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For: Govindaraj RG, Naderi M, Singha M, Lemoine J, Brylinski M. Large-scale computational drug repositioning to find treatments for rare diseases. NPJ Syst Biol Appl 2018;4:13. [PMID: 29560273 DOI: 10.1038/s41540-018-0050-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/22/2018] [Accepted: 02/03/2018] [Indexed: 11/08/2022]  Open
Number Cited by Other Article(s)
1
Napolitano G, Has C, Schwerk A, Yuan JH, Ullrich C. Potential of Artificial Intelligence to Accelerate Drug Development for Rare Diseases. Pharmaceut Med 2024;38:79-86. [PMID: 38315404 DOI: 10.1007/s40290-023-00504-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 02/07/2024]
2
Cheohen CFDAR, Esteves MEA, da Fonseca TS, Leal CM, Assis FDLF, Campos MF, Rebelo RS, Allonso D, Leitão GG, da Silva ML, Leitão SG. In silico screening of phenylethanoid glycosides, a class of pharmacologically active compounds as natural inhibitors of SARS-CoV-2 proteases. Comput Struct Biotechnol J 2023;21:1461-1472. [PMID: 36817956 PMCID: PMC9920770 DOI: 10.1016/j.csbj.2023.02.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]  Open
3
Procoxacin bidirectionally inhibits osteoblastic and osteoclastic activity in bone and suppresses bone metastasis of prostate cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023;42:45. [PMID: 36759880 PMCID: PMC9909988 DOI: 10.1186/s13046-023-02610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/21/2023] [Indexed: 02/11/2023]
4
Zhao C, Tan T, Zhang E, Wang T, Gong H, Jia Q, Liu T, Yang X, Zhao J, Wu Z, Wei H, Xiao J, Yang C. A chronicle review of new techniques that facilitate the understanding and development of optimal individualized therapeutic strategies for chordoma. Front Oncol 2022;12:1029670. [PMID: 36465398 PMCID: PMC9708744 DOI: 10.3389/fonc.2022.1029670] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 10/19/2022] [Indexed: 09/01/2023]  Open
5
Shi W, Singha M, Pu L, Srivastava G, Ramanujam J, Brylinski M. GraphSite: Ligand Binding Site Classification with Deep Graph Learning. Biomolecules 2022;12:biom12081053. [PMID: 36008947 PMCID: PMC9405584 DOI: 10.3390/biom12081053] [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: 06/03/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 12/10/2022]  Open
6
Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R. Evaluating the performance of drug-repurposing technologies. Drug Discov Today 2022;27:49-64. [PMID: 34400352 PMCID: PMC10014214 DOI: 10.1016/j.drudis.2021.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 06/20/2021] [Accepted: 08/08/2021] [Indexed: 01/22/2023]
7
Martínez-deMiguel C, Segura-Bedmar I, Chacón-Solano E, Guerrero-Aspizua S. The RareDis corpus: A corpus annotated with rare diseases, their signs and symptoms. J Biomed Inform 2021;125:103961. [PMID: 34879250 DOI: 10.1016/j.jbi.2021.103961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/08/2021] [Accepted: 11/22/2021] [Indexed: 11/26/2022]
8
Nguyen PL, Bui BP, Duong MTH, Lee K, Ahn HC, Cho J. Suppression of LPS-Induced Inflammation and Cell Migration by Azelastine through Inhibition of JNK/NF-κB Pathway in BV2 Microglial Cells. Int J Mol Sci 2021;22:ijms22169061. [PMID: 34445767 PMCID: PMC8396433 DOI: 10.3390/ijms22169061] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023]  Open
9
Del Castillo-Santaella T, Hernández-Morante JJ, Suárez-Olmos J, Maldonado-Valderrama J, Peña-García J, Martínez-Cortés C, Pérez-Sánchez H. Identification of the thistle milk component Silibinin(A) and Glutathione-disulphide as potential inhibitors of the pancreatic lipase: Potential implications on weight loss. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
10
Ibezim A, Onah E, Dim EN, Ntie-Kang F. A computational multi-targeting approach for drug repositioning for psoriasis treatment. BMC Complement Med Ther 2021;21:193. [PMID: 34225727 PMCID: PMC8258956 DOI: 10.1186/s12906-021-03359-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022]  Open
11
Traylor JI, Sheppard HE, Ravikumar V, Breshears J, Raza SM, Lin CY, Patel SR, DeMonte F. Computational Drug Repositioning Identifies Potentially Active Therapies for Chordoma. Neurosurgery 2021;88:428-436. [PMID: 33017025 PMCID: PMC7803434 DOI: 10.1093/neuros/nyaa398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 06/28/2020] [Indexed: 12/27/2022]  Open
