المؤلفون: A. Najla Hosseini, David van der Spoel

مصطلحات موضوعية: Biophysics, Neuroscience, Biotechnology, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, ∼ 1 å, specific interactions needed, numerous scientific disciplines, including drug discovery, grained force field, accurately simulate peptides, martini force field, martini 3 lacks, martini 3 coarse, structural biology, sheets increases, scale systems, problems may, organic compounds, molecular systems, melting points, important tool, evaluated using, critical evaluation, computational chemistry, biomolecular systems, backbone beads, amyloid peptide

Relation: https://figshare.com/articles/journal_contribution/Martini_on_the_Rocks_Can_a_Coarse-Grained_Force_Field_Model_Crystals_/25049906

الاتاحة: https://doi.org/10.1021/acs.jpclett.4c00012.s002
https://figshare.com/articles/journal_contribution/Martini_on_the_Rocks_Can_a_Coarse-Grained_Force_Field_Model_Crystals_/25049906

المؤلفون: Marrink, Siewert J., Monticelli, Luca, Melo, Manuel N., Alessandri, Riccardo, Tieleman, D. Peter, Souza, Paulo C.T.

المساهمون: Instituto de Tecnologia Química e Biológica António Xavier (ITQB), RUN

مصطلحات موضوعية: coarse graining, Martini force field, molecular dynamics, Biochemistry, Computer Science Applications, Physical and Theoretical Chemistry, Computational Mathematics, Materials Chemistry

وصف الملف: application/pdf

Relation: 1759-0876; PURE: 72092170

الاتاحة: http://hdl.handle.net/10362/158515

المؤلفون: Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten, Siewert J. Marrink

المصدر: Frontiers in Chemistry, Vol 11 (2023)

مصطلحات موضوعية: JCVI-syn3A, minimal cell, Martini force field, integrative modeling, coarse grain, polyply, Chemistry, QD1-999

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fchem.2023.1106495/full; https://doaj.org/toc/2296-2646

URL الوصول: https://doaj.org/article/ec6346a36976419a93f6e9f4abc90255

المؤلفون: Marrink, Siewert J., Monticelli, Luca, Melo, Manuel N., Alessandri, Riccardo, Tieleman, D. Peter, Souza, Paulo C.T.

المصدر: Marrink , S J , Monticelli , L , Melo , M N , Alessandri , R , Tieleman , D P & Souza , P C T 2023 , ' Two decades of Martini : Better beads, broader scope ' , Wiley Interdisciplinary Reviews: Computational Molecular Science , vol. 13 , no. 1 , e1620 . https://doi.org/10.1002/wcms.1620

مصطلحات موضوعية: coarse graining, Martini force field, molecular dynamics

وصف الملف: application/pdf

الاتاحة: https://hdl.handle.net/11370/13583061-b22b-4f5c-923b-245ba738dd7d
https://research.rug.nl/en/publications/13583061-b22b-4f5c-923b-245ba738dd7d
https://doi.org/10.1002/wcms.1620
https://pure.rug.nl/ws/files/574739172/WIREs_Comput_Mol_Sci_2022_Marrink_Two_decades_of_Martini_Better_beads_broader_scope.pdf
http://www.scopus.com/inward/record.url?scp=85132565104&partnerID=8YFLogxK

المؤلفون: K. Anton Feenstra, Akiko Higuchi, Kei Yura, Sanne Abeln, Halima Mouhib

المصدر: F1000Research, Vol 8 (2022)

مصطلحات موضوعية: GLUT1 glucose transporter deficiency syndrome, Human glucose transporters, SLC transporter family, transport mechanism, molecular dynamics simulation, Martini force field, eng, Medicine, Science

وصف الملف: electronic resource

Relation: https://f1000research.com/articles/8-322/v2; https://doaj.org/toc/2046-1402

URL الوصول: https://doaj.org/article/e77ce8190c6c4bb692276bad561e164f

المؤلفون: Arash Elahi (11902569), Xavier Bidault (7861847), Santanu Chaudhuri (1501243)

