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ForCE in action: Alchemical Free Energy Calculations of C H 3-C H 3 interfaces to estimate stability and recombination efficiency in bispecific antibody design

• Authors : Kokot, Janik

Subjects: Alchemische freie energie Berechnung; Antikörper; CH3-CH3 SchnittstelleUI:CP:AA

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Surface free energy calculation of the solid–fluid interfaces from molecular simulation

• Authors : Ghoufi, Aziz;

Subjects: Free energy calculations; Molecular simulations; Thermodynamic functions

• Source: ISSN: 2158-3226 ; AIP Advances ; https://hal.science/hal-04567366 ; AIP Advances, 2024, 14 (4), ⟨10.1063/5.0188578⟩.

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Molecular docking and molecular dynamics simulations reveal the clinical resistance of the gatekeeper mutation V564F of FGFR2 against Infigratinib

• Authors : Guodong Zheng; Wuxia Liu; Qian Zhang

Subjects: FGFR2; Infigratinib; gatekeeper mutation

• Source: Journal of Experimental Nanoscience, Vol 18, Iss 1 (2023)

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Molecular modeling of 1-butyl-3-methylimidazolium based ionic liquids for potential applications in the desulfurization of diesel fuel

• Authors : Miranda R. Caudle; Jason E. Thompson; Andrew S. Paluch

Subjects: Ionic liquids; Desulfurization; Molecular simulation

• Source: Journal of Ionic Liquids, Vol 3, Iss 2, Pp 100071- (2023)

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A FRET-Based Assay for the Identification of PCNA Inhibitors.

• Authors : Hardebeck S; University of Münster, Institute of Pharmaceutical and Medicinal Chemistry, Pharmacampus, 48149 Münster, Germany.; Schreiber S

Subjects: Fluorescence Resonance Energy Transfer* ; Neurodegenerative Diseases*; Humans

• Source: International journal of molecular sciences [Int J Mol Sci] 2023 Jul 24; Vol. 24 (14). Date of Electronic Publication: 2023 Jul 24.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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LSD1-Based Reversible Inhibitors Virtual Screening and Binding Mechanism Computational Study.

• Authors : Yin Z; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.; Liu S

Subjects: Enzyme Inhibitors*/Enzyme Inhibitors*/Enzyme Inhibitors*/pharmacology ; Enzyme Inhibitors*/Enzyme Inhibitors*/Enzyme Inhibitors*/chemistry ; Histones*/Histones*/Histones*/metabolism

• Source: Molecules (Basel, Switzerland) [Molecules] 2023 Jul 10; Vol. 28 (14). Date of Electronic Publication: 2023 Jul 10.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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LSD1-Based Reversible Inhibitors Virtual Screening and Binding Mechanism Computational Study

• Authors : Yang, Zhili Yin; Shaohui Liu; Xiaoyue Yang

Subjects: virtual screening; pharmacophore model; molecular docking

• Source: Molecules; Volume 28; Issue 14; Pages: 5315

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LSD1-Based Reversible Inhibitors Virtual Screening and Binding Mechanism Computational Study

• Authors : Zhili Yin; Shaohui Liu; Xiaoyue Yang

Subjects: virtual screening; pharmacophore model; molecular docking

• Source: Molecules, Vol 28, Iss 14, p 5315 (2023)

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AI-Driven De Novo Design and Molecular Modeling for Discovery of Small-Molecule Compounds as Potential Drug Candidates Targeting SARS-CoV-2 Main Protease.

