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Number Cited by Other Article(s)
1
Saganuwan SA. Structure-activity relationship of pharmacophores and toxicophores: the need for clinical strategy. Daru 2024:10.1007/s40199-024-00525-y. [PMID: 38935265 DOI: 10.1007/s40199-024-00525-y] [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: 11/20/2023] [Accepted: 06/11/2024] [Indexed: 06/28/2024]  Open
2
Sahu M, Vashishth S, Kukreti N, Gulia A, Russell A, Ambasta RK, Kumar P. Synergizing drug repurposing and target identification for neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024;205:111-169. [PMID: 38789177 DOI: 10.1016/bs.pmbts.2024.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
3
Hoogstraten CA, Koenderink JB, van Straaten CE, Scheer-Weijers T, Smeitink JAM, Schirris TJJ, Russel FGM. Pyruvate dehydrogenase is a potential mitochondrial off-target for gentamicin based on in silico predictions and in vitro inhibition studies. Toxicol In Vitro 2024;95:105740. [PMID: 38036072 DOI: 10.1016/j.tiv.2023.105740] [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: 07/10/2023] [Revised: 11/08/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
4
Odunitan TT, Saibu OA, Apanisile BT, Omoboyowa DA, Balogun TA, Awe AV, Ajayi TM, Olagunju GV, Mahmoud FM, Akinboade M, Adeniji CB, Abdulazeez WO. Integrating biocomputational techniques for Breast cancer drug discovery via the HER-2, BCRA, VEGF and ER protein targets. Comput Biol Med 2024;168:107737. [PMID: 38000249 DOI: 10.1016/j.compbiomed.2023.107737] [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: 10/05/2023] [Revised: 11/03/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023]
5
Li S, Tian T, Zhang Z, Zou Z, Zhao D, Zeng J. PocketAnchor: Learning structure-based pocket representations for protein-ligand interaction prediction. Cell Syst 2023;14:692-705.e6. [PMID: 37516103 DOI: 10.1016/j.cels.2023.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/25/2022] [Accepted: 05/19/2023] [Indexed: 07/31/2023]
6
Szwabowski GL, Daigle BJ, Baker DL, Parrill AL. Structure-based pharmacophore modeling 2. Developing a novel framework for structure-based pharmacophore model generation and selection. J Mol Graph Model 2023;122:108488. [PMID: 37121167 DOI: 10.1016/j.jmgm.2023.108488] [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: 11/06/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023]
7
Szwabowski GL, Baker DL, Parrill AL. Application of computational methods for class A GPCR Ligand discovery. J Mol Graph Model 2023;121:108434. [PMID: 36841204 DOI: 10.1016/j.jmgm.2023.108434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
8
Szwabowski GL, Cole JA, Baker DL, Parrill AL. Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation. J Mol Graph Model 2023;121:108429. [PMID: 36804368 DOI: 10.1016/j.jmgm.2023.108429] [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: 11/06/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023]
9
Singh MP, Singh N, Mishra D, Ehsan S, Chaturvedi VK, Chaudhary A, Singh V, Vamanu E. Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review. Curr Pharm Des 2023;29:2601-2617. [PMID: 37916490 DOI: 10.2174/0113816128259795231023193419] [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: 05/18/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023]
10
Hernández-Silva D, Alcaraz-Pérez F, Pérez-Sánchez H, Cayuela ML. Virtual screening and zebrafish models in tandem, for drug discovery and development. Expert Opin Drug Discov 2022:1-13. [DOI: 10.1080/17460441.2022.2147503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
11
Identification of Active Compounds against Melanoma Growth by Virtual Screening for Non-Classical Human DHFR Inhibitors. Int J Mol Sci 2022;23:ijms232213946. [PMID: 36430425 PMCID: PMC9694616 DOI: 10.3390/ijms232213946] [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: 09/06/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022]  Open
12
