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: Pang, Jiu, Mehandzhiyski, Alexandar, 1986, Zozoulenko, Igor, 1962

المصدر: Cellulose. 29:9493-9509

مصطلحات موضوعية: Martini 3, Coarse-grained molecular dynamics simulations, Cellulose nanocrystal (CNC), TEMPO surface modification, Colloidal stability

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-189314
https://liu.diva-portal.org/smash/get/diva2:1704680/FULLTEXT01.pdf

المؤلفون: Midhun Mohan Anila, Paweł Rogowski, Bartosz Różycki

المصدر: Molecules, Vol 29, Iss 12, p 2768 (2024)

مصطلحات موضوعية: galectin-3, conformational ensemble, fuzzy complexes, molecular dynamics simulations, Martini 3, Organic chemistry, QD241-441

وصف الملف: electronic resource

Relation: https://www.mdpi.com/1420-3049/29/12/2768; https://doaj.org/toc/1420-3049

URL الوصول: https://doaj.org/article/68cb348f8ea84460bb6ccbc3007b9968

المؤلفون: Chiariello, Maria Gabriella, Zarmiento-Garcia, Rubi, Marrink, Siewert Jan

المصدر: Chiariello , M G , Zarmiento-Garcia , R & Marrink , S J 2024 , ' Martini 3 Coarse-Grained Model for the Cofactors Involved in Photosynthesis ' , International Journal of Molecular Sciences , vol. 25 , no. 14 , 7947 . https://doi.org/10.3390/ijms25147947

مصطلحات موضوعية: CG parametrization, coarse-graining (CG), free energy calculations, light-harvesting cofactors, Martini 3, molecular dynamics simulations, photosystem II, protein dynamics

وصف الملف: application/pdf

الاتاحة: https://hdl.handle.net/11370/7b2f7c22-2402-4152-8795-52702f12d5da
https://research.rug.nl/en/publications/7b2f7c22-2402-4152-8795-52702f12d5da
https://doi.org/10.3390/ijms25147947
https://pure.rug.nl/ws/files/1081516119/ijms-25-07947.pdf
http://www.scopus.com/inward/record.url?scp=85199789081&partnerID=8YFLogxK

المؤلفون: Ozturk, Tugba Nur, König, Melanie, Carpenter, Timothy S., Pedersen, Kasper B., Wassenaar, Tsjerk A., Ingólfsson, Helgi I., Marrink, Siewert J.

المصدر: Ozturk , T N , König , M , Carpenter , T S , Pedersen , K B , Wassenaar , T A , Ingólfsson , H I & Marrink , S J 2024 , ' Building complex membranes with Martini 3 ' , Methods in Enzymology , vol. 701 , pp. 237-285 . https://doi.org/10.1016/bs.mie.2024.03.010

مصطلحات موضوعية: Asymmetrical membranes, Complex membranes, Curved membranes, Embedding proteins in membranes, Leaflet asymmetry, Martini 3, Membrane set up

وصف الملف: application/pdf

الاتاحة: https://hdl.handle.net/11370/c2d9cc01-c017-4dd8-b25c-eadcb1edadab
https://research.rug.nl/en/publications/c2d9cc01-c017-4dd8-b25c-eadcb1edadab
https://doi.org/10.1016/bs.mie.2024.03.010
https://pure.rug.nl/ws/files/1060273814/1-s2.0-S0076687924000946-main.pdf
http://www.scopus.com/inward/record.url?scp=85189959416&partnerID=8YFLogxK

المؤلفون: Barriga, Rodrigo

المساهمون: Melo, Manuel, RUN

مصطلحات موضوعية: Coarse-Grain, Martini 3

وصف الملف: application/pdf

الاتاحة: http://hdl.handle.net/10362/151163

المؤلفون: Pang, Jiu, Mehandzhiyski, Aleksandar Y., Zozoulenko, Igor

المصدر: Carbohydrate Polymers. 313

مصطلحات موضوعية: Cellulose regeneration, Coarse-grained molecular dynamics, simulations, Martini 3, Cellulose I ?, Cellulose II, Backmapping

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-193707
https://liu.diva-portal.org/smash/get/diva2:1757045/FULLTEXT01.pdf

المؤلفون: Ivan R. Sasselli, Ivan Coluzza

مصطلحات موضوعية: Biophysics, Biochemistry, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, systematically exploring parameters, stacking interactions due, overestimated hydrophilicity arising, identify issues stemming, focused improvements seem, even exhibit aggregation, constant ph behavior, charged backbone beads, aromatic side chains, short peptide self, reproducing peptide self, martini 3 performance, charged termini, aromatic groups, version 3, martini 3, version 2, test case, strategic modifications, parameter set, investigation demonstrates, intermolecular distances, insufficient planarity, initially developed, exceptional tool