• Authors : Andrianov AM; Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, Belarus.; Shuldau MA

Subjects: Artificial Intelligence* ; Small Molecule Libraries*/Small Molecule Libraries*/Small Molecule Libraries*/pharmacology ; Small Molecule Libraries*/Small Molecule Libraries*/Small Molecule Libraries*/therapeutic use

• Source: International journal of molecular sciences [Int J Mol Sci] 2023 Apr 29; Vol. 24 (9). Date of Electronic Publication: 2023 Apr 29.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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AI-Driven De Novo Design and Molecular Modeling for Discovery of Small-Molecule Compounds as Potential Drug Candidates Targeting SARS-CoV-2 Main Protease

• Authors : Alexander M. Andrianov; Mikita A. Shuldau; Konstantin V. Furs

Subjects: Inorganic Chemistry; Organic Chemistry; General Medicine

• Source: International Journal of Molecular Sciences; Volume 24; Issue 9; Pages: 8083

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QSAR via multisite λ-dynamics in the orphaned TSSK1B kinase.

• Authors : Liu X; Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, USA.; Tsang PK

Subjects: Molecular Dynamics Simulation* ; Quantitative Structure-Activity Relationship*; Humans

• Source: Protein science : a publication of the Protein Society [Protein Sci] 2023 Apr; Vol. 32 (4), pp. e4623.Publisher: Cold Spring Harbor Laboratory Press Country of Publication: United States NLM ID: 9211750 Publication Model: Print Cited Medium: Internet

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Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus.

• Authors : Srivastava M; Computational Biophysics and CADD Group, Computational and Mathematical Biology Center, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad 121001, India.; Mittal L

• Source: Pharmaceuticals (Basel, Switzerland) [Pharmaceuticals (Basel)] 2023 Mar 01; Vol. 16 (3). Date of Electronic Publication: 2023 Mar 01.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101238453 Publication Model: Electronic Cited Medium: Print ISSN: 1424-8247 (Print)

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Template Entrance Channel as Possible Allosteric Inhibition and Resistance Site for Quinolines Tricyclic Derivatives in RNA Dependent RNA Polymerase of Bovine Viral Diarrhea Virus

• Authors : Mitul Srivastava; Lovika Mittal; Debapriyo Sarmadhikari

Subjects: bovine viral diarrhea virus (BVDV); RNA-dependent RNA polymerase (RdRp); BVDV inhibitor

• Source: Pharmaceuticals, Vol 16, Iss 3, p 376 (2023)

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A Combined in Silico and Structural Study Opens New Perspectives on Aliphatic Sulfonamides, a Still Poorly Investigated Class of CA Inhibitors

• Authors : Davide Esposito; Giuseppina De Simone; EMMA LANGELLA

Subjects: carbonic anhydrase inhibitors; General Immunology and Microbiology; aliphatic sulfonamide

• Source: BiologyVolume 12Issue 2Pages: 281

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A Combined in Silico and Structural Study Opens New Perspectives on Aliphatic Sulfonamides, a Still Poorly Investigated Class of CA Inhibitors

• Authors : Emma Langella; Davide Esposito; Simona Maria Monti

Subjects: carbonic anhydrase inhibitors; aliphatic sulfonamide; X-ray crystallography

• Source: Biology, Vol 12, Iss 2, p 281 (2023)

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RosettaDDGPrediction for high-throughput mutational scans:From stability to binding

• Authors : Sora, Valentina; Laspiur, Adrian Otamendi; Degn, Kristine

Subjects: binding free energy; folding free energy; free energy calculations

• Source: Sora , V , Laspiur , A O , Degn , K , Arnaudi , M , Utichi , M , Beltrame , L , De Menezes , D , Orlandi , M , Stoltze , U K , Rigina , O , Sackett , P W , Wadt , K , Schmiegelow , K , Tiberti , M &

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Benchmarking Relative Binding Free Energy Calculations Using the OpenFE toolkit ...

• Authors : Alibay, Irfan; Ries, Benjamin; Henry, Michael M.

