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For: Yadav P, Mollaei P, Cao Z, Wang Y, Farimani AB. Prediction of GPCR activity using Machine Learning. Comput Struct Biotechnol J 2022. [PMID: 35685352 PMCID: PMC9163700 DOI: 10.1016/j.csbj.2022.05.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 11/20/2022]  Open
Number Cited by Other Article(s)
1
Liu W, Li X, Hang B, Wang P. EnGCI: enhancing GPCR-compound interaction prediction via large molecular models and KAN network. BMC Biol 2025;23:136. [PMID: 40375308 DOI: 10.1186/s12915-025-02238-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Accepted: 05/06/2025] [Indexed: 05/18/2025]  Open
2
Conflitti P, Lyman E, Sansom MSP, Hildebrand PW, Gutiérrez-de-Terán H, Carloni P, Ansell TB, Yuan S, Barth P, Robinson AS, Tate CG, Gloriam D, Grzesiek S, Eddy MT, Prosser S, Limongelli V. Functional dynamics of G protein-coupled receptors reveal new routes for drug discovery. Nat Rev Drug Discov 2025;24:251-275. [PMID: 39747671 PMCID: PMC11968245 DOI: 10.1038/s41573-024-01083-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2024] [Indexed: 01/04/2025]
3
Ekambaram S, Arakelov G, Dokholyan NV. The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives. J Mol Biol 2025:169060. [PMID: 40043838 DOI: 10.1016/j.jmb.2025.169060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 02/26/2025] [Accepted: 02/26/2025] [Indexed: 03/16/2025]
4
Badrinarayanan S, Guntuboina C, Mollaei P, Barati Farimani A. Multi-Peptide: Multimodality Leveraged Language-Graph Learning of Peptide Properties. J Chem Inf Model 2025;65:83-91. [PMID: 39700492 PMCID: PMC11733943 DOI: 10.1021/acs.jcim.4c01443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2024] [Revised: 12/03/2024] [Accepted: 12/04/2024] [Indexed: 12/21/2024]
5
Caniceiro AB, Orzeł U, Rosário-Ferreira N, Filipek S, Moreira IS. Leveraging Artificial Intelligence in GPCR Activation Studies: Computational Prediction Methods as Key Drivers of Knowledge. Methods Mol Biol 2025;2870:183-220. [PMID: 39543036 DOI: 10.1007/978-1-0716-4213-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2024]
6
Mollaei P, Sadasivam D, Guntuboina C, Barati Farimani A. IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins Using Large Language Models. J Phys Chem B 2024;128:12030-12037. [PMID: 39586094 DOI: 10.1021/acs.jpcb.4c02507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2024]
7
Lopez-Balastegui M, Stepniewski TM, Kogut-Günthel MM, Di Pizio A, Rosenkilde MM, Mao J, Selent J. Relevance of G protein-coupled receptor (GPCR) dynamics for receptor activation, signalling bias and allosteric modulation. Br J Pharmacol 2024. [PMID: 38978399 DOI: 10.1111/bph.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 07/10/2024]  Open
8
Nguyen ATN, Nguyen DTN, Koh HY, Toskov J, MacLean W, Xu A, Zhang D, Webb GI, May LT, Halls ML. The application of artificial intelligence to accelerate G protein-coupled receptor drug discovery. Br J Pharmacol 2024;181:2371-2384. [PMID: 37161878 DOI: 10.1111/bph.16140] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/14/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]  Open
9
Bhattacharjee A, Kar S, Ojha PK. Unveiling G-protein coupled receptor kinase-5 inhibitors for chronic degenerative diseases: Multilayered prioritization employing explainable machine learning-driven multi-class QSAR, ligand-based pharmacophore and free energy-inspired molecular simulation. Int J Biol Macromol 2024;269:131784. [PMID: 38697440 DOI: 10.1016/j.ijbiomac.2024.131784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/02/2024] [Accepted: 04/21/2024] [Indexed: 05/05/2024]
10
Kim S, Mollaei P, Antony A, Magar R, Barati Farimani A. GPCR-BERT: Interpreting Sequential Design of G Protein-Coupled Receptors Using Protein Language Models. J Chem Inf Model 2024;64:1134-1144. [PMID: 38340054 PMCID: PMC10900288 DOI: 10.1021/acs.jcim.3c01706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
11
Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024;74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
12
Huang WC, Lin WT, Hung MS, Lee JC, Tung CW. Decrypting orphan GPCR drug discovery via multitask learning. J Cheminform 2024;16:10. [PMID: 38263092 PMCID: PMC10804799 DOI: 10.1186/s13321-024-00806-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024]  Open
13
Buyanov I, Popov P. Characterizing conformational states in GPCR structures using machine learning. Sci Rep 2024;14:1098. [PMID: 38212515 PMCID: PMC10784458 DOI: 10.1038/s41598-023-47698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024]  Open
14
Mollaei P, Barati Farimani A. Unveiling Switching Function of Amino Acids in Proteins Using a Machine Learning Approach. J Chem Theory Comput 2023;19:8472-8480. [PMID: 37933128 PMCID: PMC10688191 DOI: 10.1021/acs.jctc.3c00665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/08/2023]
15
Guntuboina C, Das A, Mollaei P, Kim S, Barati Farimani A. PeptideBERT: A Language Model Based on Transformers for Peptide Property Prediction. J Phys Chem Lett 2023;14:10427-10434. [PMID: 37956397 PMCID: PMC10683064 DOI: 10.1021/acs.jpclett.3c02398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/04/2023] [Accepted: 11/07/2023] [Indexed: 11/15/2023]
16
Mollaei P, Barati Farimani A. Activity Map and Transition Pathways of G Protein-Coupled Receptor Revealed by Machine Learning. J Chem Inf Model 2023;63:2296-2304. [PMID: 37036101 PMCID: PMC10131220 DOI: 10.1021/acs.jcim.3c00032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Indexed: 04/11/2023]
17
Jundi D, Coutanceau JP, Bullier E, Imarraine S, Fajloun Z, Hong E. Expression of olfactory receptor genes in non-olfactory tissues in the developing and adult zebrafish. Sci Rep 2023;13:4651. [PMID: 36944644 PMCID: PMC10030859 DOI: 10.1038/s41598-023-30895-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/02/2023] [Indexed: 03/23/2023]  Open
18
Gutiérrez-Mondragón MA, König C, Vellido A. Layer-Wise Relevance Analysis for Motif Recognition in the Activation Pathway of the β2-Adrenergic GPCR Receptor. Int J Mol Sci 2023;24:ijms24021155. [PMID: 36674669 PMCID: PMC9865744 DOI: 10.3390/ijms24021155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023]  Open
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