publication . Other literature type . Article . 2018

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

Miszta, Przemysław; Pasznik, Paweł; Jakowiecki, Jakub; Sztyler, Agnieszka; Latek, Dorota; Filipek, Sławomir;
  • Published: 21 May 2018
  • Publisher: Oxford University Press (OUP)
Abstract
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...
Subjects
free text keywords: Genetics, Web service, computer.software_genre, computer, G protein-coupled receptor, Homology modeling, Biology, Computational biology, Web Server Issue
Related Organizations
32 references, page 1 of 3

1.Pandy-Szekeres G., Munk C., Tsonkov T.M., Mordalski S., Harpsoe K., Hauser A.S., Bojarski A.J., Gloriam D.E.GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res.2018; 46:D440–D446.29155946 [OpenAIRE] [PubMed]

2.Moreno J.L., Holloway T., Gonzalez-Maeso J.G protein-coupled receptor heterocomplexes in neuropsychiatric disorders. Prog. Mol. Biol. Transl. Sci.2013; 117:187–205.23663970 [OpenAIRE] [PubMed]

3.O’Hayre M., Degese M.S., Gutkind J.S.Novel insights into G protein and G protein-coupled receptor signaling in cancer. Curr. Opin. Cell Biol.2014; 27:126–135.24508914 [OpenAIRE] [PubMed]

4.Sodhi A., Montaner S., Gutkind J.S.Viral hijacking of G-protein-coupled-receptor signalling networks. Nat. Rev. Mol. Cell Biol.2004; 5:998–1012.15573137 [OpenAIRE] [PubMed]

5.Thathiah A., De Strooper B.The role of G protein-coupled receptors in the pathology of Alzheimer's disease. Nat. Rev. Neurosci.2011; 12:73–87.21248787 [OpenAIRE] [PubMed]

6.Claeysen S., Cochet M., Donneger R., Dumuis A., Bockaert J., Giannoni P.Alzheimer culprits: cellular crossroads and interplay. Cell Signal.2012; 24:1831–1840.22627093 [PubMed]

7.Schioth H.B., Fredriksson R.The GRAFS classification system of G-protein coupled receptors in comparative perspective. Gen. Comp. Endocrinol.2005; 142:94–101.15862553 [OpenAIRE] [PubMed]

8.Zhang J., Yang J., Jang R., Zhang Y.GPCR-I-TASSER: a hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure. 2015; 23:1538–1549.26190572 [OpenAIRE] [PubMed]

9.Rodriguez D., Brea J., Loza M.I., Carlsson J.Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. Structure. 2014; 22:1140–1151.25043551 [PubMed]

10.Latek D., Pasznik P., Carlomagno T., Filipek S.Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One. 2013; 8:e56742.23468878 [OpenAIRE] [PubMed]

11.Kufareva I., Katritch V.Participants of GPCR DOCK 2013 Participants of GPCR DOCK 2013 Stevens R.C., Abagyan R.Advances in GPCR modeling evaluated by the GPCR Dock 2013 Assessment: Meeting new chall enges. Structure. 2014; 22:1120–1139.25066135 [OpenAIRE] [PubMed]

12.Latek D., Bajda M., Filipek S.A hybrid approach to structure and function modeling of G Protein-Coupled receptors. J. Chem. Inf. Model.2016; 56:630–641.26978043 [OpenAIRE] [PubMed]

13.Marti-Solano M., Iglesias A., de Fabritiis G., Sanz F., Brea J., Loza M.I., Pastor M., Selent J.Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation. Mol. Pharmacol.2015; 87:740–746.25661038 [PubMed]

14.Stepniewski T.M., Filipek S.Non-peptide ligand binding to the formyl peptide receptor FPR2–A comparison to peptide ligand binding modes. Bioorg. Med. Chem.2015; 23:4072–4081.25882522 [OpenAIRE] [PubMed]

15.Jakowiecki J., Filipek S.Hydrophobic ligand entry and exit pathways of the CB1 cannabinoid receptor. J. Chem. Inf. Model.2016; 56:2457–2466.27966915 [OpenAIRE] [PubMed]