Subjects: Free Energy Calculations; Open Source; Python

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Identification of Activated Cdc42-Associated Kinase Inhibitors as Potential Anticancer Agents Using Pharmacoinformatic Approaches

• Authors : Kumar, V.; Kumar, R.; Parate, Shaddha, 1990

Subjects: Biochemistry and Molecular Biology; Biokemi och molekylärbiologi; ACK1

• Source: Biomolecules. 13(2)

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Electronic Notebook: Free-energy analysis of the amyloid fibrillation suppression by ATP

• Authors : Tuan Minh Do;

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-energy analysis of the amyloid fibrillation suppression by ATP ...

• Authors : Do, Tuan Minh

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-Energy Decomposition of Salt Effects on the Solubilities of Small Molecules and the Role of Excluded-Volume Effects

• Authors : Stefan Hervø-Hansen;

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-Energy Decomposition of Salt Effects on the Solubilities of Small Molecules and the Role of Excluded-Volume Effects (GAFF/SPCE/Heyda et al Force Field) ...

• Authors : Stefan Hervø-Hansen

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-Energy Decomposition of Salt Effects on the Solubilities of Small Molecules and the Role of Excluded-Volume Effects (GAFF/SPCE/Heyda et al) ...

• Authors : Stefan Hervø-Hansen

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic notebook: Free-energy decomposition of salt effects on the solubilities of small molecules and the role of excluded-volume effects (GAFF/SPCE/Heyda force field) ...

• Authors : Stefan Hervø-Hansen

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-Energy Decomposition of Salt Effects on the Solubilities of Small Molecules and the Role of Excluded-Volume Effects (Sage/OPC/Sengupta&Merz Force Field) ...

• Authors : Stefan Hervø-Hansen

Subjects: reproducible science; electronic notebooks; chemistry

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Electronic Notebook: Free-Energy Decomposition of Salt Effects on the Solubilities of Small Molecules and the Role of Excluded-Volume Effects ...

• Authors : Hervø-Hansen, Stefan

Subjects: reproducible science; electronic notebooks; chemistry

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Kartograf: An Accurate Graph-Based Atom Mapper For Hybrid Topology Relative Free Energy Calculations

• Authors : Ries, Benjamin; Alibay, Irfan; Henry, Michael M.

Subjects: Free Energy Calculations; Atom Mappings; Cheminformatics

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Modeling of transmembrane domain and full-length TLRs in membrane models

Subjects: Toll-like receptors; Membrane proteins; Molecular recognition

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On the Path to Optimal Alchemistry

Subjects: Accelerated weight histogram method; Alchemical free energy calculations; Lambda path optimization

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Probing nucleotide substrate selectivity during viral replication of SARS-CoV-2 RNA Dependent RNA Polymerase

• Authors : Romero, Moises Ernesto

Subjects: Computational chemistry; Biophysics; Free Energy Calculations

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Chasing collective variables using temporal data-driven strategies

• Authors : Haochuan Chen; Christophe Chipot

Subjects: Autoencoders; collective variables; free-energy calculations

• Source: QRB Discovery, Vol 4 (2023)

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The Open Free Energy Consortium: Alchemistry for Everyone

• Authors : Gowers, Richard; Alibay, Irfan; Swenson, David W.H.

Subjects: free energy calculations; open source

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On the Path to Optimal Alchemistry

• Authors : Lundborg, Magnus; Lidmar, Jack, 1968; Hess, Berk

Subjects: Accelerated weight histogram method; Alchemical free energy calculations; Lambda path optimization

• Source: The Protein Journal. 42(5):477-489

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A Dynamic and Responsive Host in Action Light-Controlled Molecular Encapsulation

• Authors : Sean T J Ryan; Jesús Del Barrio; Daniel F. Ryan

Subjects: Plant cell and molecular biology; Animal cell and molecular biology; DFT calculations

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Optimizing active learning for free energy calculations

• Authors : James Thompson; W Patrick Walters; Jianwen A Feng

Subjects: Artificial intelligence; Active learning; Machine learning

• Source: Artificial Intelligence in the Life Sciences, Vol 2, Iss , Pp 100050- (2022)

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Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry.

