المؤلفون: Curado Carballada, Christian

المساهمون: University/Department: Universitat de Girona. Departament de Química, University/Department: Universitat de Girona. Institut de Química Computacional i Catàlisi

Thesis Advisors: Osuna Oliveras, Sílvia, Feixas Geronès, Ferran, Swart, Marcel

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Dinàmica molecular, Dinámica molecular, Molecular dynamics, Biocatàlisi, Biocatálisis, Biocatalysis, Markov State Model, Dinàmica conformacional, Dinámica conformacional, Conformational dynamics, Amines, Superfície d'energia lliure, Superficie de energía libre, Free energy landscape, Mutacions distals, Mutaciones distales, Distal mutations

وصف الملف: application/pdf

URL الوصول: http://hdl.handle.net/10803/688466

المؤلفون: Herrera Nieto, Pablo

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

Thesis Advisors: De Fabritiis, Gianni

المصدر: TDX (Tesis Doctorals en Xarxa)

مصطلحات موضوعية: Molecular dynamics simulations, Intrinsically disordered proteins, Markov state model, Coupled-folding and binding, Partially ordered state

وصف الملف: application/pdf

URL الوصول: http://hdl.handle.net/10803/670061

المؤلفون: Huilin Wen, Hao Ouyang, Hao Shang, Chaohong Da, Tao Zhang

المصدر: Computational and Structural Biotechnology Journal, Vol 23, Iss , Pp 688-699 (2024)

مصطلحات موضوعية: Enhanced sampling strategy, ANN, Metadynamics, Markov state model, Conformational transition, Aβ peptide, Biotechnology, TP248.13-248.65

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037023004944; https://doaj.org/toc/2001-0370

URL الوصول: https://doaj.org/article/163960479b0a424092b958f55da83817

المؤلفون: Vinod Jani, Uddhavesh Sonavane, Rajendra Joshi

المصدر: Heliyon, Vol 10, Iss 16, Pp e36161- (2024)

مصطلحات موضوعية: KRAS, Molecular dynamics simulation, Markov state model, DCCM, Cancer, Science (General), Q1-390, Social sciences (General), H1-99

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2405844024121925; https://doaj.org/toc/2405-8440

URL الوصول: https://doaj.org/article/45073e227a1244d59fb05a4776181c83

المؤلفون: Wang, Lingyan, Song, Kaiyuan, Yu, Jin, Da, Lin-Tai

المصدر: Acta Biochimica et Biophysica Sinica. 54(6)

مصطلحات موضوعية: Biochemistry and Cell Biology, Biological Sciences, Genetics, 1.1 Normal biological development and functioning, Generic health relevance, DNA, DNA Repair, Nucleotides, Sugars, Thymine DNA Glycosylase, DNA repair, DNA glycosylase, Markov state model, molecular dynamics simulation, Biochemistry & Molecular Biology, Biochemistry and cell biology

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/86m3680q
https://escholarship.org/content/qt86m3680q/qt86m3680q.pdf

المؤلفون: Cathrine Bergh, Urška Rovšnik, Rebecca Howard, Erik Lindahl

المصدر: eLife, Vol 12 (2024)

مصطلحات موضوعية: Gloeobacter violaceus, cryo-EM, Markov state model, lipid binding site, gating, conformational transition, Medicine, Science, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://elifesciences.org/articles/86016; https://doaj.org/toc/2050-084X

URL الوصول: https://doaj.org/article/39f32a52a8d143c2a0b65fd8e0cf1df6

المؤلفون: Minghao Liu, Siyun Zheng, Yijia Tang, Weiwei Han, Wannan Li, Tao Li

المصدر: International Journal of Molecular Sciences, Vol 25, Iss 18, p 10074 (2024)

مصطلحات موضوعية: polyphenol oxidase, conformational changes, molecular dynamics simulation, Markov state model, Biology (General), QH301-705.5, Chemistry, QD1-999

Relation: https://www.mdpi.com/1422-0067/25/18/10074; https://doaj.org/toc/1661-6596; https://doaj.org/toc/1422-0067; https://doaj.org/article/a556e0d5327c42708e3898a7554b82ff

الاتاحة: https://doi.org/10.3390/ijms251810074
https://doaj.org/article/a556e0d5327c42708e3898a7554b82ff

