Temat: "Molecular Docking Simulation" - OpacWWW

Skocz do pozycji: 1.

Tytuł:: Bis(triazinyl)pyridine complexes of Pt(II) and Pd(II): studies of the nucleophilic substitution reactions, DNA/HSA interactions, molecular docking and biological activity.
Autorzy:: Jovanović-Stević S; Department of Natural Science, University of Kragujevac, Institute for Information Technologies Kragujevac, Jovana Cvijića Bb, 34000, Kragujevac, Serbia. .
Radisavljević S; Faculty of Science, University of Kragujevac, R. Domanovića 12, P. O. Box 60, 34000, Kragujevac, Serbia.
Scheurer A; Inorganic Chemistry, Department of Chemistry and Pharmacy, University of Erlangen-Nürnberg, Erlangen, Germany.
Ćoćić D; Faculty of Science, University of Kragujevac, R. Domanovića 12, P. O. Box 60, 34000, Kragujevac, Serbia.
Šmit B; Department of Natural Science, University of Kragujevac, Institute for Information Technologies Kragujevac, Jovana Cvijića Bb, 34000, Kragujevac, Serbia.
Petković M; 'Vinča' Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Mike Petrovića Alasa 12-14, 11001, Belgrade, Serbia.
Živanović MN; Department of Natural Science, University of Kragujevac, Institute for Information Technologies Kragujevac, Jovana Cvijića Bb, 34000, Kragujevac, Serbia.
Virijević K; Department of Natural Science, University of Kragujevac, Institute for Information Technologies Kragujevac, Jovana Cvijića Bb, 34000, Kragujevac, Serbia.
Petrović B; Faculty of Science, University of Kragujevac, R. Domanovića 12, P. O. Box 60, 34000, Kragujevac, Serbia.; Pokaż więcej
Źródło:: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2021 Aug; Vol. 26 (5), pp. 625-637. Date of Electronic Publication: 2021 Jul 15.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Molecular Docking Simulation*
Antineoplastic Agents/*pharmacology
Coordination Complexes/*pharmacology
DNA/*chemistry
Palladium/*pharmacology
Platinum/*pharmacology
Pyridines/*pharmacology
Serum Albumin, Human/*chemistry
Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Cell Proliferation/drug effects ; Cells, Cultured ; Coordination Complexes/chemical synthesis ; Coordination Complexes/chemistry ; Drug Screening Assays, Antitumor ; Humans ; Kinetics ; Palladium/chemistry ; Platinum/chemistry ; Pyridines/chemistry

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Skocz do pozycji: 2.

Tytuł:: Investigating the anticancer properties of the two new platinum complexes with iso- and tert-pentylglycine by the DFT, molecular docking, and ADMET assessment and experimental confirmations.
Autorzy:: Ramezani N; Department of Chemistry, Semnan University, Semnan, Iran.
Eslami Moghadam M; Chemistry & Chemical Engineering Research Center of Iran, Tehran, Iran. eslami_.
Behzad M; Department of Chemistry, Semnan University, Semnan, Iran.; Pokaż więcej
Źródło:: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2021 May; Vol. 26 (2-3), pp. 283-298. Date of Electronic Publication: 2021 Feb 22.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Density Functional Theory*
Molecular Docking Simulation*
Antineoplastic Agents/*chemistry
Antineoplastic Agents/*pharmacology
Glycine/*chemistry
Organoplatinum Compounds/*chemistry
Organoplatinum Compounds/*pharmacology
Antineoplastic Agents/metabolism ; DNA/chemistry ; DNA/metabolism ; Humans ; MCF-7 Cells ; Nucleic Acid Conformation ; Organoplatinum Compounds/metabolism

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Skocz do pozycji: 3.

Tytuł:: Efficient screening of protein-ligand complexes in lipid bilayers using LoCoMock score.
Autorzy:: Morita R; Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan. .
Shigeta Y; Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan.
Harada R; Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8577, Tsukuba, Ibaraki, Japan. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2023 Apr; Vol. 37 (4), pp. 217-225. Date of Electronic Publication: 2023 Mar 21.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Lipid Bilayers*
Membrane Proteins*
Ligands ; Protein Binding ; Drug Discovery ; Molecular Docking Simulation

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Skocz do pozycji: 4.