مصطلحات موضوعية: Biophysics, Medicine, Ecology, Cancer, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, micelle diameter similar, micelle core size, many potential applications, atom force fields, 3500 g mol, martini force field, atomistic free energy, po block parameterization, spanning many eo, existing models significantly, dependent model reproduces, critical micelle temperature, propylene oxide trimer, high po content, triblock copolymers thermo, propylene oxide, po content, martini platform, atomistic bond, ethylene oxide, po ratios, po ratio, po mass

Relation: https://figshare.com/articles/journal_contribution/Temperature-Transferable_Coarse-Grained_Model_for_Poly_propylene_oxide_to_Study_Thermo-Responsive_Behavior_of_Triblock_Copolymers/17866539

الاتاحة: https://doi.org/10.1021/acs.jpcb.1c06318.s001

المؤلفون: Cheng Zhou, Kefu Liu

المصدر: BioMedical Engineering OnLine, Vol 18, Iss 1, Pp 1-16 (2019)

مصطلحات موضوعية: Molecular dynamics simulation, Martini force field, Reversible electroporation, Phospholipid membrane, Medical technology, R855-855.5

وصف الملف: electronic resource

Relation: https://doaj.org/toc/1475-925X

URL الوصول: https://doaj.org/article/7a7dbb825da74b06839a607bcd1f1cc8

المؤلفون: Md. Iqbal Mahmood, Adolfo B. Poma, Kei-ichi Okazaki

المصدر: Frontiers in Molecular Biosciences, Vol 8 (2021)

مصطلحات موضوعية: molecular dynamics simulation, MARTINI force field, Gō model, membrane remodeling, Pacsin, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2021.619381/full; https://doaj.org/toc/2296-889X

URL الوصول: https://doaj.org/article/6c78d80ba08949efbd1251bb8e6ef880

المؤلفون: S. Mahajan & T. Tang

مصطلحات موضوعية: Martini Force Field, Polyethyleneimine

Relation: https://era.library.ualberta.ca/items/920aab64-b2cc-4231-b67b-45d43286f4ba

الاتاحة: https://era.library.ualberta.ca/items/920aab64-b2cc-4231-b67b-45d43286f4ba
https://doi.org/10.7939/r3-gnte-kp69

المؤلفون: Luís Borges-Araújo (11882748), Paulo C. T. Souza (7421693), Fábio Fernandes (4512166), Manuel N. Melo (191945)

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Neuroscience, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, relevant phosphoinositide interaction, provide stable topologies, potential long times, play crucial roles, pi ­( 4, phosphoinositide aggregation tendencies, phosphatidylinositide lipid headgroups, develop improve upon, 5 )­ p, membrane regulatory events, martini force field, involved membrane processes, earlier martini versions, included correct behavior, grain force field, lipid membrane simulations, 2 , martini 3 coarse, martini 3, membrane phospholipids, employing coarse, behavior seen, atomistic simulations

Relation: https://figshare.com/articles/journal_contribution/Improved_Parameterization_of_Phosphatidylinositide_Lipid_Headgroups_for_the_Martini_3_Coarse-Grain_Force_Field/17698107

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00615.s001

المؤلفون: Thomas D. Potter (11377881), Elin L. Barrett (11377884), Mark A. Miller (11377887)

مصطلحات موضوعية: Biophysics, Biochemistry, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, martini force field, extracting partition coefficients, broader chemical space, parameterizing organic molecules, grained mapping algorithm, grained beads, throughput simulations, structural rigidity, stable frameworks, preserving symmetry, molecule ’, mapping process, latter case, larger molecules, interfacial region, existing schemes, energy profiles, diverse set, cholesterol content, building efficient, bonding network, based analysis, automated system, aromatic rings

Relation: https://figshare.com/articles/journal_contribution/Automated_Coarse-Grained_Mapping_Algorithm_for_the_Martini_Force_Field_and_Benchmarks_for_Membrane_Water_Partitioning/16560039