Relation: https://figshare.com/articles/journal_contribution/Assessment_of_the_MARTINI_3_Performance_for_Short_Peptide_Self-Assembly/24870662

الاتاحة: https://doi.org/10.1021/acs.jctc.3c01015.s001
https://figshare.com/articles/journal_contribution/Assessment_of_the_MARTINI_3_Performance_for_Short_Peptide_Self-Assembly/24870662

المؤلفون: Borges-Araújo, Luís, Borges-Araújo, Ana, C, Ozturk, Tugba Nur, Ramirez-Echemendia, Daniel, P, Fábián, Balázs, Carpenter, Timothy, S, Thallmair, Sebastian, Barnoud, Jonathan, Ingólfsson, Helgi, I, Hummer, Gerhard, Tieleman, D. Peter, Marrink, Siewert, J, Souza, Paulo, C T, Melo, Manuel, N

المساهمون: Microbiologie moléculaire et biochimie structurale / Molecular Microbiology and Structural Biochemistry (MMSB), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)

المصدر: ISSN: 1549-9618.

مصطلحات موضوعية: Martini 3 Cholesterol Membrane simulations Molecular dynamics, Martini 3, Cholesterol, Membrane simulations, Molecular dynamics, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, [CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation

Relation: hal-04296756; https://hal.science/hal-04296756; https://hal.science/hal-04296756/document; https://hal.science/hal-04296756/file/martini-3-coarse-grained-force-field-for-cholesterol.pdf

الاتاحة: https://hal.science/hal-04296756
https://hal.science/hal-04296756/document
https://hal.science/hal-04296756/file/martini-3-coarse-grained-force-field-for-cholesterol.pdf
https://doi.org/10.1021/acs.jctc.3c00547

المؤلفون: Kai Steffen Stroh, Paulo C. T. Souza, Luca Monticelli, Herre Jelger Risselada

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Biotechnology, Evolutionary Biology, Cancer, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, variable optimization problem, gained tremendous popularity, g ., rdfs, concomitant hysteresis introduce, grained force fields, grained force field, variable optimization coarse, chemically relevant molecules, transition temperatures ), possible nonbonded interactions, metaheuristic search methods, martini model entail, martini 3 coarse, block cg ffs, variable pso methods, block cg approach, molecules within building, cg ffs

Relation: https://figshare.com/articles/journal_contribution/CGCompiler_Automated_Coarse-Grained_Molecule_Parametrization_via_Noise-Resistant_Mixed-Variable_Optimization/24574179

الاتاحة: https://doi.org/10.1021/acs.jctc.3c00637.s001
https://figshare.com/articles/journal_contribution/CGCompiler_Automated_Coarse-Grained_Molecule_Parametrization_via_Noise-Resistant_Mixed-Variable_Optimization/24574179

المؤلفون: Panagiotis I. Koukos, Sepehr Dehghani-Ghahnaviyeh, Camilo Velez-Vega, John Manchester, D. Peter Tieleman, José S. Duca, Paulo C. T. Souza, Zoe Cournia

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Biotechnology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, reproduces key dynamical, bilayer penetration depth, accessible surface area, grained force field, atom force field, tether lipid tails, martini 3 coarse, protein lipidation post, anchored proteins include, protein trafficking, grained models, anchored proteins, anchored peptides, vital co, various diseases, undergo farnesylation, translational modifications, thus crucial, targeting myristoylation, targeting farnesylation

Relation: https://figshare.com/articles/journal_contribution/Martini_3_Force_Field_Parameters_for_Protein_Lipidation_Post-Translational_Modifications/24665664

الاتاحة: https://doi.org/10.1021/acs.jctc.3c00604.s004
https://figshare.com/articles/journal_contribution/Martini_3_Force_Field_Parameters_for_Protein_Lipidation_Post-Translational_Modifications/24665664

المؤلفون: Launay, Romain, Teppa, Elin, Martins, Carla, Abby, Sophie, S, Pierrel, Fabien, André, Isabelle, Esque, Jérémy

المساهمون: Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Translational Innovation in Medicine and Complexity / Recherche Translationnelle et Innovation en Médecine et Complexité - UMR 5525 (TIMC), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP), Université Grenoble Alpes (UGA), ANR-19-CE45-0013,dEEPEN,Principes moléculaires et évolutifs gouvernant la régiosélectivité des enzymes(2019)

المصدر: ISSN: 1661-6596.