• Authors : Stratilová B; Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia.; Stratilová E

Subjects: Computational Chemistry* ; beta-Glucans*; Glucose

• Source: International journal of molecular sciences [Int J Mol Sci] 2022 Oct 05; Vol. 23 (19). Date of Electronic Publication: 2022 Oct 05.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry

• Authors : Barbora Stratilová; Eva Stratilová; Maria Hrmova

Subjects: Glycosylation; Xylose; beta-Glucans

• Source: International Journal of Molecular Sciences; Volume 23; Issue 19; Pages: 11838

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Computational study of ion permeation through claudin-4 paracellular channels.

• Authors : Berselli A; Center for Synaptic Neuroscience and Technology (), Istituto Italiano di Tecnologia, Genova, Italy.; Department of Experimental Medicine, Università degli Studi di Genova, Genova, Italy.

Subjects: Chlorides*/Chlorides*/Chlorides*/analysis ; Chlorides*/Chlorides*/Chlorides*/metabolism ; Claudins*/Claudins*/Claudins*/metabolism

• Source: Annals of the New York Academy of Sciences [Ann N Y Acad Sci] 2022 Oct; Vol. 1516 (1), pp. 162-174. Date of Electronic Publication: 2022 Jul 10.Publisher: New York Academy of Sciences Country of Publication: United States NLM ID: 7506858 Publication Model: Print-Electronic Cited Medium: Internet

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Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations

• Authors : Hossam Nada; Ahmed Elkamhawy; Kyeong Lee

Subjects: E-pharmacophore modeling; Structure-based virtual screening (SBVS); Molecular dynamics (MD) simulation

• Source: PeerJ, Vol 10, p e14120 (2022)

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Phyto-Computational Intervention of Diabetes Mellitus at Multiple Stages Using Isoeugenol from Ocimum tenuiflorum : A Combination of Pharmacokinetics and Molecular Modelling Approaches.

• Authors : Martiz RM; Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysore 570015, India.; Department of Microbiology, School of Life Sciences, JSS Academy of Higher Education and Research, Mysore 570015, India.

Subjects: Diabetes Mellitus* ; Oils, Volatile*; Aldehyde Reductase

• Source: Molecules (Basel, Switzerland) [Molecules] 2022 Sep 22; Vol. 27 (19). Date of Electronic Publication: 2022 Sep 22.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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Phyto-Computational Intervention of Diabetes Mellitus at Multiple Stages Using Isoeugenol from Ocimum tenuiflorum: A Combination of Pharmacokinetics and Molecular Modelling Approaches

• Authors : Reshma Mary Martiz; Shashank M. Patil; Deepika Thirumalapura Hombegowda

Subjects: Chemistry (miscellaneous); Organic Chemistry; Drug Discovery

• Source: Molecules; Volume 27; Issue 19; Pages: 6222

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Computer-Aided Screening of Phytoconstituents from Ocimum tenuiflorum against Diabetes Mellitus Targeting DPP4 Inhibition: A Combination of Molecular Docking, Molecular Dynamics, and Pharmacokinetics Approaches.

• Authors : Sajal H; Department of Biotechnology and Bioinformatics, JSS Academy of Higher Education and Research, Mysuru 570015, India.; Patil SM

Subjects: Diabetes Mellitus* ; Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/Diabetes Mellitus, Type 2*/drug therapy ; Dipeptidyl-Peptidase IV Inhibitors*/Dipeptidyl-Peptidase IV Inhibitors*/Dipeptidyl-Peptidase IV Inhibitors*/pharmacology

• Source: Molecules (Basel, Switzerland) [Molecules] 2022 Aug 12; Vol. 27 (16). Date of Electronic Publication: 2022 Aug 12.Publisher: MDPI Country of Publication: Switzerland NLM ID: 100964009 Publication Model: Electronic Cited Medium: Internet ISSN: 1420-3049

