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For: Xue LC, Dobbs D, Bonvin AMJJ, Honavar V. Computational prediction of protein interfaces: A review of data driven methods. FEBS Lett 2015;589:3516-26. [PMID: 26460190 PMCID: PMC4655202 DOI: 10.1016/j.febslet.2015.10.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/01/2015] [Accepted: 10/02/2015] [Indexed: 01/06/2023]
Number Cited by Other Article(s)
1
Vicidomini C, Fontanella F, D’Alessandro T, Roviello GN. A Survey on Computational Methods in Drug Discovery for Neurodegenerative Diseases. Biomolecules 2024;14:1330. [PMID: 39456263 PMCID: PMC11506269 DOI: 10.3390/biom14101330] [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: 09/13/2024] [Revised: 10/14/2024] [Accepted: 10/16/2024] [Indexed: 10/28/2024]  Open
2
Abbas MKG, Rassam A, Karamshahi F, Abunora R, Abouseada M. The Role of AI in Drug Discovery. Chembiochem 2024;25:e202300816. [PMID: 38735845 DOI: 10.1002/cbic.202300816] [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: 12/03/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
3
Waman VP, Ashford P, Lam SD, Sen N, Abbasian M, Woodridge L, Goldtzvik Y, Bordin N, Wu J, Sillitoe I, Orengo CA. Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics. Sci Rep 2024;14:14208. [PMID: 38902252 PMCID: PMC11190248 DOI: 10.1038/s41598-024-61541-1] [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: 11/07/2023] [Accepted: 05/07/2024] [Indexed: 06/22/2024]  Open
4
Nandigrami P, Fiser A. Assessing the functional impact of protein binding site definition. Protein Sci 2024;33:e5026. [PMID: 38757384 PMCID: PMC11099757 DOI: 10.1002/pro.5026] [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: 10/06/2023] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
5
Yang Q, Jin X, Zhou H, Ying J, Zou J, Liao Y, Lu X, Ge S, Yu H, Min X. SurfPro-NN: A 3D point cloud neural network for the scoring of protein-protein docking models based on surfaces features and protein language models. Comput Biol Chem 2024;110:108067. [PMID: 38714420 DOI: 10.1016/j.compbiolchem.2024.108067] [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: 01/18/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 05/09/2024]
6
Zeng T, Zhou Y, Zheng JW, Zhuo X, Zhu L, Wan LH. Rosmarinic acid alleviates septic acute respiratory distress syndrome in mice by suppressing the bronchial epithelial RAS-mediated ferroptosis. Int Immunopharmacol 2024;135:112304. [PMID: 38776851 DOI: 10.1016/j.intimp.2024.112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
7
Graef J, Ehrt C, Reim T, Rarey M. Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J Chem Inf Model 2024;64:3332-3349. [PMID: 38470439 DOI: 10.1021/acs.jcim.3c01462] [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: 03/13/2024]
8
Parvathy J, Yazhini A, Srinivasan N, Sowdhamini R. Interfacial residues in protein-protein complexes are in the eyes of the beholder. Proteins 2024;92:509-528. [PMID: 37982321 DOI: 10.1002/prot.26628] [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: 05/13/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
9
Yang Z, Hao T, Ma J, Yang D, Qiu M, Wang R. Tribuloside: Mechanisms and Efficacy in Treating Acute Lung Injury Revealed by Network Pharmacology and Experimental Validation. Dose Response 2024;22:15593258241251594. [PMID: 38725454 PMCID: PMC11080732 DOI: 10.1177/15593258241251594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024]  Open
10
Xiong D, Qiu Y, Zhao J, Zhou Y, Lee D, Gupta S, Torres M, Lu W, Liang S, Kang JJ, Eng C, Loscalzo J, Cheng F, Yu H. Structurally-informed human interactome reveals proteome-wide perturbations by disease mutations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.24.538110. [PMID: 37162909 PMCID: PMC10168245 DOI: 10.1101/2023.04.24.538110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
11
Giulini M, Honorato RV, Rivera JL, Bonvin AMJJ. ARCTIC-3D: automatic retrieval and clustering of interfaces in complexes from 3D structural information. Commun Biol 2024;7:49. [PMID: 38184711 PMCID: PMC10771469 DOI: 10.1038/s42003-023-05718-w] [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: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024]  Open
12
