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For: Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, MacKerell AD. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 2010;31:671-90. [PMID: 19575467 PMCID: PMC2888302 DOI: 10.1002/jcc.21367] [Citation(s) in RCA: 3000] [Impact Index Per Article: 214.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Number Cited by Other Article(s)
151
Kumar A, Maiti A, Verma S, Daschakraborty S. How do Photoswitchable Lipids Influence the Intercalation of Anticancer Drug in Lipid Membrane? Investigation using Molecular Dynamics Simulation. Chem Asian J 2024:e202400416. [PMID: 38949780 DOI: 10.1002/asia.202400416] [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: 04/15/2024] [Revised: 06/09/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
152
Zhang Q, Sun T, Yu F, Liu W, Gao J, Chen J, Zheng H, Liu J, Miao C, Guo H, Tian W, Su M, Guo Y, Liu X, Pei Y, Wang Z, Chen S, Mu C, Lam SM, Shui G, Li Z, Yu Z, Zhang Y, Chen G, Lu C, Midgley AC, Li C, Bian X, Liao X, Wang Y, Xiong W, Zhu H, Li Y, Chen Q. PAFAH2 suppresses synchronized ferroptosis to ameliorate acute kidney injury. Nat Chem Biol 2024;20:835-846. [PMID: 38287154 DOI: 10.1038/s41589-023-01528-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
153
Zelenovskii P, Soares M, Bornes C, Marin-Montesinos I, Sardo M, Kopyl S, Kholkin A, Mafra L, Figueiredo F. Detection of helical water flows in sub-nanometer channels. Nat Commun 2024;15:5516. [PMID: 38951494 PMCID: PMC11217464 DOI: 10.1038/s41467-024-49878-7] [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: 03/31/2023] [Accepted: 06/21/2024] [Indexed: 07/03/2024]  Open
154
Zeng Y, Pavlova A, Nelson PM, Glick ZL, Yang L, Pang YT, Spivak M, Licari G, Tajkhorshid E, Sherrill CD, Gumbart JC. Broadening access to small-molecule parameterization with the force field toolkit. J Chem Phys 2024;160:242501. [PMID: 38916266 DOI: 10.1063/5.0196848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024]  Open
155
Costanzo A, Fata F, Freda I, De Sciscio ML, Gugole E, Bulfaro G, Di Renzo M, Barbizzi L, Exertier C, Parisi G, D'Abramo M, Vallone B, Savino C, Montemiglio LC. Binding of steroid substrates reveals the key to the productive transition of the cytochrome P450 OleP. Structure 2024:S0969-2126(24)00223-5. [PMID: 38971159 DOI: 10.1016/j.str.2024.06.005] [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: 01/05/2024] [Revised: 05/08/2024] [Accepted: 06/11/2024] [Indexed: 07/08/2024]
156
Kern NR, Lee J, Choi YK, Im W. CHARMM-GUI Multicomponent Assembler for modeling and simulation of complex multicomponent systems. Nat Commun 2024;15:5459. [PMID: 38937468 PMCID: PMC11211406 DOI: 10.1038/s41467-024-49700-4] [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: 09/13/2023] [Accepted: 06/17/2024] [Indexed: 06/29/2024]  Open
157
Giuliatti S, Benedetti AFF, Ramos RM, Petroli RJ, Domenice S, Mendonca BB, Batista RL. Hydropathic AF-2 variants in the androgen receptor gene among androgen insensitivity patients. Andrology 2024. [PMID: 38923406 DOI: 10.1111/andr.13680] [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: 12/14/2023] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
158
Suh D, Arattu Thodika AR, Kim S, Nam K, Im W. CHARMM-GUI QM/MM Interfacer for a Quantum Mechanical and Molecular Mechanical (QM/MM) Simulation Setup: 1. Semiempirical Methods. J Chem Theory Comput 2024;20:5337-5351. [PMID: 38856971 PMCID: PMC11209942 DOI: 10.1021/acs.jctc.4c00439] [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: 04/02/2024] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024]
159
Rubio V, McInchak N, Fernandez G, Benavides D, Herrera D, Jimenez C, Mesa H, Meade J, Zhang Q, Stawikowski MJ. Modular Fluorescent Cholesterol Naphthalimide Probes And Their Application For Cholesterol Trafficking Studies In Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600118. [PMID: 38979187 PMCID: PMC11230193 DOI: 10.1101/2024.06.24.600118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