Tytuł:: Identification of potential inhibitors of Mycobacterium tuberculosis shikimate kinase: molecular docking, in silico toxicity and in vitro experiments.
Autorzy:: Freitas de Freitas T; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Roth CD; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
Abbadi BL; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
Hopf FSM; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Perelló MA; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.
de Matos Czeczot A; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
de Souza EV; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Borsoi AF; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Machado P; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Bizarro CV; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Basso LA; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.; Programa de Pós-Graduação em Medicina e Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.; Programa de Pós-Graduação em Biologia Celular e Molecular, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, 90616-900, Brazil.
Timmers LFSM; Centro de Pesquisas em Biologia Molecular e Funcional (CPBMF), Instituto Nacional de Ciência e Tecnologia em Tuberculose (INCT-TB), Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, Brazil. .; Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul, 95914-014, Brazil. .; Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul, 95914-014, Brazil. .; Programa de Pós-Graduação em Ciências Médicas, Universidade do Vale do Taquari (Univates), Lajeado, Rio Grande do Sul, 95914-014, Brazil. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2023 Mar; Vol. 37 (3), pp. 117-128. Date of Electronic Publication: 2022 Dec 22.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Mycobacterium tuberculosis*
Tuberculosis*/drug therapy
Humans ; Molecular Docking Simulation ; Antitubercular Agents/pharmacology ; Antitubercular Agents/chemistry

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Skocz do pozycji: 5.

Tytuł:: GPCRLigNet: rapid screening for GPCR active ligands using machine learning.
Autorzy:: Remington JM; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA.
McKay KT; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA.
Beckage NB; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA.
Ferrell JB; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA.
Schneebeli ST; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA.; Department of Industrial and Physical Pharmacy, Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA.; Department of Pathology, University of Vermont, Burlington, VT, 05405, USA.
Li J; Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA. .; Department of Pathology, University of Vermont, Burlington, VT, 05405, USA. .; Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47906, USA. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2023 Mar; Vol. 37 (3), pp. 147-156. Date of Electronic Publication: 2023 Feb 25.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:: Receptors, G-Protein-Coupled*/chemistry
Machine Learning*
Ligands ; Molecular Docking Simulation ; High-Throughput Screening Assays

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Skocz do pozycji: 6.

Tytuł:: Insights into the role of the cobalt(III)-thiosemicarbazone complex as a potential inhibitor of the Chikungunya virus nsP4.
Autorzy:: Martins DOS; Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil.; São Paulo State University, IBILCE, São José do Rio Preto, SP, Brazil.
Souza RAC; Bioinorganic Chemistry Group, Institute of Chemistry, Federal University of Uberlândia, Uberlândia, MG, 38408-100, Brazil.
Freire MCLC; Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil.
de Moraes Roso Mesquita NC; Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil.
Santos IA; Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil.
de Oliveira DM; Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil.
Junior NN; Molecular Modeling Laboratory, Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Brazil.
de Paiva REF; Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil.
Harris M; Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
Oliveira CG; Bioinorganic Chemistry Group, Institute of Chemistry, Federal University of Uberlândia, Uberlândia, MG, 38408-100, Brazil. .
Oliva G; Physics Institute of São Carlos, University of São Paulo, São Carlos, SP, Brazil.
Jardim ACG; Institute of Biomedical Sciences, Federal University of Uberlândia, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, 38405-302, Brazil. .; São Paulo State University, IBILCE, São José do Rio Preto, SP, Brazil. .; Pokaż więcej
Źródło:: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2023 Feb; Vol. 28 (1), pp. 101-115. Date of Electronic Publication: 2022 Dec 09.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Chikungunya Fever*/drug therapy
Chikungunya Fever*/metabolism
Chikungunya virus*/metabolism
Humans ; Viral Nonstructural Proteins/metabolism ; Viral Nonstructural Proteins/pharmacology ; Viral Nonstructural Proteins/therapeutic use ; Cobalt/pharmacology ; Molecular Docking Simulation ; Antiviral Agents/pharmacology ; Antiviral Agents/therapeutic use

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Skocz do pozycji: 7.

