jens Meiler
3. Lim Heo

In Molecular Biology

1. Lim Heo
2. Michael Feig
3. Jens Meiler
4. Brian Joseph Bender
5. Brennica Marlow
6. David Baker
7. Collin F Arbour
8. Yang Zhang

In Radiology, Nuclear Medicine and Imaging

1. Lim Heo
2. Michael Feig
3. Jens Meiler
4. Brian Joseph Bender
5. Brennica Marlow

Citations in the corpus

• Multi-State Modeling of G-protein Coupled Receptors at Experimental Accuracy (2021, methodology): “For example, GPCR models predicted using templates with sequence identities higher than 20%–40% were assumed to be confident.(24,33,34) Likewise, it may be used to infer the success of modeling prior to the active state modeling via”
• Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “Servers for the prediction of GPCRs from multiple templates are available including GPCR-ModSim [12], GPCR-I-Tasser [13], GPCRM [14], GPCR-SSFE [15], and GPCRdb [16].”