Liu S, Zhou J, Feng Z, Zhang J, Li S, Jin Z, Zhang C, Li S, He G, Li H. VRPharmer: Bringing Virtual Reality into Pharmacophore-based Virtual Screening with Interactive Exploration and Realistic Visualization. Bioinformatics 2022;38:4953-4955. [PMID: 36073903 DOI: 10.1093/bioinformatics/btac615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/01/2022] [Accepted: 09/07/2022] [Indexed: 11/13/2022]  Open
13
Drug Design by Pharmacophore and Virtual Screening Approach. Pharmaceuticals (Basel) 2022;15:ph15050646. [PMID: 35631472 PMCID: PMC9145410 DOI: 10.3390/ph15050646] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 12/20/2022]  Open
14
Mapping of Protein Binding Sites using clustering algorithms development of a pharmacophore based drug discovery tool. J Mol Graph Model 2022;115:108228. [DOI: 10.1016/j.jmgm.2022.108228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/28/2022] [Accepted: 05/19/2022] [Indexed: 11/22/2022]
15
Molecular Docking as a Potential Approach in Repurposing Drugs Against COVID-19: a Systematic Review and Novel Pharmacophore Models. CURRENT PHARMACOLOGY REPORTS 2022;8:212-226. [PMID: 35381996 PMCID: PMC8970976 DOI: 10.1007/s40495-022-00285-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/14/2022] [Indexed: 12/12/2022]
16
Tran QH, Nguyen QT, Vo NQH, Mai TT, Tran TTN, Tran TD, Le MT, Trinh DTT, Thai KM. Structure-based 3D-Pharmacophore modeling to discover novel interleukin 6 inhibitors: An in silico screening, molecular dynamics simulations and binding free energy calculations. PLoS One 2022;17:e0266632. [PMID: 35385549 PMCID: PMC8986010 DOI: 10.1371/journal.pone.0266632] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022]  Open
17
Kumar SP, Dixit NY, Patel CN, Rawal RM, Pandya HA. PharmRF: A machine-learning scoring function to identify the best protein-ligand complexes for structure-based pharmacophore screening with high enrichments. J Comput Chem 2022;43:847-863. [PMID: 35301752 DOI: 10.1002/jcc.26840] [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: 12/18/2021] [Revised: 02/14/2022] [Accepted: 02/26/2022] [Indexed: 11/09/2022]
18
Identification of potential interleukin-8 inhibitors acting on the interactive site between chemokine and CXCR2 receptor: A computational approach. PLoS One 2022;17:e0264385. [PMID: 35202450 PMCID: PMC8870564 DOI: 10.1371/journal.pone.0264385] [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: 10/02/2021] [Accepted: 02/09/2022] [Indexed: 11/19/2022]  Open
19
Kandwal S, Fayne D. Repurposing drugs for treatment of SARS-CoV-2 infection: computational design insights into mechanisms of action. J Biomol Struct Dyn 2022;40:1316-1330. [PMID: 32964805 PMCID: PMC7544922 DOI: 10.1080/07391102.2020.1825232] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/12/2020] [Indexed: 12/15/2022]
20
Castro LHE, Sant'Anna CMR. Molecular Modeling Techniques Applied to the Design of Multitarget Drugs: Methods and Applications. Curr Top Med Chem 2021;22:333-346. [PMID: 34844540 DOI: 10.2174/1568026621666211129140958] [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: 07/01/2021] [Revised: 10/23/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022]
21
N Vijayan A, Refaei MA, Silva RN, Tsang P, Zhang P. Detection of Sortase A and Identification of Its Inhibitors by Paramagnetic Nanoparticle-Assisted Nuclear Relaxation. Anal Chem 2021;93:15430-15437. [PMID: 34757710 DOI: 10.1021/acs.analchem.1c03271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
22
Kumar P, Mohanty D. Development of a Novel Pharmacophore Model Guided by the Ensemble of Waters and Small Molecule Fragments Bound to SARS-CoV-2 Main Protease. Mol Inform 2021;41:e2100178. [PMID: 34633768 PMCID: PMC8646684 DOI: 10.1002/minf.202100178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]
23
Vásquez AF, Muñoz AR, Duitama J, González Barrios A. Non-Extensive Fragmentation of Natural Products and Pharmacophore-Based Virtual Screening as a Practical Approach to Identify Novel Promising Chemical Scaffolds. Front Chem 2021;9:700802. [PMID: 34422762 PMCID: PMC8377161 DOI: 10.3389/fchem.2021.700802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022]  Open
24
MUHAMMED MT, AKI-YALCIN E. Pharmacophore Modeling in Drug Discovery: Methodology and Current Status. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2021. [DOI: 10.18596/jotcsa.927426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]  Open