Xu X, Bonvin AMJJ. DeepRank-GNN-esm: a graph neural network for scoring protein-protein models using protein language model. BIOINFORMATICS ADVANCES 2024;4:vbad191. [PMID: 38213822 PMCID: PMC10782804 DOI: 10.1093/bioadv/vbad191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/19/2023] [Indexed: 01/13/2024]
13
Jiang LD, Zhang WD, Wang BS, Cai YZ, Qin X, Zhao WB, Ji P, Yuan ZW, Wei YM, Yao WL. Exploration of the Potential Mechanism of Yujin Powder Treating Dampness-heat Diarrhea by Integrating UPLC-MS/MS and Network Pharmacology Prediction. Comb Chem High Throughput Screen 2024;27:1466-1479. [PMID: 37818576 DOI: 10.2174/0113862073246096230926045428] [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: 02/13/2023] [Revised: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/12/2023]
14
Yang Y, Bi C, Li B, Li Y, Song Y, Zhang M, Peng L, Fan D, Duan R, Li Z. Exploring the Molecular Mechanism of HongTeng Decoction against Inflammation based on Network Analysis and Experiments Validation. Curr Comput Aided Drug Des 2024;20:170-182. [PMID: 37309760 PMCID: PMC10641852 DOI: 10.2174/1573409919666230612103201] [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: 04/20/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]
15
Kiani YS, Jabeen I. Challenges of Protein-Protein Docking of the Membrane Proteins. Methods Mol Biol 2024;2780:203-255. [PMID: 38987471 DOI: 10.1007/978-1-0716-3985-6_12] [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: 07/12/2024]
16
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez‐Lumbreras LA, Fernandez‐Recio J, Harmalkar A, Chu L, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang S, Roel‐Touris J, Jimenez‐Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas‐Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman‐Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota‐Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda‐Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Velankar S, Wodak SJ. Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins 2023;91:1658-1683. [PMID: 37905971 PMCID: PMC10841881 DOI: 10.1002/prot.26609] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 11/02/2023]
17
Genz LR, Mulvaney T, Nair S, Topf M. PICKLUSTER: a protein-interface clustering and analysis plug-in for UCSF ChimeraX. Bioinformatics 2023;39:btad629. [PMID: 37846034 PMCID: PMC10629935 DOI: 10.1093/bioinformatics/btad629] [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: 06/13/2023] [Revised: 09/07/2023] [Accepted: 10/13/2023] [Indexed: 10/18/2023]  Open
18
Liu Z, Qian W, Cai W, Song W, Wang W, Maharjan DT, Cheng W, Chen J, Wang H, Xu D, Lin GN. Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations. RESEARCH (WASHINGTON, D.C.) 2023;6:0219. [PMID: 37701056 PMCID: PMC10494974 DOI: 10.34133/research.0219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/20/2023] [Indexed: 09/14/2023]
19
Mishra M, Jiang H, Wei Q. New insights on the differential interaction of sulfiredoxin with members of the peroxiredoxin family revealed by protein-protein docking and experimental studies. Eur J Pharmacol 2023;954:175873. [PMID: 37353187 PMCID: PMC10426277 DOI: 10.1016/j.ejphar.2023.175873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
20
Kotb HM, Davey NE. xProtCAS: A Toolkit for Extracting Conserved Accessible Surfaces from Protein Structures. Biomolecules 2023;13:906. [PMID: 37371487 DOI: 10.3390/biom13060906] [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: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023]  Open
21
Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023;18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
22
Zhi G, Shao B, Zheng T, Mu J, Li J, Feng Y, Zhu S, Dang Y, Liu F, Wang D. Exploring the molecular mechanism of Gan Shuang granules for the treatment of non-alcoholic steatohepatitis using network pharmacology, molecular docking, and experimental verification. Front Pharmacol 2023;14:1082451. [PMID: 36762105 PMCID: PMC9902723 DOI: 10.3389/fphar.2023.1082451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/13/2023] [Indexed: 01/25/2023]  Open
23
Rogers JR, Nikolényi G, AlQuraishi M. Growing ecosystem of deep learning methods for modeling protein-protein interactions. Protein Eng Des Sel 2023;36:gzad023. [PMID: 38102755 DOI: 10.1093/protein/gzad023] [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: 10/10/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]  Open
24
