المؤلفون: Carlos Ramírez-Palacios, Siewert J. Marrink

المصدر: QRB Discovery, Vol 4 (2023)

مصطلحات موضوعية: Deep learning, enantioselectivity predictions, molecular dynamics trajectories, ω-transaminases, Biotechnology, TP248.13-248.65, Biology (General), QH301-705.5

وصف الملف: electronic resource

Relation: https://www.cambridge.org/core/product/identifier/S2633289222000229/type/journal_article; https://doaj.org/toc/2633-2892

URL الوصول: https://doaj.org/article/2326c7c04986491f9a1a8b33d6807a09

المؤلفون: Jacob Stamm, Sung Kwon, Shawn Sandhu, Moaid Shaik, Rituparna Das, Jesse Sandhu, Bradley Curenton, Clayton Wicka, Benjamin G. Levine, Liangliang Sun, Marcos Dantus

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Pharmacology, Evolutionary Biology, Mental Health, Infectious Diseases, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, pump – probe, membered cyclic intermediate, important stepwise reaction, field tunnel ionization, ab initio <, mclafferty product ion, report femtosecond time, molecular dynamics trajectories, mclafferty rearrangement following, latter two compounds, fast time scale, time scale, mclafferty rearrangement, time constants, surprising dynamics, bond rearrangement, resolved measurements, mass spectrometry, facilitates transfer, experimental measurements

Relation: https://figshare.com/articles/journal_contribution/The_Surprising_Dynamics_of_the_McLafferty_Rearrangement/24492265

الاتاحة: https://doi.org/10.1021/acs.jpclett.3c02102.s002
https://figshare.com/articles/journal_contribution/The_Surprising_Dynamics_of_the_McLafferty_Rearrangement/24492265

المؤلفون: Rajitha Rajeshwar T (11320165), Moumita Saharay (360963), Jeremy C. Smith (192295), Marimuthu Krishnan (1422733)

مصطلحات موضوعية: Biophysics, Biochemistry, Cell Biology, Molecular Biology, Biotechnology, Hematology, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, linear correlation established, large flexibility changes, adaptive biasing force, protein makes possible, molecular dynamics trajectories, conformational entropy change, 2 , heterogeneous fast side, conformational entropy, protein side, fast side, molecular recognition, chain dynamics, side chains, transition decreases, thermodynamic correlates, potential indicator, increasing magnitude, functional importance, free (<, correlated response

Relation: https://figshare.com/articles/journal_contribution/Correlated_Response_of_Protein_Side-Chain_Fluctuations_and_Conformational_Entropy_to_Ligand_Binding/16413223

الاتاحة: https://doi.org/10.1021/acs.jpcb.1c01227.s001

المؤلفون: Rui Wang (52434), Brandon C. Bukowski (4039403), Jiaxin Duan (4867468), Jingyi Sui (6520184), Randall Q. Snurr (767831), Joseph T. Hupp (1270782)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Physiology, Biotechnology, Cancer, Plant Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, NU -600. Atomistic simulations, confocal fluorescence microscopy, dye molecules, Topology Guest transport, NU -600, guest transport behavior, MOF, transport efficiency advantage, dye transport processes, macroscopic crystallite morphologies, Molecular dynamics trajectories, solvated dye diffusion

Relation: https://figshare.com/articles/journal_contribution/Art_of_Architecture_Efficient_Transport_through_Solvent-Filled_Metal_Organic_Frameworks_Regulated_by_Topology/16415818

الاتاحة: https://doi.org/10.1021/acs.chemmater.1c01536.s001

المؤلفون: Zhi-Xin Qin (7900934), Matthew Tremblay (9303362), Xin Hong (95011), Zhongyue J. Yang (11437471)

مصطلحات موضوعية: Biophysics, Neuroscience, Infectious Diseases, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, using cyclopentadiene dimerization, potential energy drop, free energy minimum, flat energy region, enhanced conformational flexibility, cyclopentadiene dimerization involves, approach product formation, reacting species enter, reacting species along, entropic path sampling, molecular dynamics trajectories, involve entropic intermediates, entropy maximum along, computational protocol known, reaction path based, reacting species, entropy maximum, computational protocol, reaction path, entropic variation, intermediates form, dynamic intermediates

Relation: https://figshare.com/articles/journal_contribution/Entropic_Path_Sampling_Computational_Protocol_to_Evaluate_Entropic_Profile_along_a_Reaction_Path/16900014

الاتاحة: https://doi.org/10.1021/acs.jpclett.1c03116.s001

المؤلفون: Andrei Y. Kostritskii (10725347), Claudia Alleva (10725350), Saskia Cönen (10725353), Jan-Philipp Machtens (10725356)

مصطلحات موضوعية: Biophysics, Biochemistry, Molecular Biology, Sociology, Cancer, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, particle mesh Ewald method, biomolecular processes, secondary-active transporter Glt Ph, TMEM 16 lipid scramblases, biomolecule, electrostatic, P 2X receptor, Molecular Dynamics Trajectories, biomolecular MD simulations, DNA, Quantifying Biomolecular Electrostatics, MD trajectories

Relation: https://figshare.com/articles/journal_contribution/g_elpot_A_Tool_for_Quantifying_Biomolecular_Electrostatics_from_Molecular_Dynamics_Trajectories/14515112

