المؤلفون: Zhe Li, Mei-Yan Jiang, Runduo Liu, Quan Wang, Qian Zhou, Yi-You Huang, Yinuo Wu, Chang-Guo Zhan, Hai-Bin Luo

المصدر: Acta Pharmaceutica Sinica B, Vol 14, Iss 12, Pp 5357-5369 (2024)

مصطلحات موضوعية: Free energy perturbation, Drug design, Phosphodiesterase 1, Relative binding free energy, Molecular simulation, Therapeutics. Pharmacology, RM1-950

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211383524002521; https://doaj.org/toc/2211-3835

URL الوصول: https://doaj.org/article/ff830aced8fd4213a2fd0578606f3c13

المؤلفون: Drechsel, Nils Jan Daniel

المساهمون: University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Thesis Advisors: Villà i Freixa, Jordi, Dill, Ken A.

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Multiscale molecular dynamics, Coarse-grained force-field, Free energy perturbation, Non-polar solvation free energy, Solvent accessible surface area, Collective variable, Chicken villin headpiece, Triforce, Exposed boundary, Dinámica molecular multiescala, Campos de fuerza de grano grueso, Perturbación de energía libre, Solvatación energía libre no-polar, Superficie accesible al disolvente, Variables colectiva, Expuestos límite

وصف الملف: application/pdf

URL الوصول: http://hdl.handle.net/10803/125071

المؤلفون: Vaia-Argyro Bakalakou, Barbara Mavroidi, Amalia D. Kalampaliki, Béatrice Josselin, Stéphane Bach, Alexios-Leandros Skaltsounis, Panagiotis Marakos, Nicole Pouli, Maria Pelecanou, Vassilios Myrianthopoulos, Sandrine Ruchaud, Ioannis K. Kostakis

المصدر: European Journal of Medicinal Chemistry Reports, Vol 12, Iss , Pp 100193- (2024)

مصطلحات موضوعية: Kinase inhibitors, Metadynamics, pyrazolo[4,3-c]pyrazoles, Solvent mapping, Alzheimer's disease, Free energy perturbation, Pharmacy and materia medica, RS1-441, Other systems of medicine, RZ201-999

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2772417424000657; https://doaj.org/toc/2772-4174

URL الوصول: https://doaj.org/article/eb0021815ee9431cabe5edd011eff369

المؤلفون: Hongze Fu, Yinbang Zhu, Qu Chen

المصدر: Frontiers in Physics, Vol 12 (2024)

مصطلحات موضوعية: MM/PBSA, free energy perturbation (FEP), thermodynamic integration, Bennett acceptance ratio (BAR), umbrella sampling (US), Jarzynski equality, Physics, QC1-999

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fphy.2024.1469515/full; https://doaj.org/toc/2296-424X

URL الوصول: https://doaj.org/article/a7db51c25e0148bea61df6e0d74922cd

المؤلفون: Khan, Abdul Kareem

المساهمون: University/Department: Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut

Thesis Advisors: Villà i Freixa, Jordi

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: dinàmica, centre actiu, relacions d'estructura activitat, preorganització, reorganització, estat de transició, estat actiu, estabilitat electrostàtica, interacción proteïna-proteïna, test de ranks de Wilcoxon, P-loop, G1 motif, HVR, metastability, RMSD, substrate assisted catalysis, sequence alignment, beta sheet, helix, Z-test, wilcoxon rank test, protein-protein interactions, electrostatic stability, active state, dynamics, signal transduction, electrostatic stabilization, ras effectors, guanine exchange factor, GTPase-activating proteins, quantum mechanics/molecular, PDLD/S-LRA, X-ray crystallography, solvation energy, free energy perturbation, statistical analysis, GTP hydrolysis, guanosine diphosphate, guanosine triphosphate, computer simulation, thermodynamics, protein conformation, electrostatics, interruptor II, interruptor I, llaç P, motiu G1, HVR (regions altament variables), metaestabilita, catàlisi assistida pel substrat, aliniament de seqüència, fulla beta, hèlix, test Z, transducció del senyal, estabilització electrostàtica, efectors de ras, factor de bescamvi de guanina, proteïnes activadores de l'activitat, mecànica quàntica/mecànica, cristalografia de raigs X, energia de solvatació, perturbació de l'energia lliure, anàlisi estadística, hidròlisi de GTP, difosfat de guanosina, trifosfat de guanosina, simulació computacional, termodinàmica, conformació proteïca, electrostàtica, switch-I, switch-II

وصف الملف: application/pdf

URL الوصول: http://www.tdx.cat/TDX-0714109-112338
http://hdl.handle.net/10803/7161

المؤلفون: Castellano, Steven

المساهمون: Luisi, Ben, Faraldo-Gómez, José

مصطلحات موضوعية: multidrug resistance pumps, molecular dynamics simulations, free energy perturbation, metadynamics, cryo-EM, styrene maleic acid, Multidrug and Toxic Compound Extrusion family, Major Facilitator Superfamily, Resistance-Nodulation-Cell Division superfamily