Sarkar C, Das B, Rawat VS, Wahlang JB, Nongpiur A, Tiewsoh I, Lyngdoh NM, Das D, Bidarolli M, Sony HT. Artificial Intelligence and Machine Learning Technology Driven Modern Drug Discovery and Development. Int J Mol Sci 2023;24:ijms24032026. [PMID: 36768346 PMCID: PMC9916967 DOI: 10.3390/ijms24032026] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/22/2023]  Open
25
Jung Y, Geng C, Bonvin AMJJ, Xue LC, Honavar VG. MetaScore: A Novel Machine-Learning-Based Approach to Improve Traditional Scoring Functions for Scoring Protein-Protein Docking Conformations. Biomolecules 2023;13:121. [PMID: 36671507 PMCID: PMC9855734 DOI: 10.3390/biom13010121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023]  Open
26
Ozdemir ES, Nussinov R. Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions. Front Oncol 2023;13:1061595. [PMID: 36910650 PMCID: PMC9997845 DOI: 10.3389/fonc.2023.1061595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023]  Open
27
Mechanisms of Xiaochaihu Decoction on Treating Hepatic Fibrosis Explored by Network Pharmacology. DISEASE MARKERS 2022;2022:8925637. [PMID: 36246566 PMCID: PMC9553551 DOI: 10.1155/2022/8925637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022]
28
Walder M, Edelstein E, Carroll M, Lazarev S, Fajardo JE, Fiser A, Viswanathan R. Integrated structure-based protein interface prediction. BMC Bioinformatics 2022;23:301. [PMID: 35879651 PMCID: PMC9316365 DOI: 10.1186/s12859-022-04852-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]  Open
29
Sen N, Anishchenko I, Bordin N, Sillitoe I, Velankar S, Baker D, Orengo C. Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs. Brief Bioinform 2022;23:bbac187. [PMID: 35641150 PMCID: PMC9294430 DOI: 10.1093/bib/bbac187] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 12/12/2022]  Open
30
Tubiana J, Schneidman-Duhovny D, Wolfson HJ. ScanNet: A web server for structure-based prediction of protein binding sites with geometric deep learning. J Mol Biol 2022;434:167758. [DOI: 10.1016/j.jmb.2022.167758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/28/2022]
31
Chi Q, Yang Z, Liang HP. A Transendothelial Leukocyte Transmigration Model Based on Computational Fluid Dynamics and BP Neural Network. Front Bioeng Biotechnol 2022;10:881797. [PMID: 35800330 PMCID: PMC9253467 DOI: 10.3389/fbioe.2022.881797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022]  Open
32
Rajendran M, Ferran MC, Babbitt GA. Identifying vaccine escape sites via statistical comparisons of short-term molecular dynamics. BIOPHYSICAL REPORTS 2022;2:100056. [PMID: 35403093 PMCID: PMC8978532 DOI: 10.1016/j.bpr.2022.100056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/31/2022] [Indexed: 01/08/2023]
33
ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction. Nat Methods 2022;19:730-739. [DOI: 10.1038/s41592-022-01490-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/12/2022] [Indexed: 11/08/2022]
34
Rodrigues CHM, Ascher DB. CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning. Nucleic Acids Res 2022;50:W204-W209. [PMID: 35609999 PMCID: PMC9252741 DOI: 10.1093/nar/gkac381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022]  Open
35
Biró B, Zhao B, Kurgan L. Complementarity of the residue-level protein function and structure predictions in human proteins. Comput Struct Biotechnol J 2022;20:2223-2234. [PMID: 35615015 PMCID: PMC9118482 DOI: 10.1016/j.csbj.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/02/2022] [Accepted: 05/02/2022] [Indexed: 11/24/2022]  Open
36
Li L, Lu Y, Liu Y, Wang D, Duan L, Cheng S, Liu G. Network Pharmacology Analysis of Huangqi Jianzhong Tang Targets in Gastric Cancer. Front Pharmacol 2022;13:882147. [PMID: 35462892 PMCID: PMC9024123 DOI: 10.3389/fphar.2022.882147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 03/18/2022] [Indexed: 11/13/2022]  Open
37
Grassmann G, Miotto M, Di Rienzo L, Gosti G, Ruocco G, Milanetti E. A novel computational strategy for defining the minimal protein molecular surface representation. PLoS One 2022;17:e0266004. [PMID: 35421111 PMCID: PMC9009619 DOI: 10.1371/journal.pone.0266004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/12/2022] [Indexed: 11/18/2022]  Open
38
Schweke H, Mucchielli MH, Chevrollier N, Gosset S, Lopes A. SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features. J Chem Inf Model 2022;62:1595-1601. [DOI: 10.1021/acs.jcim.1c01269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