Tytuł:: Combining fragment docking with graph theory to improve ligand docking for homology model structures.
Autorzy:: Sarfaraz S; School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
Muneer I; School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China.
Liu H; School of life sciences, University of Science and Technology of China, Hefei, 230026, Anhui, China. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Dec; Vol. 34 (12), pp. 1237-1259. Date of Electronic Publication: 2020 Oct 09.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Molecular Docking Simulation*
Pandemics*
Betacoronavirus/*enzymology
Coronavirus Infections/*drug therapy
Cysteine Endopeptidases/*drug effects
Pneumonia, Viral/*drug therapy
Viral Nonstructural Proteins/*drug effects
ATPases Associated with Diverse Cellular Activities/chemistry ; ATPases Associated with Diverse Cellular Activities/metabolism ; COVID-19 ; Coronavirus 3C Proteases ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/metabolism ; Cytochrome P-450 Enzyme System/chemistry ; Cytochrome P-450 Enzyme System/metabolism ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Humans ; Ligands ; Models, Chemical ; Models, Molecular ; Molecular Chaperones/chemistry ; Molecular Chaperones/metabolism ; Peptide Fragments/chemistry ; Peptide Fragments/metabolism ; Protein Binding ; Protein Conformation ; Receptors, G-Protein-Coupled/chemistry ; Receptors, G-Protein-Coupled/metabolism ; SARS-CoV-2 ; Transcription Factors/chemistry ; Transcription Factors/metabolism ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/metabolism

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Skocz do pozycji: 8.

Tytuł:: Benchmarking GPCR homology model template selection in combination with de novo loop generation.
Autorzy:: Szwabowski GL; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
Castleman PN; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
Sears CK; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
Wink LH; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
Cole JA; Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA.
Baker DL; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
Parrill AL; Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA. .; The University of Memphis, 107 Scates Hall, Memphis, TN, 38152, USA. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Oct; Vol. 34 (10), pp. 1027-1044. Date of Electronic Publication: 2020 Jul 31.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:: Molecular Docking Simulation*
Molecular Dynamics Simulation*
Software*
Receptors, G-Protein-Coupled/*chemistry
Receptors, G-Protein-Coupled/*metabolism
Benchmarking ; Humans ; Ligands ; Protein Binding ; Protein Conformation

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Skocz do pozycji: 9.

Tytuł:: Flexi-pharma: a molecule-ranking strategy for virtual screening using pharmacophores from ligand-free conformational ensembles.
Autorzy:: Lans I; Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
Palacio-Rodríguez K; Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
Cavasotto CN; Computational Drug Design and Biomedical Informatics Laboratory, Translational Medicine Research Institute (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.; Facultad de Ciencias Biomédicas, and Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina.; Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina.
Cossio P; Biophysics of Tropical Diseases Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia. .; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438, Frankfurt am Main, Germany. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Oct; Vol. 34 (10), pp. 1063-1077. Date of Electronic Publication: 2020 Jul 12.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Drug Evaluation, Preclinical*
Molecular Docking Simulation*
Molecular Dynamics Simulation*
Drug Discovery/*methods
Pharmaceutical Preparations/*analysis
Pharmaceutical Preparations/*chemistry
Humans ; Ligands ; Models, Molecular ; Pharmaceutical Preparations/metabolism ; Protein Binding

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Skocz do pozycji: 10.

Tytuł:: Side chain virtual screening of matched molecular pairs: a PDB-wide and ChEMBL-wide analysis.
Autorzy:: Baumgartner MP; Computational Chemistry and Cheminformatics, Eli Lilly and Company Inc., San Diego, CA, USA.
Evans DA; Computational Chemistry and Cheminformatics, Eli Lilly and Company Ltd., Windlesham, UK. evans_david_.; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Sep; Vol. 34 (9), pp. 953-963. Date of Electronic Publication: 2020 Jun 12.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Algorithms*
Databases, Protein*
Molecular Docking Simulation*
Drug Discovery/*methods
Drug Evaluation, Preclinical/*methods
Proteins/*chemistry
Proteins/*metabolism
Humans ; Ligands ; Models, Molecular ; Protein Binding ; Retrospective Studies

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Skocz do pozycji: 11.

Tytuł:: A study of Pt(II)-phenanthroline complex interactions with double-stranded and G-quadruplex DNA by ESI-MS, circular dichroism, and computational docking.
Autorzy:: Ang DL; Nanoscale Organisation and Dynamics Group, School of Science, Western Sydney University, Penrith, NSW, 2751, Australia.
Kelso C; School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia.
Beck JL; School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia.
Ralph SF; School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, 2522, Australia.
Harman DG; School of Medicine, Western Sydney University, Locked Bag 1797, Penrith South DC, NSW, 2751, Australia.
Aldrich-Wright JR; Nanoscale Organisation and Dynamics Group, School of Science, Western Sydney University, Penrith, NSW, 2751, Australia. .; School of Medicine, Western Sydney University, Locked Bag 1797, Penrith South DC, NSW, 2751, Australia. .; Pokaż więcej
Źródło:: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2020 May; Vol. 25 (3), pp. 429-440. Date of Electronic Publication: 2020 Mar 26.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Density Functional Theory*
Molecular Docking Simulation*
Coordination Complexes/*chemistry
DNA/*chemistry
Phenanthrolines/*chemistry
Platinum/*chemistry
Circular Dichroism ; DNA/isolation & purification ; G-Quadruplexes ; Molecular Structure ; Spectrometry, Mass, Electrospray Ionization

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Skocz do pozycji: 12.