160
Baldo AP, Ilgen AG, Leung K. Deprotonation of formic, acetic acids and bicarbonate ion in slit silica nanopores at infinite dilution and in the presence of electrolytes. J Colloid Interface Sci 2024;674:482-489. [PMID: 38941940 DOI: 10.1016/j.jcis.2024.05.160] [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: 03/28/2024] [Revised: 05/09/2024] [Accepted: 05/21/2024] [Indexed: 06/30/2024]
161
Vikraman D, Majumdar BB, Sk S, Weichbrodt C, Fertig N, Winterhalter M, Mondal J, Mahendran KR. Conformational flexibility driving charge-selective substrate translocation across a bacterial transporter. Chem Sci 2024;15:9333-9344. [PMID: 38903220 PMCID: PMC11186346 DOI: 10.1039/d4sc00345d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024]  Open
162
Ponnuchamy V, Sandak A, Sandak J. Advanced Molecular Dynamics Model for Investigating Biological-Origin Microfibril Structures. ACS OMEGA 2024;9:25646-25654. [PMID: 38911769 PMCID: PMC11191132 DOI: 10.1021/acsomega.3c08853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/28/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024]
163
Sarfraz M, Ayyaz M, Rauf A, Yaqoob A, Tooba, Arif Ali M, Siddique SA, Qureshi AM, Sarfraz MH, Aljowaie RM, Almutairi SM, Arshad M. New Pyrimidinone Bearing Aminomethylenes and Schiff Bases as Potent Antioxidant, Antibacterial, SARS-CoV-2, and COVID-19 Main Protease MPro Inhibitors: Design, Synthesis, Bioactivities, and Computational Studies. ACS OMEGA 2024;9:25730-25747. [PMID: 38911743 PMCID: PMC11191110 DOI: 10.1021/acsomega.3c09393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/25/2024]
164
Mittal S, Nisler C, Szostak JW. Simulations predict preferred Mg2+ coordination in a nonenzymatic primer-extension reaction center. Biophys J 2024;123:1579-1591. [PMID: 38702884 PMCID: PMC11214020 DOI: 10.1016/j.bpj.2024.04.032] [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: 12/28/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]  Open
165
He X, Zhao L, Tian Y, Li R, Chu Q, Gu Z, Zheng M, Wang Y, Li S, Jiang H, Jiang Y, Wen L, Wang D, Cheng X. Highly accurate carbohydrate-binding site prediction with DeepGlycanSite. Nat Commun 2024;15:5163. [PMID: 38886381 PMCID: PMC11183243 DOI: 10.1038/s41467-024-49516-2] [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: 11/27/2023] [Accepted: 06/10/2024] [Indexed: 06/20/2024]  Open
166
Mustafa NF, Cheng KK, Nadri MH, Razali SA, Zakaria II, Salin NH, Amran SI. Discovery of azaleatin as a potential allosteric inhibitor for dengue NS2B-NS3 protease using in vitro and in silico studies. J Biomol Struct Dyn 2024:1-12. [PMID: 38881303 DOI: 10.1080/07391102.2024.2335296] [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: 11/30/2023] [Accepted: 03/21/2024] [Indexed: 06/18/2024]
167
Wang C, Cao S, Shi C, Guo M, Sun D, Liu Z, Xiu P, Wang Y, Wang G, Liu Y. The novel function of an orphan pheromone receptor reveals the sensory specializations of two potential distinct types of sex pheromones in noctuid moth. Cell Mol Life Sci 2024;81:259. [PMID: 38878072 PMCID: PMC11335300 DOI: 10.1007/s00018-024-05303-2] [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: 01/27/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 08/22/2024]
168
Yetek İ, Mert S, Tunca E, Bayrakdar A, Kasımoğulları R. Synthesis, molecular docking and molecular dynamics simulations, drug-likeness studies, ADMET prediction and biological evaluation of novel pyrazole-carboxamides bearing sulfonamide moiety as potent carbonic anhydrase inhibitors. Mol Divers 2024:10.1007/s11030-024-10901-0. [PMID: 38869737 DOI: 10.1007/s11030-024-10901-0] [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: 03/06/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024]
169
McFarlane NR, Gui J, Oláh J, Harvey JN. Gaseous inhibition of the transsulfuration pathway by cystathionine β-synthase. Phys Chem Chem Phys 2024;26:16579-16588. [PMID: 38832404 DOI: 10.1039/d4cp01321b] [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: 06/05/2024]