32 references, page 1 of 3
Abstract
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...
Subjects
free text keywords: Genetics, Web service, computer.software_genre, computer, G protein-coupled receptor, Homology modeling, Biology, Computational biology, Web Server Issue
Related Organizations
32 references, page 1 of 3

1.Pandy-Szekeres G., Munk C., Tsonkov T.M., Mordalski S., Harpsoe K., Hauser A.S., Bojarski A.J., Gloriam D.E.GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res.2018; 46:D440–D446.29155946 [OpenAIRE] [PubMed]

2.Moreno J.L., Holloway T., Gonzalez-Maeso J.G protein-coupled receptor heterocomplexes in neuropsychiatric disorders. Prog. Mol. Biol. Transl. Sci.2013; 117:187–205.23663970 [OpenAIRE] [PubMed]

3.O’Hayre M., Degese M.S., Gutkind J.S.Novel insights into G protein and G protein-coupled receptor signaling in cancer. Curr. Opin. Cell Biol.2014; 27:126–135.24508914 [OpenAIRE] [PubMed]

4.Sodhi A., Montaner S., Gutkind J.S.Viral hijacking of G-protein-coupled-receptor signalling networks. Nat. Rev. Mol. Cell Biol.2004; 5:998–1012.15573137 [OpenAIRE] [PubMed]

5.Thathiah A., De Strooper B.The role of G protein-coupled receptors in the pathology of Alzheimer's disease. Nat. Rev. Neurosci.2011; 12:73–87.21248787 [OpenAIRE] [PubMed]

6.Claeysen S., Cochet M., Donneger R., Dumuis A., Bockaert J., Giannoni P.Alzheimer culprits: cellular crossroads and interplay. Cell Signal.2012; 24:1831–1840.22627093 [PubMed]

7.Schioth H.B., Fredriksson R.The GRAFS classification system of G-protein coupled receptors in comparative perspective. Gen. Comp. Endocrinol.2005; 142:94–101.15862553 [OpenAIRE] [PubMed]

8.Zhang J., Yang J., Jang R., Zhang Y.GPCR-I-TASSER: a hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome. Structure. 2015; 23:1538–1549.26190572 [OpenAIRE] [PubMed]

9.Rodriguez D., Brea J., Loza M.I., Carlsson J.Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. Structure. 2014; 22:1140–1151.25043551 [PubMed]

10.Latek D., Pasznik P., Carlomagno T., Filipek S.Towards improved quality of GPCR models by usage of multiple templates and profile-profile comparison. PLoS One. 2013; 8:e56742.23468878 [OpenAIRE] [PubMed]

11.Kufareva I., Katritch V.Participants of GPCR DOCK 2013 Participants of GPCR DOCK 2013 Stevens R.C., Abagyan R.Advances in GPCR modeling evaluated by the GPCR Dock 2013 Assessment: Meeting new chall enges. Structure. 2014; 22:1120–1139.25066135 [OpenAIRE] [PubMed]

12.Latek D., Bajda M., Filipek S.A hybrid approach to structure and function modeling of G Protein-Coupled receptors. J. Chem. Inf. Model.2016; 56:630–641.26978043 [OpenAIRE] [PubMed]

13.Marti-Solano M., Iglesias A., de Fabritiis G., Sanz F., Brea J., Loza M.I., Pastor M., Selent J.Detection of new biased agonists for the serotonin 5-HT2A receptor: modeling and experimental validation. Mol. Pharmacol.2015; 87:740–746.25661038 [PubMed]

14.Stepniewski T.M., Filipek S.Non-peptide ligand binding to the formyl peptide receptor FPR2–A comparison to peptide ligand binding modes. Bioorg. Med. Chem.2015; 23:4072–4081.25882522 [OpenAIRE] [PubMed]

15.Jakowiecki J., Filipek S.Hydrophobic ligand entry and exit pathways of the CB1 cannabinoid receptor. J. Chem. Inf. Model.2016; 56:2457–2466.27966915 [OpenAIRE] [PubMed]

32 references, page 1 of 3
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publication . Other literature type . Article . 2018

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

Miszta, Przemysław; Pasznik, Paweł; Jakowiecki, Jakub; Sztyler, Agnieszka; Latek, Dorota; Filipek, Sławomir;