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00322.s001

المؤلفون: Yang Liu (4829), Alex H. de Vries (7421696), Weria Pezeshkian (3589226), Siewert J. Marrink (135518)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Microbiology, Cell Biology, Molecular Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, plasma membranes, Capturing Membrane Phase Separation, Martini force field, AA, phase separation, CG, VS scheme couples, Dual Resolution Molecular Dynamics ., leaflet

Relation: https://figshare.com/articles/journal_contribution/Capturing_Membrane_Phase_Separation_by_Dual_Resolution_Molecular_Dynamics_Simulations/14839158

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00151.s001

المؤلفون: Anne-Elisabeth Molza (1890415), Ping Gao (172038), Justine Jakpou (10942363), Julien Nicolas (1356393), Nicolas Tsapis (1506610), Tâp Ha-Duong (5574005)

مصطلحات موضوعية: Biophysics, Medicine, Biotechnology, Developmental Biology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, 370 K show, Poly, phase diagram, version 2.2, drug delivery nanoparticles, ureido-based polymers, polymer solution, dissolution processes, MD, UCST, MARTINI force field, thermoresponsive nanoparticles, Upper Critical Solution Temperature., gain insight, phase separation, solution temperature, reparametrized version 3.0, Multi-microsecond simulations, citrulline, exhibit tunable, drug delivery systems, simulation study

Relation: https://figshare.com/articles/journal_contribution/Simulations_of_the_Upper_Critical_Solution_Temperature_Behavior_of_Poly_ornithine-_i_co_i_-citrulline_s_Using_MARTINI-Based_Coarse-Grained_Force_Fields/14751115

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00140.s001

المؤلفون: Konstantinos D. Papavasileiou (5545907), Loukas D. Peristeras (4926331), Andreas Bick (1720555), Ioannis G. Economou (559797)

مصطلحات موضوعية: Biophysics, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, H 2 O diffusivity, Molecular Dynamics Simulation, presence, Co NP, mixture, GTL, CG MD simulations, emission transportation fuels, C 28, catalyst support materials, MARTINI force field, FTS reaction, pore, study FTS-related processes, phase separation, Co NP surface, van der Waals, CG simulation methods, TIP 4P force field, AA, center, novel CGMD simulations

Relation: https://figshare.com/articles/journal_contribution/Molecular_Dynamics_Simulation_of_the_i_n_i_Octacosane_Water_Mixture_Confined_in_Graphene_Mesopores_Comparison_of_Atomistic_and_Coarse-Grained_Calculations_and_the_Effect_of_Catalyst_Nanoparticle/13836574

الاتاحة: https://doi.org/10.1021/acs.energyfuels.0c04151.s001

المؤلفون: Jiramate Kitjanon, Wasinee Khuntawee, Saree Phongphanphanee, Thana Sutthibutpong, Nattaporn Chattham, Mikko Karttunen, Jirasak Wong-ekkabut

المصدر: Polymers; Volume 13; Issue 22; Pages: 4044

مصطلحات موضوعية: molecular dynamics simulations, natural rubber, cis -1,4-polyisoprene, MARTINI force field

وصف الملف: application/pdf

Relation: Polymer Physics and Theory; https://dx.doi.org/10.3390/polym13224044

الاتاحة: https://doi.org/10.3390/polym13224044

المؤلفون: Christos Lamprakis (10723116), Ioannis Andreadelis (6331535), John Manchester (2303572), Camilo Velez-Vega (1487623), José S. Duca (1487629), Zoe Cournia (650343)

مصطلحات موضوعية: Biophysics, Biochemistry, Physiology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, Martini open-beta 3, Study Protein Dimerization, supramolecular protein aggregation, association, membrane proteins, near-native dimer complexes, minima, coarse-grained force field, protein dimerization process, Martini 2.2 P, Martini Force Field, Martini 2.2 P multimer simulations, Martini 3 results

Relation: https://figshare.com/articles/journal_contribution/Evaluating_the_Efficiency_of_the_Martini_Force_Field_to_Study_Protein_Dimerization_in_Aqueous_and_Membrane_Environments/14510988