170
Batebi H, Pérez-Hernández G, Rahman SN, Lan B, Kamprad A, Shi M, Speck D, Tiemann JKS, Guixà-González R, Reinhardt F, Stadler PF, Papasergi-Scott MM, Skiniotis G, Scheerer P, Kobilka BK, Mathiesen JM, Liu X, Hildebrand PW. Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor. Nat Struct Mol Biol 2024:10.1038/s41594-024-01334-2. [PMID: 38867113 DOI: 10.1038/s41594-024-01334-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/14/2024] [Indexed: 06/14/2024]
171
Luo X, Yu T, Li NK, Zuckermann RN, Jiang X, Balsara NP, Prendergast D. Thermodynamic Driving Forces for the Self-Assembly of Diblock Polypeptoids. ACS NANO 2024;18:14917-14924. [PMID: 38811008 PMCID: PMC11171762 DOI: 10.1021/acsnano.3c12228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/07/2024] [Accepted: 05/15/2024] [Indexed: 05/31/2024]
172
Ishraaq R, Das S. All-atom molecular dynamics simulations of polymer and polyelectrolyte brushes. Chem Commun (Camb) 2024;60:6093-6129. [PMID: 38819435 DOI: 10.1039/d4cc01557f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
173
Cogo RM, Pavani TFA, Mengarda ACA, Cajas RA, Teixeira TR, Fukui-Silva L, Sun YU, Liu LJ, Amarasinghe DK, Yoon MC, Santos-Filho OA, de Moraes J, Caffrey CR, G G Rando D. Pharmacophore Virtual Screening Identifies Riboflavin as an Inhibitor of the Schistosome Cathepsin B1 Protease with Antiparasitic Activity. ACS OMEGA 2024;9:25356-25369. [PMID: 38882094 PMCID: PMC11170711 DOI: 10.1021/acsomega.4c03376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024]
174
Lagardère L, Maurin L, Adjoua O, El Hage K, Monmarché P, Piquemal JP, Hénin J. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation. J Chem Theory Comput 2024;20:4481-4498. [PMID: 38805379 DOI: 10.1021/acs.jctc.3c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
175
Alobaida A, Abouzied AS, Younes KM, Alzhrani RM, Alsaab HO, Huwaimel B. Analyzing energetics and dynamics of hepatitis C virus polymerase interactions with marine bacterial compounds: a computational study. Mol Divers 2024:10.1007/s11030-024-10904-x. [PMID: 38856834 DOI: 10.1007/s11030-024-10904-x] [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: 04/01/2024] [Accepted: 05/25/2024] [Indexed: 06/11/2024]
176
Lei YK, Yagi K, Sugita Y. Learning QM/MM potential using equivariant multiscale model. J Chem Phys 2024;160:214109. [PMID: 38828815 DOI: 10.1063/5.0205123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024]  Open
177
Prabhakaran A, Jha KK, Sia RCE, Arellano Reyes RA, Sarangi NK, Kogut M, Guthmuller J, Czub J, Dietzek-Ivanšić B, Keyes TE. Triplet-Triplet Annihilation Upconverting Liposomes: Mechanistic Insights into the Role of Membranes in Two-Dimensional TTA-UC. ACS APPLIED MATERIALS & INTERFACES 2024;16:29324-29337. [PMID: 38776974 PMCID: PMC11163426 DOI: 10.1021/acsami.4c00990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
178
Yang R, Zhang L, Bu F, Sun F, Cheng B. AI-based prediction of protein-ligand binding affinity and discovery of potential natural product inhibitors against ERK2. BMC Chem 2024;18:108. [PMID: 38831341 PMCID: PMC11145815 DOI: 10.1186/s13065-024-01219-x] [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: 02/24/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]  Open
179
Interlandi G. Exploring ligands that target von Willebrand factor selectively under oxidizing conditions through docking and molecular dynamics simulations. Proteins 2024. [PMID: 38829206 DOI: 10.1002/prot.26706] [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: 01/29/2024] [Revised: 04/25/2024] [Accepted: 05/13/2024] [Indexed: 06/05/2024]
180