12
Giorgio E, Pesce E, Pozzi E, Sondo E, Ferrero M, Morerio C, Borrelli G, Della Sala E, Lorenzati M, Cortelli P, Buffo A, Pedemonte N, Brusco A. A high-content drug screening strategy to identify protein level modulators for genetic diseases: A proof-of-principle in autosomal dominant leukodystrophy. Hum Mutat 2020;42:102-116. [PMID: 33252173 DOI: 10.1002/humu.24147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 11/07/2022]
13
Paludo GP, Thompson CE, Miyamoto KN, Guedes RLM, Zaha A, de Vasconcelos ATR, Cancela M, Ferreira HB. Cestode strobilation: prediction of developmental genes and pathways. BMC Genomics 2020;21:487. [PMID: 32677885 PMCID: PMC7367335 DOI: 10.1186/s12864-020-06878-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 07/02/2020] [Indexed: 02/06/2023]  Open
14
Zhu L, Roberts R, Huang R, Zhao J, Xia M, Delavan B, Mikailov M, Tong W, Liu Z. Drug Repositioning for Noonan and LEOPARD Syndromes by Integrating Transcriptomics With a Structure-Based Approach. Front Pharmacol 2020;11:927. [PMID: 32676024 PMCID: PMC7333460 DOI: 10.3389/fphar.2020.00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 06/08/2020] [Indexed: 01/24/2023]  Open
15
Peng Y, Wang M, Xu Y, Wu Z, Wang J, Zhang C, Liu G, Li W, Li J, Tang Y. Drug repositioning by prediction of drug's anatomical therapeutic chemical code via network-based inference approaches. Brief Bioinform 2020;22:2058-2072. [PMID: 32221552 DOI: 10.1093/bib/bbaa027] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/05/2020] [Accepted: 02/17/2020] [Indexed: 12/17/2022]  Open
16
Naderi M, Lemoine JM, Govindaraj RG, Kana OZ, Feinstein WP, Brylinski M. Binding site matching in rational drug design: algorithms and applications. Brief Bioinform 2019;20:2167-2184. [PMID: 30169563 PMCID: PMC6954434 DOI: 10.1093/bib/bby078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/18/2018] [Accepted: 07/29/2018] [Indexed: 01/06/2023]  Open
17
Misselbeck K, Parolo S, Lorenzini F, Savoca V, Leonardelli L, Bora P, Morine MJ, Mione MC, Domenici E, Priami C. A network-based approach to identify deregulated pathways and drug effects in metabolic syndrome. Nat Commun 2019;10:5215. [PMID: 31740673 PMCID: PMC6861239 DOI: 10.1038/s41467-019-13208-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/25/2019] [Indexed: 12/11/2022]  Open
18
Thilakasiri PS, Dmello RS, Nero TL, Parker MW, Ernst M, Chand AL. Repurposing of drugs as STAT3 inhibitors for cancer therapy. Semin Cancer Biol 2019;68:31-46. [PMID: 31711994 DOI: 10.1016/j.semcancer.2019.09.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/20/2019] [Accepted: 09/24/2019] [Indexed: 02/06/2023]
19
Comparing AutoDock and Vina in Ligand/Decoy Discrimination for Virtual Screening. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9214538] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
20
Pu L, Govindaraj RG, Lemoine JM, Wu HC, Brylinski M. DeepDrug3D: Classification of ligand-binding pockets in proteins with a convolutional neural network. PLoS Comput Biol 2019;15:e1006718. [PMID: 30716081 PMCID: PMC6375647 DOI: 10.1371/journal.pcbi.1006718] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/14/2019] [Accepted: 12/16/2018] [Indexed: 01/19/2023]  Open
21
Hu G, Wang K, Song J, Uversky VN, Kurgan L. Taxonomic Landscape of the Dark Proteomes: Whole-Proteome Scale Interplay Between Structural Darkness, Intrinsic Disorder, and Crystallization Propensity. Proteomics 2018;18:e1800243. [PMID: 30198635 DOI: 10.1002/pmic.201800243] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/30/2018] [Indexed: 12/14/2022]
22
Naderi M, Govindaraj RG, Brylinski M. eModel-BDB: a database of comparative structure models of drug-target interactions from the Binding Database. Gigascience 2018;7:5057873. [PMID: 30052959 PMCID: PMC6131211 DOI: 10.1093/gigascience/giy091] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 07/16/2018] [Indexed: 01/14/2023]  Open
23
Govindaraj RG, Brylinski M. Comparative assessment of strategies to identify similar ligand-binding pockets in proteins. BMC Bioinformatics 2018. [PMID: 29523085 PMCID: PMC5845264 DOI: 10.1186/s12859-018-2109-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]  Open
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