مصطلحات موضوعية: ubiquinone, MD simulations, Alphafold2, molecular modelling, Martini 3 force field, peripheral membrane protein, co-evolutionary information, protein-protein interaction, umbrella sampling, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, [CHIM]Chemical Sciences

Relation: info:eu-repo/semantics/altIdentifier/pmid/36142227; PUBMED: 36142227; WOS: 000858236200001

الاتاحة: https://hal.inrae.fr/hal-03800688
https://hal.inrae.fr/hal-03800688v1/document
https://hal.inrae.fr/hal-03800688v1/file/2022_Launay_I.J.of-Molecular-Sciences.pdf
https://doi.org/10.3390/ijms231810323

المؤلفون: Rodrigo A. Moreira, Stefan A. L. Weber, Adolfo B. Poma

المصدر: Molecules; Volume 27; Issue 3; Pages: 976

مصطلحات موضوعية: cellulose I allomorphs, cellulose II, Martini 3, large conformational changes, twist, molecular dynamics, coarse-grained model, aggregation

جغرافية الموضوع: agris

وصف الملف: application/pdf

Relation: Computational and Theoretical Chemistry; https://dx.doi.org/10.3390/molecules27030976

الاتاحة: https://doi.org/10.3390/molecules27030976

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: Vainikka, Petteri, Thallmair, Sebastian, Souza, Paulo Cesar Telles, Marrink, Siewert J.

المصدر: Vainikka , P , Thallmair , S , Souza , P C T & Marrink , S J 2021 , ' Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents : Thermodynamic, Structural, and Extraction Properties ' , ACS Sustainable Chemistry and Engineering , vol. 9 , no. 51 , pp. 17338-17350 . https://doi.org/10.1021/acssuschemeng.1c06521

مصطلحات موضوعية: Coarse-grained simulations, Deep eutectic solvents, Extraction properties, Martini 3, Molecular dynamics

وصف الملف: application/pdf

الاتاحة: https://hdl.handle.net/11370/a79c6ec6-b53c-48f3-8d21-11ec46cc477d
https://research.rug.nl/en/publications/a79c6ec6-b53c-48f3-8d21-11ec46cc477d
https://doi.org/10.1021/acssuschemeng.1c06521
https://pure.rug.nl/ws/files/198932156/acssuschemeng.1c06521.pdf
http://www.scopus.com/inward/record.url?scp=85121972418&partnerID=8YFLogxK

المؤلفون: Petteri Vainikka (11840553), Sebastian Thallmair (1339593), Paulo Cesar Telles Souza (11840556), Siewert J. Marrink (135518)

مصطلحات موضوعية: Biophysics, Genetics, Physiology, Biotechnology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, morphological shape changes, opening new possibilities, currently available models, martini 3 coarse, grained models, new dess, surfactant aggregates, recyclable alternative, rapid screening, physicochemical nature, ionic liquids, grained model, grained approach, environmentally friendly, built coarse, acceptable accuracy

Relation: https://figshare.com/articles/journal_contribution/Martini_3_Coarse-Grained_Model_for_Type_III_Deep_Eutectic_Solvents_Thermodynamic_Structural_and_Extraction_Properties/17207406

الاتاحة: https://doi.org/10.1021/acssuschemeng.1c06521.s001

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: Abdul, Wasim, Menon, Sneha, Mondal, Jagannath

المساهمون: Abdul, Wasim, Menon, Sneha, Mondal, Jagannath

المصدر: eLife, (2024-04-02)

مصطلحات موضوعية: molecular dynamics, parkinson's disease, liquid liquid phase separation, LLPS, Martini 3, coarse grained, Inrinsically disordered protein, IDP

Relation: https://zenodo.org/communities/mdsimidp; https://doi.org/10.5281/zenodo.10926367; https://doi.org/10.5281/zenodo.10926368; oai:zenodo.org:10926368

الاتاحة: https://doi.org/10.5281/zenodo.10926368

المؤلفون: Luis Borges-Araújo (10941165), Paulo Souza (8925965), Fábio Fernandes (10950154), Manuel N. Melo (6696638)

مصطلحات موضوعية: Computational Chemistry and Modeling, PIP2, Martini force field, Martini 3 forcefield, phosphoinositide, parameterization

Relation: https://figshare.com/articles/preprint/Improved_Parameterization_of_Phosphatidylinositide_Lipid_Headgroups_for_the_Martini_3_Coarse_Grain_Force_Field/14759991

الاتاحة: https://doi.org/10.26434/chemrxiv.14759991.v2

المؤلفون: Cea Klapp, Esteban, Arroyo Avirama, Andrés Felipe, Ormazábal Latorre, Sebastián Alejandro, Gajardo Parra, Nicolás F., Pazo Carballo, César Alexander, Quinteros Lama, Héctor, Marzialetti, Teresita, Held, Christoph, Canales Muñoz, Roberto, Garrido, José Matías

مصطلحات موضوعية: Furfuryl alcohol, Liquid-liquid extraction, Hydrophobic deep eutectic solvents, PC-SAFT, Martini 3

وصف الملف: 9 páginas; application/pdf

Relation: https://doi.org/10.1016/j.molliq.2023.122232; https://repositorio.uc.cl/handle/11534/73504

الاتاحة: https://repositorio.uc.cl/handle/11534/73504
https://doi.org/10.1016/j.molliq.2023.122232