Wu D, Hierons SJ, Polepalli S, Gucwa M, Fritzen R, Markiewicz M, Sabín J, Minor W, Murzyn K, Blindauer CA, Stewart AJ. Targeted removal of the FA2 site on human albumin prevents fatty acid-mediated inhibition of Zn2+ binding. J Lipid Res 2024;65:100560. [PMID: 38750995 PMCID: PMC11179626 DOI: 10.1016/j.jlr.2024.100560] [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: 03/07/2024] [Revised: 05/01/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024]  Open
181
Gangwal A, Lavecchia A. Unleashing the power of generative AI in drug discovery. Drug Discov Today 2024;29:103992. [PMID: 38663579 DOI: 10.1016/j.drudis.2024.103992] [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: 02/09/2024] [Revised: 03/22/2024] [Accepted: 04/18/2024] [Indexed: 05/04/2024]
182
Bisht A, Tewari D, Kumar S, Chandra S. Network pharmacology, molecular docking, and molecular dynamics simulation to elucidate the mechanism of anti-aging action of Tinospora cordifolia. Mol Divers 2024;28:1743-1763. [PMID: 37439907 DOI: 10.1007/s11030-023-10684-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023]
183
Ruan P, Wang S, Yi P, Yang M, Chen Y, Yang M. Identification of the potential TLR7 antagonists by virtual screening and experimental validation. Mol Divers 2024;28:1335-1346. [PMID: 37217769 DOI: 10.1007/s11030-023-10660-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
184
Ichale R, Kanhed AM, Vora A. Coumarin linked thiazole derivatives as potential α-glucosidase inhibitors to treat diabetes mellitus. Mol Divers 2024;28:1239-1247. [PMID: 37118160 DOI: 10.1007/s11030-023-10652-4] [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: 02/18/2023] [Accepted: 04/14/2023] [Indexed: 04/30/2023]
185
Brown TP, Santa DE, Berger BA, Kong L, Wittenberg NJ, Im W. CHARMM GUI Membrane Builder for oxidized phospholipid membrane modeling and simulation. Curr Opin Struct Biol 2024;86:102813. [PMID: 38598982 PMCID: PMC11102286 DOI: 10.1016/j.sbi.2024.102813] [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: 02/07/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/12/2024]
186
Olukunle OF, Olowosoke CB, Khalid A, Oke GA, Omoboyede V, Umar HI, Ibrahim O, Adeboboye CF, Iwaloye O, Olawale F, Adedeji AA, Bello T, Alabere HO, Chukwuemeka PO. Identification of a 1, 8-naphthyridine-containing compound endowed with the inhibition of p53-MDM2/X interaction signaling: a computational perspective. Mol Divers 2024;28:1109-1127. [PMID: 37029281 DOI: 10.1007/s11030-023-10637-3] [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: 01/05/2023] [Accepted: 03/17/2023] [Indexed: 04/09/2023]
187
Włodek F, Kulig W, Stachowicz-Kuśnierz A. Insights into short chain polyethylene penetration of phospholipid bilayers via atomistic molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024;1866:184327. [PMID: 38679310 DOI: 10.1016/j.bbamem.2024.184327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
188
Jayaraman M, Kumar R, Panchalingam S, Jeyaraman J. Mechanistic insights into the conformational changes and alterations in residual communications due to the mutations in the pncA Gene of Mycobacterium tuberculosis: A computational perspective for effective therapeutic solutions. Comput Biol Chem 2024;110:108065. [PMID: 38615420 DOI: 10.1016/j.compbiolchem.2024.108065] [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: 12/04/2023] [Revised: 03/11/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
189
Mukhaleva E, Ma N, van der Velden WJC, Gogoshin G, Branciamore S, Bhattacharya S, Rodin AS, Vaidehi N. Bayesian network models identify cooperative GPCR:G protein interactions that contribute to G protein coupling. J Biol Chem 2024;300:107362. [PMID: 38735478 PMCID: PMC11176750 DOI: 10.1016/j.jbc.2024.107362] [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: 11/03/2023] [Revised: 05/03/2024] [Accepted: 05/04/2024] [Indexed: 05/14/2024]  Open
190
Abdelmalek D, Smaoui F, Frikha F, Ben Marzoug R, Msalbi D, Souissi A, Aifa MS. Computational identification of new TKI as potential noncovalent reversible EGFRL858R/T790M inhibitors: VHTS, molecular docking, DFT study and molecular dynamic simulation. J Biomol Struct Dyn 2024;42:4870-4887. [PMID: 37349947 DOI: 10.1080/07391102.2023.2223663] [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: 12/12/2022] [Accepted: 06/05/2023] [Indexed: 06/24/2023]