URL الوصول: https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.841290

المؤلفون: Dazhi Feng, Bo Liu, Zhiwei Chen, Jinyi Xu, Meiyu Geng, Wenhu Duan, Jing Ai, Hefeng Zhang

مصطلحات موضوعية: Biochemistry, Cell Biology, Pharmacology, Biotechnology, Hematology, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, HPK1 inhibitor, machine learning, virtual screening, free energy perturbation, structural modification

Relation: https://figshare.com/articles/journal_contribution/Discovery_of_hematopoietic_progenitor_kinase_1_inhibitors_using_machine_learning-based_screening_and_free_energy_perturbation/24975736

الاتاحة: https://doi.org/10.6084/m9.figshare.24975736.v1
https://figshare.com/articles/journal_contribution/Discovery_of_hematopoietic_progenitor_kinase_1_inhibitors_using_machine_learning-based_screening_and_free_energy_perturbation/24975736

المؤلفون: Renling Hu, Jintu Zhang, Yu Kang, Zhe Wang, Peichen Pan, Yafeng Deng, Chang-Yu Hsieh, Tingjun Hou

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Molecular Biology, Pharmacology, Biotechnology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, various simulation techniques, simulation process limits, previously published methods, perturbing group size, improving computational efficiency, ideal perturbation patterns, free energy perturbation, cartesian coordinate reconstruction, allowing straightforward integration, complex data preparation, based alignment algorithm, 08 ± 0, scale congeneric ligands, samples multiple ligands, large perturbing groups, guide lead optimization, fully connected via, blade dynamics engine, average unsigned error, msld calculations based

Relation: https://figshare.com/articles/journal_contribution/Comprehensive_Open-Source_and_Automated_Workflow_for_Multisite_Dynamics_in_Lead_Optimization/25127585

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01154.s001
https://figshare.com/articles/journal_contribution/Comprehensive_Open-Source_and_Automated_Workflow_for_Multisite_Dynamics_in_Lead_Optimization/25127585

المؤلفون: Madapally, Hridya Valia, Abe, Kazuhiro, Dubey, Vikas, Khandelia, Himanshu

المصدر: Madapally , H V , Abe , K , Dubey , V & Khandelia , H 2024 , ' Specific protonation of acidic residues confers K + selectivity to the gastric proton pump ' , Journal of Biological Chemistry , vol. 300 , no. 1 , 105542 . https://doi.org/10.1016/j.jbc.2023.105542

مصطلحات موضوعية: cryo-EM, free energy perturbation, H,K-ATPase, ion selectivity, membrane protein, molecular dynamics, proton pump

وصف الملف: application/pdf

الاتاحة: https://portal.findresearcher.sdu.dk/da/publications/7867f252-a6da-428c-983c-f360d1d53d12
https://doi.org/10.1016/j.jbc.2023.105542
https://findresearcher.sdu.dk/ws/files/252955385/1-s2.0-S002192582302570X-main.pdf

المؤلفون: Zachary Smith, Michael Strobel, Bodhi P. Vani, Pratyush Tiwary

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Physiology, Pharmacology, Computational Biology, Biological Sciences not elsewhere classified, Information Systems not elsewhere classified, site prediction workflow, nearly every step, minimize wasted computation, important early step, free energy perturbation, data set preparation, aided drug discovery, recovering binding sites, binding sites, priori <, pdb structures, model evaluation, high degree, evaluate assumptions, downstream tasks, difficult task, campaigns rely, attention identifying, art performance, achieve state

Relation: https://figshare.com/articles/journal_contribution/Graph_Attention_Site_Prediction_GrASP_Identifying_Druggable_Binding_Sites_Using_Graph_Neural_Networks_with_Attention/25367097

الاتاحة: https://doi.org/10.1021/acs.jcim.3c01698.s001

المؤلفون: Saha, Aakash

مصطلحات موضوعية: Bioengineering, Alchemical Free Energy Perturbation, Biophysics, Computational Chemistry, CRISPR-Cas, Molecular Simulation

URL الوصول: https://escholarship.org/uc/item/2zp5v2p9

المؤلفون: Tuckerman, Mark E., author

المصدر: Statistical Mechanics: Theory and Molecular Simulation, 2023, ill.