39
Abbasi WA, Ajaz SA, Arshad K, Liaqat S, Andleeb S, Bibi M, Abbas SA. SIP: A computational prediction of S-Adenosyl methionine (SAM) interacting proteins and their interaction sites through primary structures. Comput Biol Chem 2022;98:107662. [DOI: 10.1016/j.compbiolchem.2022.107662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/26/2022] [Accepted: 03/03/2022] [Indexed: 11/03/2022]
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BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction. J Mol Biol 2022;434:167556. [DOI: 10.1016/j.jmb.2022.167556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/12/2022] [Accepted: 03/16/2022] [Indexed: 11/20/2022]
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Kumari S, Shivakrishna P, Sreenivasulu K. Molecular docking analysis of two bioactive molecules KLUF10 and KLUF13 isolated from the marine bacteria Micrococcus sp. OUS9 with TNF alpha. Bioinformation 2022;17:530-535. [PMID: 35095226 PMCID: PMC8770404 DOI: 10.6026/97320630017530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/21/2021] [Accepted: 04/30/2021] [Indexed: 11/29/2022]  Open
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Ke K, Jiang X, Zhang Y, Zhou Y, Zhao J, Zhang J, Liu Y, An M. Exploring the Mechanism of Wu Ling San plus Flavor for the Treatment of Diabetic Macular Edema Based on Network Pharmacology and Molecular Docking Techniques. Chin Med 2022. [DOI: 10.4236/cm.2022.133004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
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Zhang F, Zhao B, Shi W, Li M, Kurgan L. DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning. Brief Bioinform 2021;23:6461158. [PMID: 34905768 DOI: 10.1093/bib/bbab521] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/30/2021] [Accepted: 11/14/2021] [Indexed: 12/14/2022]  Open
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Renaud N, Geng C, Georgievska S, Ambrosetti F, Ridder L, Marzella DF, Réau MF, Bonvin AMJJ, Xue LC. DeepRank: a deep learning framework for data mining 3D protein-protein interfaces. Nat Commun 2021;12:7068. [PMID: 34862392 PMCID: PMC8642403 DOI: 10.1038/s41467-021-27396-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 11/12/2021] [Indexed: 11/08/2022]  Open
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Gao F, Glaser J, Glotzer SC. The role of complementary shape in protein dimerization. SOFT MATTER 2021;17:7376-7383. [PMID: 34304260 DOI: 10.1039/d1sm00468a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
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Dara S, Dhamercherla S, Jadav SS, Babu CHM, Ahsan MJ. Machine Learning in Drug Discovery: A Review. Artif Intell Rev 2021;55:1947-1999. [PMID: 34393317 PMCID: PMC8356896 DOI: 10.1007/s10462-021-10058-4] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Liu J, Liu J, Tong X, Peng W, Wei S, Sun T, Wang Y, Zhang B, Li W. Network Pharmacology Prediction and Molecular Docking-Based Strategy to Discover the Potential Pharmacological Mechanism of Huai Hua San Against Ulcerative Colitis. DRUG DESIGN DEVELOPMENT AND THERAPY 2021;15:3255-3276. [PMID: 34349502 PMCID: PMC8326529 DOI: 10.2147/dddt.s319786] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
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Identifying hydrophobic protein patches to inform protein interaction interfaces. Proc Natl Acad Sci U S A 2021;118:2018234118. [PMID: 33526682 DOI: 10.1073/pnas.2018234118] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
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Das S, Scholes HM, Sen N, Orengo C. CATH functional families predict functional sites in proteins. Bioinformatics 2021;37:1099-1106. [PMID: 33135053 PMCID: PMC8150129 DOI: 10.1093/bioinformatics/btaa937] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/30/2020] [Accepted: 10/27/2020] [Indexed: 01/12/2023]  Open
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Beytur S. Marker residue types at the structural regions of transmembrane alpha-helical and beta-barrel interfaces. Proteins 2021;89:1145-1157. [PMID: 33890696 DOI: 10.1002/prot.26087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/11/2022]
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