Tytuł:: Evaluation of interactions between the hepatitis C virus NS3/4A and sulfonamidobenzamide based molecules using molecular docking, molecular dynamics simulations and binding free energy calculations.
Autorzy:: Ren J; Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.; BeiGene (Beijing) Co., Ltd, No. 30 Science Park Road, Zhong-Guan-Cun Life Sciences Park, Changping District, Beijing, 102206, People's Republic of China.
Vaid TM; Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
Lee H; Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.; Biophysics Core at Research Resource Center, University of Illinois at Chicago, 1100 S. Ashland Ave, Chicago, IL, 60607, USA.
Ojeda I; Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA.
Johnson ME; Center for Biomolecular Sciences and Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave, Chicago, IL, 60607, USA. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2023 Jan; Vol. 37 (1), pp. 53-65. Date of Electronic Publication: 2022 Nov 25.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural
MeSH Terms:: Hepacivirus*
Hepatitis C*/drug therapy
Humans ; Molecular Dynamics Simulation ; Molecular Docking Simulation ; Protease Inhibitors/pharmacology ; Viral Nonstructural Proteins/chemistry ; Antiviral Agents/pharmacology ; Antiviral Agents/chemistry

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Skocz do pozycji: 13.

Tytuł:: Brucine-Induced Neurotoxicity by Targeting Caspase 3: Involvement of PPARγ/NF-κB/Apoptosis Signaling Pathway.
Autorzy:: Lei Y; School of Pharmacy, Zunyi Medical University, Zunyi, China.; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China.
Hou F; School of Pharmacy, Zunyi Medical University, Zunyi, China.; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China.
Wu X; School of Pharmacy, Zunyi Medical University, Zunyi, China.; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China.
Yi Y; School of Pharmacy, Zunyi Medical University, Zunyi, China.; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China.
Xu F; Spemann Graduate School of Biology and Medicine (SGBM), Albert-Ludwigs-University Freiburg, 79085, Freiburg, Germany.
Gong Q; School of Pharmacy, Zunyi Medical University, Zunyi, China.; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China.
Gao J; School of Pharmacy, Zunyi Medical University, Zunyi, China. .; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, 6 Xuefu West Road, Zunyi City, Guizhou Province, 563000, People's Republic of China. .; Pokaż więcej
Źródło:: Neurotoxicity research [Neurotox Res] 2022 Dec; Vol. 40 (6), pp. 2117-2131. Date of Electronic Publication: 2022 Sep 24.
Typ publikacji:: Journal Article
MeSH Terms:: NF-kappa B*
PPAR gamma*
Caspase 3 ; Molecular Docking Simulation ; Apoptosis ; Anti-Inflammatory Agents/pharmacology ; Signal Transduction

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Skocz do pozycji: 14.