25
Identification of potential COVID-19 main protease inhibitors using structure-based pharmacophore approach, molecular docking and repurposing studies. ACTA PHARMACEUTICA (ZAGREB, CROATIA) 2021;71:163-174. [PMID: 33151166 DOI: 10.2478/acph-2021-0016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/02/2020] [Indexed: 01/19/2023]
26
Agrawal PK, Agrawal C, Blunden G. Rutin: A Potential Antiviral for Repurposing as a SARS-CoV-2 Main Protease (Mpro) Inhibitor. Nat Prod Commun 2021. [DOI: 10.1177/1934578x21991723] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
27
Temml V, Kutil Z. Structure-based molecular modeling in SAR analysis and lead optimization. Comput Struct Biotechnol J 2021;19:1431-1444. [PMID: 33777339 PMCID: PMC7979990 DOI: 10.1016/j.csbj.2021.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/21/2021] [Accepted: 02/23/2021] [Indexed: 12/13/2022]  Open
28
Unraveling the binding mechanism of an Oxovanadium(IV) - Curcumin complex on albumin, DNA and DNA gyrase by in vitro and in silico studies and evaluation of its hemocompatibility. J Inorg Biochem 2021;221:111402. [PMID: 33975249 DOI: 10.1016/j.jinorgbio.2021.111402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 11/20/2022]
29
Lombino J, Gulotta MR, De Simone G, Mekni N, De Rosa M, Carbone D, Parrino B, Cascioferro SM, Diana P, Padova A, Perricone U. Dynamic-shared Pharmacophore Approach as Tool to Design New Allosteric PRC2 Inhibitors, Targeting EED Binding Pocket. Mol Inform 2020;40:e2000148. [PMID: 32833314 DOI: 10.1002/minf.202000148] [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: 06/15/2020] [Accepted: 08/23/2020] [Indexed: 11/09/2022]
30
Jiang S, Feher M, Williams C, Cole B, Shaw DE. AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. J Chem Inf Model 2020;60:4326-4338. [PMID: 32639159 DOI: 10.1021/acs.jcim.0c00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
31
D'Abadia PL, BailÃo EFLC, Lino JÚnior RS, Oliveira MG, Silva VB, Oliveira LAR, ConceiÇÃo EC, Melo-Reis PR, Borges LL, GonÇalves PJ, Almeida LM. Hancornia speciosa serum fraction latex stimulates the angiogenesis and extracellular matrix remodeling processes. AN ACAD BRAS CIENC 2020;92:e20190107. [PMID: 32556049 DOI: 10.1590/0001-3765202020190107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/03/2019] [Indexed: 11/21/2022]  Open
32
Vásquez AF, Reyes Muñoz A, Duitama J, González Barrios A. Discovery of new potential CDK2/VEGFR2 type II inhibitors by fragmentation and virtual screening of natural products. J Biomol Struct Dyn 2020;39:3285-3299. [DOI: 10.1080/07391102.2020.1763839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
33
Kumar SP, Patel CN, Rawal RM, Pandya HA. Energetic contributions of amino acid residues and its cross‐talk to delineate ligand‐binding mechanism. Proteins 2020;88:1207-1225. [DOI: 10.1002/prot.25894] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/20/2020] [Accepted: 04/03/2020] [Indexed: 02/02/2023]
34
Liu Q, Miao Y, Wang X, Lv G, Peng Y, Li K, Li M, Qiu L, Lin J. Structure-based virtual screening and biological evaluation of novel non-bisphosphonate farnesyl pyrophosphate synthase inhibitors. Eur J Med Chem 2020;186:111905. [DOI: 10.1016/j.ejmech.2019.111905] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 02/09/2023]
35
Multiple Virtual Screening Strategies for the Discovery of Novel Compounds Active Against Dengue Virus: A Hit Identification Study. Sci Pharm 2019. [DOI: 10.3390/scipharm88010002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
36
Tuffaha GO, Hatmal MM, Taha MO. Discovery of new JNK3 inhibitory chemotypes via QSAR-Guided selection of docking-based pharmacophores and comparison with other structure-based pharmacophore modeling methods. J Mol Graph Model 2019;91:30-51. [PMID: 31158642 DOI: 10.1016/j.jmgm.2019.05.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022]
37
Al-Sha'er MA, Al-Aqtash RA, Taha MO. Discovery of New Phosphoinositide 3-kinase Delta (PI3Kδ) Inhibitors via Virtual Screening using Crystallography-derived Pharmacophore Modelling and QSAR Analysis. Med Chem 2019;15:588-601. [PMID: 30799792 DOI: 10.2174/1573406415666190222125333] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 01/31/2019] [Accepted: 02/07/2019] [Indexed: 01/29/2023]