191
Kaya S, Tatar-Yılmaz G, Aktar BSK, Emre EEO. Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis. Protein J 2024;43:577-591. [PMID: 38642318 DOI: 10.1007/s10930-024-10196-y] [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] [Accepted: 03/23/2024] [Indexed: 04/22/2024]
192
Wu Z, Chen S, Wang Y, Li F, Xu H, Li M, Zeng Y, Wu Z, Gao Y. Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis. Int J Surg 2024;110:3848-3878. [PMID: 38502850 PMCID: PMC11175770 DOI: 10.1097/js9.0000000000001289] [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: 11/08/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
193
Sureshan M, Brintha S, Jothi A. Identification of Mulberrofuran as a potent inhibitor of hepatitis A virus 3Cpro and RdRP enzymes through structure-based virtual screening, dynamics simulation, and DFT studies. Mol Divers 2024;28:1609-1628. [PMID: 37386350 DOI: 10.1007/s11030-023-10679-7] [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: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 07/01/2023]
194
Heidarnejad F, Namvar A, Sadat SM, Pordanjani PM, Rezaei F, Namdari H, Arjmand S, Bolhassani A. In silico designing of novel epitope-based peptide vaccines against HIV-1. Biotechnol Lett 2024;46:315-354. [PMID: 38403788 DOI: 10.1007/s10529-023-03464-x] [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: 11/16/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
195
Aslan A, Ari Yuka S. Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives. Amino Acids 2024;56:37. [PMID: 38822212 PMCID: PMC11143054 DOI: 10.1007/s00726-024-03397-3] [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: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
196
Szlasa W, Sauer N, Baczyńska D, Ziętek M, Haczkiewicz-Leśniak K, Karpiński P, Fleszar M, Fortuna P, Kulus MJ, Piotrowska A, Kmiecik A, Barańska A, Michel O, Novickij V, Tarek M, Kasperkiewicz P, Dzięgiel P, Podhorska-Okołów M, Saczko J, Kulbacka J. Pulsed electric field induces exocytosis and overexpression of MAGE antigens in melanoma. Sci Rep 2024;14:12546. [PMID: 38822068 PMCID: PMC11143327 DOI: 10.1038/s41598-024-63181-x] [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: 11/22/2023] [Accepted: 05/27/2024] [Indexed: 06/02/2024]  Open
197
Si W, Chen H, Lin X, Wu G, Zhao J, Sha J. Actuation mechanism of a nanoscale drilling rig based on nested carbon nanotubes. NANOSCALE 2024;16:10414-10427. [PMID: 38742415 DOI: 10.1039/d4nr00902a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
198
Inan T, Flinko R, Lewis GK, MacKerell AD, Kurkcuoglu O. Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation. J Phys Chem B 2024;128:5157-5174. [PMID: 38647430 PMCID: PMC11139592 DOI: 10.1021/acs.jpcb.4c00925] [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: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
199
Stachowicz-Kuśnierz A, Rychlik P, Korchowiec J, Korchowiec B. Insights into Transfer of Supramolecular Doxorubicin/Congo Red Aggregates through Phospholipid Membranes. Molecules 2024;29:2567. [PMID: 38893446 PMCID: PMC11173802 DOI: 10.3390/molecules29112567] [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: 05/13/2024] [Revised: 05/26/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]  Open
200
Rawat V, DeLear P, Prashanth P, Ozgurses ME, Tebeje A, Burns PA, Conger KO, Solís C, Hasnain Y, Novikova A, Endress JE, González-Sánchez P, Dong W, Stephanopoulos G, DeNicola GM, Harris IS, Sept D, Mason FM, Coloff JL. Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy. JCI Insight 2024;9:e174329. [PMID: 38815134 DOI: 10.1172/jci.insight.174329] [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: 07/27/2023] [Accepted: 05/29/2024] [Indexed: 06/01/2024]  Open
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