Tytuł:: JM-20, a Benzodiazepine-Dihydropyridine Hybrid Molecule, Inhibits the Formation of Alpha-Synuclein-Aggregated Species.
Autorzy:: Santos CC; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Cardim-Pires TR; Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Shvachiy L; Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Gottingen, Göttingen, Germany.; Faculdade de Medicina, Centro Cardiovascular da Universidade de Lisboa, Universidade de Lisboa, Av Prof Egas Moniz, 1649-028, Lisbon, Portugal.
Fonseca-Fonseca LA; Centro de Investigación y Desarrollo de Medicamentos (CIDEM), La Habana, Cuba.
Muñoz P; Instituto de Ciencias Biomedicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile.
Almeida ÁMAN; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Costa ACS; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Teles-Souza J; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Ochoa-Rodríguez E; Organic Synthesis Laboratory of the Faculty of Chemistry of the University of Havana, Havana, Cuba.
de Fátima Dias Costa M; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Palhano FL; Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Segura-Aguilar J; Molecular & Clinical Pharmacology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile.
Barbosa DB; Laboratory of Molecular Modeling, Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.
do Bomfim MR; Laboratory of Molecular Modeling, Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.
Dos Santos Junior MC; Laboratory of Molecular Modeling, Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.
Leite FHA; Laboratory of Molecular Modeling, Department of Health, State University of Feira de Santana, Feira de Santana, Brazil.
da Rocha Pita SS; Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia - College of Pharmacy, Salvador, Brazil.
Costa SL; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil.
Núñez-Figueredo Y; Centro de Investigación y Desarrollo de Medicamentos (CIDEM), La Habana, Cuba.
Outeiro TF; Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Gottingen, Göttingen, Germany.; Max Planck Institute for Multidisciplinary Sciences, Goettingen, Germany.; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4HH, UK.; Scientific Employee With an Honorary Contract at German Center for Neurodegenerative Diseases (DZNE), 37075, Göttingen, Germany.
Foguel D; Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.
Silva VDA; Laboratory of Neurochemistry and Cell Biology, Department of Biochemistry and Biophysics, Federal University of Bahia - Institute of Health Sciences, Salvador, 40110-100, Brazil. .; Pokaż więcej
Źródło:: Neurotoxicity research [Neurotox Res] 2022 Dec; Vol. 40 (6), pp. 2135-2147. Date of Electronic Publication: 2022 Aug 23.
Typ publikacji:: Journal Article
MeSH Terms:: Neuroblastoma*
Parkinson Disease*/drug therapy
Dihydropyridines*
Humans ; alpha-Synuclein ; Benzodiazepines ; Molecular Docking Simulation

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Skocz do pozycji: 15.

Tytuł:: Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant.
Autorzy:: Liu X; School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China. .
Zheng L; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China.
Cong Y; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
Gong Z; School of Micro-Nano Electronics, Zhejiang University, Hangzhou, 310027, China.; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
Yin Z; School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai, 201620, China.
Zhang JZH; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, 200062, China. .; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China. .; Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China. .; Department of Chemistry, New York University, NY, NY, 10003, USA. .
Liu Z; College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
Sun Z; College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2022 Dec; Vol. 36 (12), pp. 879-894. Date of Electronic Publication: 2022 Nov 17.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Carboxylic Acids*
Proteins*/chemistry
Entropy ; Ligands ; Molecular Docking Simulation

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Skocz do pozycji: 16.

Tytuł:: Cytotoxicity, alpha-glucosidase inhibition and molecular docking studies of hydroxamic acid chromium(III) complexes.
Autorzy:: Hassan LR; Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam, 40450, Selangor, Malaysia.
Anouar EH; Department of Chemistry, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia. .
Bahron H; Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam, 40450, Selangor, Malaysia.; University of Malaya Centre for Ionic Liquid (UMCIL), Universiti Malaya, 50603, Kuala Lumpur, Malaysia.
Abdullah F; Centre of Foundation Studies, Universiti Teknologi MARA, Dengkil, 43800, Selangor, Malaysia.
Mohd Tajuddin A; Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam, 40450, Selangor, Malaysia. .; Atta-ur-Rahman Institute for Natural Product Discovery (AuRIns), Universiti Teknologi MARA, Level 9, FF3 Building, 42300 Puncak Alam, Selangor, Malaysia. .; Pokaż więcej
Źródło:: Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry [J Biol Inorg Chem] 2020 Mar; Vol. 25 (2), pp. 239-252. Date of Electronic Publication: 2020 Jan 23.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Molecular Docking Simulation*
Antineoplastic Agents/*pharmacology
Chromium/*pharmacology
Coordination Complexes/*pharmacology
Glycoside Hydrolase Inhibitors/*pharmacology
Hydroxamic Acids/*pharmacology
alpha-Glucosidases/*metabolism
Antineoplastic Agents/chemical synthesis ; Antineoplastic Agents/chemistry ; Cell Proliferation/drug effects ; Chromium/chemistry ; Coordination Complexes/chemical synthesis ; Coordination Complexes/chemistry ; Drug Screening Assays, Antitumor ; Glycoside Hydrolase Inhibitors/chemical synthesis ; Glycoside Hydrolase Inhibitors/chemistry ; HCT116 Cells ; Humans ; Hydroxamic Acids/chemistry ; Molecular Structure ; Tumor Cells, Cultured

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Skocz do pozycji: 17.