38
Mortier J, Dhakal P, Volkamer A. Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. Molecules 2018;23:molecules23081959. [PMID: 30082611 PMCID: PMC6222449 DOI: 10.3390/molecules23081959] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/27/2018] [Accepted: 07/27/2018] [Indexed: 12/19/2022]  Open
39
Protein‐protein interactions as antibiotic targets: A medicinal chemistry perspective. Med Res Rev 2018;40:469-494. [DOI: 10.1002/med.21519] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/28/2018] [Accepted: 06/03/2018] [Indexed: 12/27/2022]
40
Hatmal MM, Taha MO. Combining Stochastic Deformation/Relaxation and Intermolecular Contacts Analysis for Extracting Pharmacophores from Ligand-Receptor Complexes. J Chem Inf Model 2018. [PMID: 29529367 DOI: 10.1021/acs.jcim.7b00708] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
41
Shiri F, Pirhadi S, Rahmani A. Identification of new potential HIV-1 reverse transcriptase inhibitors by QSAR modeling and structure-based virtual screening. J Recept Signal Transduct Res 2017;38:37-47. [PMID: 29254400 DOI: 10.1080/10799893.2017.1414844] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
42
Ghanakota P, Carlson HA. Comparing pharmacophore models derived from crystallography and NMR ensembles. J Comput Aided Mol Des 2017;31:979-993. [PMID: 29047011 DOI: 10.1007/s10822-017-0077-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
43
Wieder M, Garon A, Perricone U, Boresch S, Seidel T, Almerico AM, Langer T. Common Hits Approach: Combining Pharmacophore Modeling and Molecular Dynamics Simulations. J Chem Inf Model 2017;57:365-385. [PMID: 28072524 DOI: 10.1021/acs.jcim.6b00674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
44
Combining molecular dynamics simulation and ligand-receptor contacts analysis as a new approach for pharmacophore modeling: beta-secretase 1 and check point kinase 1 as case studies. J Comput Aided Mol Des 2016;30:1149-1163. [PMID: 27722817 DOI: 10.1007/s10822-016-9984-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/03/2016] [Indexed: 01/19/2023]
45
Ngo T, Kufareva I, Coleman JL, Graham RM, Abagyan R, Smith NJ. Identifying ligands at orphan GPCRs: current status using structure-based approaches. Br J Pharmacol 2016;173:2934-51. [PMID: 26837045 PMCID: PMC5341249 DOI: 10.1111/bph.13452] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 11/18/2015] [Accepted: 01/29/2016] [Indexed: 12/26/2022]  Open
46
Wieder M, Perricone U, Seidel T, Langer T. Pharmacophore Models Derived from Molecular Dynamics Simulations of Protein-Ligand Complexes: A Case Study. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601101019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
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Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations. MONATSHEFTE FUR CHEMIE 2016;147:553-563. [PMID: 27069282 PMCID: PMC4785218 DOI: 10.1007/s00706-016-1674-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/14/2016] [Indexed: 01/23/2023]
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Wieder M, Perricone U, Boresch S, Seidel T, Langer T. Evaluating the stability of pharmacophore features using molecular dynamics simulations. Biochem Biophys Res Commun 2016;470:685-689. [PMID: 26785387 DOI: 10.1016/j.bbrc.2016.01.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/14/2016] [Indexed: 01/10/2023]
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Kumar A, Zhang KYJ. Application of Shape Similarity in Pose Selection and Virtual Screening in CSARdock2014 Exercise. J Chem Inf Model 2015;56:965-73. [PMID: 26247231 DOI: 10.1021/acs.jcim.5b00279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Wang X, Sun C, Fang L, Yin D. Discovery of novel sphingosine kinase 1 inhibitorsvia structure-based hierarchical virtual screening. MEDCHEMCOMM 2015. [DOI: 10.1039/c4md00312h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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