الاتاحة: https://doi.org/10.1021/acs.jctc.0c00507.s001

المؤلفون: Wojciech Plazinski, Valery Lutsyk, Anita Plazinska

مصطلحات موضوعية: Biophysics, Biochemistry, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, lipid membrane composition, inherent elastic network, exploring free energies, defined structures (<, coupling parameter λ, surfactant protein b, predefined conformational states, proposed method may, martini force field, five biomolecular systems, protein conformational transitions, protein ’, unfolded states, various factors, valuable tool, use within, terminal segment, straightforward method, staphylococcal <, routinely used, results show, native conformation, multiple factors, method using

Relation: https://figshare.com/articles/dataset/Exploring_Free_Energies_of_Specific_Protein_Conformations_Using_the_Martini_Force_Field/25326231

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01155.s001
https://figshare.com/articles/dataset/Exploring_Free_Energies_of_Specific_Protein_Conformations_Using_the_Martini_Force_Field/25326231

المؤلفون: Marchetto, Alessandro, Si Chaib, Zeineb, Rossi, Carlo Alberto, Ribeiro, Rui, Pantano, Sergio, Rossetti, Giulia, Giorgetti, Alejandro

المساهمون: Marchetto, Alessandro, Si Chaib, Zeineb, Rossi, Carlo Alberto, Ribeiro, Rui, Pantano, Sergio, Rossetti, Giulia, Giorgetti, Alejandro

مصطلحات موضوعية: CGMD, SIRAH, backmapping, martini force field

وصف الملف: ELETTRONICO

Relation: info:eu-repo/semantics/altIdentifier/pmid/33333836; info:eu-repo/semantics/altIdentifier/wos/WOS:000603266000001; volume:25; issue:24; firstpage:1; lastpage:12; numberofpages:12; journal:MOLECULES; http://hdl.handle.net/11562/1035461; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85098675370

الاتاحة: http://hdl.handle.net/11562/1035461
https://doi.org/10.3390/molecules25245934

المؤلفون: Si Chaib, Zeineb, Marchetto, Alessandro, Dishnica, Klevia, Carloni, Paolo, Giorgetti, Alejandro, Rossetti, Giulia

المساهمون: Si Chaib, Zeineb, Marchetto, Alessandro, Dishnica, Klevia, Carloni, Paolo, Giorgetti, Alejandro, Rossetti, Giulia

مصطلحات موضوعية: TSPO, Martini force-field, cholesterol

وصف الملف: ELETTRONICO

Relation: info:eu-repo/semantics/altIdentifier/wos/WOS:000580248700001; volume:25; issue:18; firstpage:1; lastpage:18; numberofpages:18; journal:MOLECULES; http://hdl.handle.net/11562/1025044; info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85091591182

الاتاحة: http://hdl.handle.net/11562/1025044
https://doi.org/10.3390/molecules25184299

المؤلفون: Sun, Fude, Schroer, Carsten F E, Palacios, Carlos R, Xu, Lida, Luo, Shi-Zhong, Marrink, Siewert J

المصدر: Sun , F , Schroer , C F E , Palacios , C R , Xu , L , Luo , S-Z & Marrink , S J 2020 , ' Molecular mechanism for bidirectional regulation of CD44 for lipid raft affiliation by palmitoylations and PIP2 ' , PLoS Computational Biology , vol. 16 , no. 4 , e1007777 . https://doi.org/10.1371/journal.pcbi.1007777

مصطلحات موضوعية: MARTINI FORCE-FIELD, PHOSPHATIDYLINOSITOL, 4,5-BISPHOSPHATE, COMPUTATIONAL LIPIDOMICS, CYTOPLASMIC DOMAIN, L-SELECTIN, DYNAMICS, PROTEINS, INSIGHTS, ASSOCIATION, SITES

وصف الملف: application/pdf

الاتاحة: https://hdl.handle.net/11370/b01c5e77-34fd-4709-ac3f-3c64fdfc97c7
https://research.rug.nl/en/publications/b01c5e77-34fd-4709-ac3f-3c64fdfc97c7
https://doi.org/10.1371/journal.pcbi.1007777
https://pure.rug.nl/ws/files/132285366/journal.pcbi.1007777.pdf