Tytuł:: Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.
Autorzy:: Kotelnikov S; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.; Innopolis University, Innopolis, Russia.
Alekseenko A; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
Liu C; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.
Ignatov M; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.; Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, USA.
Padhorny D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
Brini E; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
Lukin M; Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA.
Coutsias E; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.
Dill KA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.; Department of Chemistry, Stony Brook University, Stony Brook, NY, USA.; Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, USA.
Kozakov D; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA. .; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA. .; Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, USA. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Feb; Vol. 34 (2), pp. 179-189. Date of Electronic Publication: 2019 Dec 26.
Typ publikacji:: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:: Drug Design*
Molecular Docking Simulation*
Amyloid Precursor Protein Secretases/*metabolism
Aspartic Acid Endopeptidases/*metabolism
Macrocyclic Compounds/*chemistry
Macrocyclic Compounds/*pharmacology
Amyloid Precursor Protein Secretases/chemistry ; Aspartic Acid Endopeptidases/chemistry ; Binding Sites ; Humans ; Ligands ; Molecular Dynamics Simulation ; Monte Carlo Method ; Protein Binding ; Thermodynamics

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Skocz do pozycji: 18.

Tytuł:: Deep neural network affinity model for BACE inhibitors in D3R Grand Challenge 4.
Autorzy:: Wang B; Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Rd., Manhattan, KS, 66506, USA.
Ng HL; Biochemistry & Molecular Biophysics, Kansas State University, 141 Chalmers Hall, 1711 Claflin Rd., Manhattan, KS, 66506, USA. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Feb; Vol. 34 (2), pp. 201-217. Date of Electronic Publication: 2020 Jan 08.
Typ publikacji:: Journal Article; Research Support, U.S. Gov't, Non-P.H.S.
MeSH Terms:: Drug Design*
Molecular Docking Simulation*
Neural Networks, Computer*
Amyloid Precursor Protein Secretases/*antagonists & inhibitors
Aspartic Acid Endopeptidases/*antagonists & inhibitors
Enzyme Inhibitors/*pharmacology
Macrocyclic Compounds/*pharmacology
Amyloid Precursor Protein Secretases/chemistry ; Amyloid Precursor Protein Secretases/metabolism ; Aspartic Acid Endopeptidases/chemistry ; Aspartic Acid Endopeptidases/metabolism ; Binding Sites ; Enzyme Inhibitors/chemistry ; Humans ; Ligands ; Macrocyclic Compounds/chemistry ; Protein Binding

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Skocz do pozycji: 19.

Tytuł:: Docking rigid macrocycles using Convex-PL, AutoDock Vina, and RDKit in the D3R Grand Challenge 4.
Autorzy:: Kadukova M; Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, 38000, Grenoble, France.; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141700.
Chupin V; Moscow Institute of Physics and Technology, Dolgoprudny, Russia, 141700.
Grudinin S; Univ. Grenoble Alpes, CNRS, Inria, Grenoble INP, LJK, 38000, Grenoble, France. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2020 Feb; Vol. 34 (2), pp. 191-200. Date of Electronic Publication: 2019 Nov 29.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Drug Design*
Molecular Docking Simulation*
Macrocyclic Compounds/*pharmacology
Proteins/*metabolism
Binding Sites ; Databases, Protein ; Humans ; Ligands ; Macrocyclic Compounds/chemistry ; Protein Binding ; Protein Conformation ; Proteins/chemistry ; Software

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Skocz do pozycji: 20.

Tytuł:: Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset.
Autorzy:: Elisée E; Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France.
Gapsys V; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Mele N; Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France.
Chaput L; Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France.; Sorbonne Université, UPMC Paris 06, Institut National de la Santé et de la Recherche Médicale, Unité Mixte de Recherche S 1155, Paris, France.
Selwa E; Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France.
de Groot BL; Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. .
Iorga BI; Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, Labex LERMIT, Gif-sur-Yvette, France. .; Pokaż więcej
Źródło:: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2019 Dec; Vol. 33 (12), pp. 1031-1043. Date of Electronic Publication: 2019 Nov 01.
Typ publikacji:: Journal Article; Research Support, Non-U.S. Gov't
MeSH Terms:: Drug Design*
Molecular Docking Simulation*
Binding Sites/*drug effects
Protein Binding/*drug effects
Computer-Aided Design ; Crystallography, X-Ray ; Entropy ; Humans ; Ligands ; Protein Conformation/drug effects ; Software ; Thermodynamics

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