المؤلفون: Polzin, Robert M., Klebanov, Ilja, Nüsken, Nikolas, Koltai, Péter

مصطلحات موضوعية: Low rank modeling, Coherent sets, Maximum likelihood, Nonnegative matrix factorization, Clustering, Markov state model, ddc:510

وصف الملف: 44 Seiten; application/pdf

الاتاحة: https://refubium.fu-berlin.de/handle/fub188/45445
https://doi.org/10.17169/refubium-45157
https://doi.org/10.1007/s00332-024-10091-x

المؤلفون: Satyajit Khatua, Srabani Taraphder

المصدر: Chemical Physics Impact, Vol 7, Iss , Pp 100329- (2023)

مصطلحات موضوعية: Carbonic anhydrase, 2-[(S)-benzylsulfinyl]Benzoic acid (3G1), Mechanism of unbinding, Transition path sampling, Markov state model (MSM), Physics, QC1-999, Chemistry, QD1-999

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667022423001688; https://doaj.org/toc/2667-0224

URL الوصول: https://doaj.org/article/a646a38aa9c844e5973d435993be957e

المؤلفون: Zhuang, Yuxuan, 1994

المساهمون: Lindahl, Erik, Professor, 1972, Brannigan, Grace, Associate Professor

مصطلحات موضوعية: ion channels, molecular dynamics, markov state model, lipid modulation, nicotinic receptor, protein conformational transitions, Biophysics, biofysik

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-220676
https://su.diva-portal.org/smash/get/diva2:1794307/FULLTEXT01.pdf
https://su.diva-portal.org/smash/get/diva2:1794307/PREVIEW01.jpg

المؤلفون: Taylor, Bryn C, Lee, Christopher T, Amaro, Rommie E

المصدر: Proceedings of the National Academy of Sciences of the United States of America. 116(17)

مصطلحات موضوعية: Diabetes, Autoimmune Disease, Neurodegenerative, 1.1 Normal biological development and functioning, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, Allosteric Site, Amino Acid Motifs, Binding Sites, Humans, Ligands, Molecular Dynamics Simulation, Protein Binding, Protein Conformation, Receptors, CCR2, CC chemokine receptor 2, CCR2, GPCR, Markov-state model, molecular dynamics simulations

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/7f6377vs

المؤلفون: Bodrenko Igor V., Milenkovic Stefan, Ceccarelli Matteo

المصدر: Biomolecular Concepts, Vol 13, Iss 1, Pp 207-219 (2022)

مصطلحات موضوعية: nanopores, diffusive transport, molecular current, saturation, markov state model, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1868-503X

URL الوصول: https://doaj.org/article/53ca7bfb545447d79b3960f0cc80e251

المؤلفون: Ying Wang, Mingyu Li, Wenqi Liang, Xinchao Shi, Jigang Fan, Ren Kong, Yaqin Liu, Jian Zhang, Ting Chen, Shaoyong Lu

المصدر: Computational and Structural Biotechnology Journal, Vol 20, Iss , Pp 628-639 (2022)

مصطلحات موضوعية: GPCR, Molecular dynamics simulations, Markov state model, Allosteric modulator, Biotechnology, TP248.13-248.65

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037022000228; https://doaj.org/toc/2001-0370

URL الوصول: https://doaj.org/article/0c11371a0f244c42ad04128dec6bbf8c

المؤلفون: Alves da Silva, Leticia, Lazzarin, Erica, Gradisch, Ralph, Clarke, Amy, Stockner, Thomas

المساهمون: Alves da Silva, Leticia, Lazzarin, Erika, Gradisch, Ralph, Clarke, Amy, Stockner, Thomas

مصطلحات موضوعية: Serotonin transporter, SERT, Free energy, Markov state Model, tICA, occlusion

Relation: https://doi.org/10.1016/j.jbc.2022.101613; https://doi.org/10.5281/zenodo.7902686; https://doi.org/10.5281/zenodo.7902687; oai:zenodo.org:7902687

الاتاحة: https://doi.org/10.5281/zenodo.7902687

المؤلفون: Robert M. Raddi, Vincent A. Voelz

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, zhou et al, scale distributed computing, p53 transactivation domain, markov state model, desolvation transitions along, based structural features, accelerated implied timescales, remarkably similar landscape, first tica eigenvector, solvent shells contributing, important solvent shells, p53 tad peptide, tica analysis, similar hyperparameters, subsequently built, slowest motions, reveal solvation, results provide, peptide binding, hydrophobic effect, centric view, binding reaction, 2017 )