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Computer-Aided Screening of Phytoconstituents from Ocimum tenuiflorum against Diabetes Mellitus Targeting DPP4 Inhibition: A Combination of Molecular Docking, Molecular Dynamics, and Pharmacokinetics Approaches

• Authors : Harshit Sajal; Shashank M. Patil; Ranjith Raj

Subjects: Chemistry (miscellaneous); DPP4 inhibition; Ocimum tenuiflorum

• Source: Molecules; Volume 27; Issue 16; Pages: 5133

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Synthesis, Characterization, Hirshfeld Surface Analysis, Crystal Structure and Molecular Modeling Studies of 1-(4-(Methoxy(phenyl)methyl)-2-methylphenoxy)butan-2-one Derivative as a Novel α-Glucosidase Inhibitor

• Authors : Chandra Shivanna; Shashank M. Patil; C. Mallikarjunaswamy

Subjects: Inorganic Chemistry; General Chemical Engineering; General Materials Science

• Source: Crystals; Volume 12; Issue 7; Pages: 960

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Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease.

• Authors : Hognon C; Grupo de Reactividad y Estructura Molecular (RESMOL), Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, Alcalá de Henares, 28801 Madrid, Spain.; Marazzi M

Subjects: Protons* ; COVID-19 Drug Treatment*; Coronavirus Papain-Like Proteases

• Source: International journal of molecular sciences [Int J Mol Sci] 2022 May 23; Vol. 23 (10). Date of Electronic Publication: 2022 May 23.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Atomistic-Level Description of the Covalent Inhibition of SARS-CoV-2 Papain-like Protease

• Authors : Cécilia Hognon; Marco Marazzi; Cristina Garcia Iriepa

Subjects: SARS-CoV-2; papain-like protease; covalent inhibitor

• Source: International Journal of Molecular Sciences; Volume 23; Issue 10; Pages: 5855

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Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase.

• Authors : Conde-Giménez M; Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain.; Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain.

Subjects: Phenylalanine Hydroxylase*/Phenylalanine Hydroxylase*/Phenylalanine Hydroxylase*/chemistry ; Phenylketonurias*/Phenylketonurias*/Phenylketonurias*/metabolism; Calorimetry

• Source: International journal of molecular sciences [Int J Mol Sci] 2022 Apr 19; Vol. 23 (9). Date of Electronic Publication: 2022 Apr 19.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067

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Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2.

• Authors : Zhang ZB; State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China.; Yunnan Key Laboratory of Stem Cell and Regenerative Medicine and Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China.

Subjects: Angiotensin-Converting Enzyme 2*/Angiotensin-Converting Enzyme 2*/Angiotensin-Converting Enzyme 2*/metabolism ; Severe acute respiratory syndrome-related coronavirus*/Severe acute respiratory syndrome-related coronavirus*/Severe acute respiratory syndrome-related coronavirus*/metabolism ; SARS-CoV-2*/SARS-CoV-2*/SARS-CoV-2*/metabolism SARS-CoV-2 variants

• Source: Cells [Cells] 2022 Apr 09; Vol. 11 (8). Date of Electronic Publication: 2022 Apr 09.Publisher: MDPI Country of Publication: Switzerland NLM ID: 101600052 Publication Model: Electronic Cited Medium: Internet ISSN: 2073-4409

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Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2

• Authors : Zhi-Bi Zhang; Yuan-Ling Xia; Jian-Xin Shen

Subjects: molecular dynamics; binding free energy calculations; electrostatic interactions

• Source: Cells, Vol 11, Iss 8, p 1274 (2022)

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Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase

• Authors : María Conde-Giménez; Juan José Galano-Frutos; María Galiana-Cameo

Subjects: phenylketonuria; pharmacological chaperones; lead optimization

• Source: International Journal of Molecular Sciences, Vol 23, Iss 9, p 4502 (2022)

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