الاتاحة: https://doi.org/10.1093/oso/9780198825562.003.0008

المؤلفون: Panel, Nicolas, Vo, Duc Duy, Kahlous, Nour Aldin, Huebner, Harald, Tiedt, Stephanie, Matricon, Pierre, Pacalon, Jody, Fleetwood, Oliver, Kampen, Stefanie, Luttens, Andreas, 1993, Delemotte, Lucie, Kihlberg, Jan, Gmeiner, Peter, Carlsson, Jens

المصدر: Angewandte Chemie International Edition. 62(22)

مصطلحات موضوعية: Agonist, beta(2) Adrenergic Receptor, Drug Design, Free Energy Perturbation, G-Protein-Coupled Receptor, Molecular Dynamics

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-524663
https://doi.org/10.1002/anie.202218959
https://uu.diva-portal.org/smash/get/diva2:1844020/FULLTEXT01.pdf

المؤلفون: Ekberg, Vilhelm

مصطلحات موضوعية: free energy perturbation, drug design, ligand-binding affinity, entropy, molecular mechanics, molecular dynamics, Naturvetenskap, Kemi, Teoretisk kemi, Natural Sciences, Chemical Sciences, Theoretical Chemistry

وصف الملف: electronic

URL الوصول: https://lup.lub.lu.se/record/9b0b1b60-c233-4709-ad14-98b4bf1d73f0
https://portal.research.lu.se/files/156152167/Vilhelm_Ekberg_avhandling_spikning.pdf

المؤلفون: Brickel, Sebastian, Demkiv, Andrey O., Crean, Rory M., Pinto, Gaspar P., Kamerlin, Shina C. Lynn, 1981

المصدر: Journal of Molecular Graphics and Modelling. 119

مصطلحات موضوعية: Enhanced sampling, Empirical valence bond, Free energy perturbation, Replica exchange molecular dynamics, Q6

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-496586
https://doi.org/10.1016/j.jmgm.2022.108402
https://uu.diva-portal.org/smash/get/diva2:1737728/FULLTEXT01.pdf

المؤلفون: Yang, Qingyi, Burchett, Woodrow, Steeno, Gregory S, Liu, Shuai, Yang, Mingjun, Mobley, David L, Hou, Xinjun

المصدر: Journal of Computational Chemistry. 41(3)

مصطلحات موضوعية: Chemical Sciences, Physical Chemistry, Theoretical and Computational Chemistry, binding affinity, binding free energy, free energy perturbation, pairwise comparison, perturbation graph, design topology, experimental error, mean squared error, Spearman correlation, experimental design, Physical Chemistry (incl. Structural), Nanotechnology, Chemical Physics, Physical chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/91d6v4w0

المؤلفون: Jespers, Willem, Verdon, Gregory, Azuaje, Jhonny, Majellaro, Maria, Keränen, Henrik, 1983, Garcia-Mera, Xerardo, Congreve, Miles, Deflorian, Francesca, de Graaf, Chris, Zhukov, Andrei, Dore, Andrew S., Mason, Jonathan S., Åqvist, Johan, Cooke, Robert M., Sotelo, Eddy, Gutiérrez-de-Terán, Hugo

المصدر: Angewandte Chemie International Edition. 59(38):16536-16543

مصطلحات موضوعية: adenosine receptors, biophysical mapping (BPM), free energy perturbation (FEP), G protein-coupled receptor (GPCR)

وصف الملف: print

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-439264
https://doi.org/10.1002/anie.202003788

المؤلفون: Deyan Wu, Xuehua Zheng, Runduo Liu, Zhe Li, Zan Jiang, Qian Zhou, Yue Huang, Xu-Nian Wu, Chen Zhang, Yi-You Huang, Hai-Bin Luo

المصدر: Acta Pharmaceutica Sinica B, Vol 12, Iss 3, Pp 1351-1362 (2022)

مصطلحات موضوعية: Free energy perturbation, Scaffold hopping, Privileged scaffolds, Drug discovery, Binding potencies, Molecular design, Therapeutics. Pharmacology, RM1-950

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211383521003889; https://doaj.org/toc/2211-3835

URL الوصول: https://doaj.org/article/35e8bd3e764c47488baa224bfba360df

المؤلفون: Cleves, Ann E, Jain, Ajay N

المصدر: Journal of Computer-Aided Molecular Design. 32(7)

مصطلحات موضوعية: Medicinal and Biomolecular Chemistry, Chemical Sciences, Bioengineering, Benzodiazepinones, Binding Sites, Dihydrotestosterone, Estradiol, Ligands, Machine Learning, Models, Molecular, Physical Phenomena, Protein Binding, Protein Conformation, Quantitative Structure-Activity Relationship, Quantum Theory, Sex Hormone-Binding Globulin, Thermodynamics, QSAR, Binding affinity, Machine learning, Multiple-instance learning, Free-energy perturbation, Pose prediction, Confidence estimation, Theoretical and Computational Chemistry, Medicinal & Biomolecular Chemistry, Medicinal and biomolecular chemistry, Theoretical and computational chemistry

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/73t1g5tc
https://escholarship.org/content/qt73t1g5tc/qt73t1g5tc.pdf

المؤلفون: Deng Li, Mona S. Minkara

المصدر: Computational and Structural Biotechnology Journal, Vol 20, Iss , Pp 4984-5000 (2022)

مصطلحات موضوعية: Surfactant Protein D, Protein-Glycan Complexes, Molecular Dynamics Simulation, Free Energy Perturbation, Biotechnology, TP248.13-248.65

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037022003798; https://doaj.org/toc/2001-0370

URL الوصول: https://doaj.org/article/36359ce1c7424d9b9123019055518fd1