Relation: https://figshare.com/articles/journal_contribution/Markov_State_Model_of_Solvent_Features_Reveals_Water_Dynamics_in_Protein-Peptide_Binding/24787541

الاتاحة: https://doi.org/10.1021/acs.jpcb.3c04775.s001
https://figshare.com/articles/journal_contribution/Markov_State_Model_of_Solvent_Features_Reveals_Water_Dynamics_in_Protein-Peptide_Binding/24787541

المؤلفون: Xiaokun Hong (14339876), Kaiyuan Song (14339879), Mueed Ur Rahman (6859931), Ting Wei (113015), Yan Zhang (8098), Lin-Tai Da (399373), Hai-Feng Chen (141242)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Cell Biology, Genetics, Molecular Biology, Immunology, Computational Biology, Biological Sciences not elsewhere classified, Physical Sciences not elsewhere classified, still poorly understood, shortest path according, order conformation conversion, main driving force, hydrophobic interaction disturbing, dynamic regulation pathway, transition path theory, molecular switch inhibiting, markov state model, reach steady states, achieving steady states, β2 integrin acts, phosphorylation regulation mechanism, β2 integrin, regulation mechanism, switch mechanism, transition paths, p4 state, phosphorylated states, threonine 758

Relation: https://figshare.com/articles/journal_contribution/Phosphorylation_Regulation_Mechanism_of_2_Integrin_for_the_Binding_of_Filamin_Revealed_by_Markov_State_Model/21830135

الاتاحة: https://doi.org/10.1021/acs.jcim.2c01177.s001

المؤلفون: Mayar Tarek Ibrahim, Gennady M. Verkhivker, Jyoti Misra, Peng Tao

المصدر: International Journal of Molecular Sciences; Volume 24; Issue 10; Pages: 9009

مصطلحات موضوعية: Hippo pathway, TEAD4/YAP1 interaction, chemical modification, Markov state model, free energy perturbation

جغرافية الموضوع: agris

وصف الملف: application/pdf

Relation: Molecular Biophysics; https://dx.doi.org/10.3390/ijms24109009

الاتاحة: https://doi.org/10.3390/ijms24109009

المؤلفون: Liuba Mazzanti, Tâp Ha-Duong

المصدر: International Journal of Molecular Sciences; Volume 24; Issue 5; Pages: 5021

مصطلحات موضوعية: peptide membrane permeability, molecular dynamics simulation, umbrella sampling, Markov State Model, free energy profile

جغرافية الموضوع: agris

وصف الملف: application/pdf

Relation: Molecular Pharmacology; https://dx.doi.org/10.3390/ijms24055021

الاتاحة: https://doi.org/10.3390/ijms24055021

المؤلفون: Clarissa A. Seidler, Janik Kokot, Monica L. Fernández-Quintero, Klaus R. Liedl

المصدر: Biomolecules; Volume 13; Issue 2; Pages: 380

مصطلحات موضوعية: camelid V H H antibodies, affinity maturation, molecular dynamics, enhanced sampling, Markov-state model

جغرافية الموضوع: agris

وصف الملف: application/pdf

Relation: https://dx.doi.org/10.3390/biom13020380

الاتاحة: https://doi.org/10.3390/biom13020380

المؤلفون: Kaifeng Liu, Fangfang Guo, Yingying Ma, Xiangyu Yu, Xueqi Fu, Wannan Li, Weiwei Han

المصدر: International Journal of Molecular Sciences, Vol 24, Iss 14471, p 14471 (2023)

مصطلحات موضوعية: molecular dynamics simulation, SARS-CoV-2, sulfated polysaccharide, functionalized fullerene, Markov state model, Biology (General), QH301-705.5, Chemistry, QD1-999

Relation: https://www.mdpi.com/1422-0067/24/19/14471; https://doaj.org/toc/1661-6596; https://doaj.org/toc/1422-0067; https://doaj.org/article/ebf96217cf3f453795b9a0bbb63762ed

الاتاحة: https://doi.org/10.3390/ijms241914471
https://doaj.org/article/ebf96217cf3f453795b9a0bbb63762ed