الاتاحة: https://doi.org/10.1021/acs.jctc.0c01246.s001

المؤلفون: Gervasio, Francesco Luigi, Galdadas, Yiannis

المساهمون: 0446f23f-962b-4fca-ac18-4a1a4cde77ca Gervasio Group, Gervasio, Francesco Luigi

مصطلحات موضوعية: Molecular dynamics trajectories, EGFR

وصف الملف: text/plain; application/vnd.visio; application/octet-stream; text/xml

Relation: https://yareta.unige.ch/archives/2f052659-2a39-4d10-bb43-b6dea49ed2d9; ark:ark:/64642/rt9qtkuoibmhndc3jxcwtwzo7eeey

الاتاحة: https://doi.org/10.26037/yareta:qtkuoibmhndc3jxcwtwzo7eeey
https://yareta.unige.ch/archives/2f052659-2a39-4d10-bb43-b6dea49ed2d9

المؤلفون: Salma Jamal, Abhinav Grover, Sonam Grover

المصدر: Frontiers in Pharmacology, Vol 10 (2019)

مصطلحات موضوعية: Alzheimer’s, caspase-8, machine learning, molecular dynamics trajectories, descriptors, Therapeutics. Pharmacology, RM1-950

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fphar.2019.00780/full; https://doaj.org/toc/1663-9812

URL الوصول: https://doaj.org/article/cac1901c7002473f943bbe99d8cd3a36

المؤلفون: Gobbo, Dorothea, Gervasio, Francesco Luigi

المساهمون: 0446f23f-962b-4fca-ac18-4a1a4cde77ca Gervasio Group, Gervasio, Francesco Luigi

مصطلحات موضوعية: Molecular dynamics trajectories, p38α, ΜΚΚ6, Bayesian/Maximum Entropy, SAXS, MD simulations, Adaptive sampling

وصف الملف: text/plain; application/octet-stream; text/xml

Relation: https://yareta.unige.ch/archives/47a31841-f8e1-477e-ba3d-2f2356592681; ark:ark:/64642/rt95w7luymjcncd3ipjm3v76bqezm

الاتاحة: https://doi.org/10.26037/yareta:5w7luymjcncd3ipjm3v76bqezm
https://yareta.unige.ch/archives/47a31841-f8e1-477e-ba3d-2f2356592681

المؤلفون: Gervasio, Francesco Luigi, Galdadas, Yiannis, Gobbo, Dorothea

المساهمون: 0446f23f-962b-4fca-ac18-4a1a4cde77ca Gervasio Group, Gervasio, Francesco Luigi

مصطلحات موضوعية: Molecular dynamics trajectories, p38α, MKK6

وصف الملف: text/plain; application/octet-stream; text/xml

Relation: https://yareta.unige.ch/archives/3e516368-075f-48c2-b75a-c18ecc5ed7e0

الاتاحة: https://doi.org/10.26037/yareta:jmnbt6lzkrfrpdcf3m3343smxq
https://yareta.unige.ch/archives/3e516368-075f-48c2-b75a-c18ecc5ed7e0

المؤلفون: Buchner, Franziska, Nakayama, Akira, Yamazaki, Shohei, Ritze, Hans-Hermann, Lübcke, Andrea

مصطلحات موضوعية: Ground state, Ionization, Liquids, Molecular dynamics, Photoelectron spectroscopy, Photoelectrons, Photoionization, Photons, Relaxation processes, Solutions, Conical intersection, Excited state relaxation, Molecular dynamics simulations, Molecular dynamics trajectories, Relaxation mechanism, Temporal evolution, Theoretical calculations, Time-resolved photoelectron spectroscopy, Excited states, thymidine, thymine, hydrogen, water, ab initio calculation, aqueous solution, Article, controlled study, electron, excitation

Time: 540

وصف الملف: application/pdf

الاتاحة: https://oa.tib.eu/renate/handle/123456789/9457
https://doi.org/10.34657/8495

المؤلفون: Rui Wang, Brandon C. Bukowski, Jiaxin Duan, Jingyi Sui, Randall Q. Snurr, Joseph T. Hupp

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Physiology, Biotechnology, Cancer, Plant Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, NU -600. Atomistic simulations, confocal fluorescence microscopy, dye molecules, Topology Guest transport, NU -600, guest transport behavior, MOF, transport efficiency advantage, dye transport processes, macroscopic crystallite morphologies, Molecular dynamics trajectories, solvated dye diffusion, info, socio

Relation: https://doi.org/10.1021/acs.chemmater.1c01536.s002

الاتاحة: https://doi.org/10.1021/acs.chemmater.1c01536.s002

المؤلفون: Maxime Ducamp (5057957), François-Xavier Coudert (2492920)

مصطلحات موضوعية: Biophysics, Microbiology, Molecular Biology, Biotechnology, Ecology, Developmental Biology, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Melting, perovskite, MD, Molecular dynamics trajectories, dataset, ldquo

Relation: https://figshare.com/articles/dataset/Molecular_dynamics_trajectories_for_Melting_of_hybrid_organic_inorganic_perovskites_/14431167

الاتاحة: https://doi.org/10.5281/zenodo.4694088

المؤلفون: Salma Jamal, Abhinav Grover, Sonam Grover

مصطلحات موضوعية: Pharmacology, Basic Pharmacology, Clinical Pharmacology and Therapeutics, Clinical Pharmacy and Pharmacy Practice, Pharmaceutical Sciences, Pharmacogenomics, Toxicology (incl. Clinical Toxicology), Pharmacology and Pharmaceutical Sciences not elsewhere classified, Alzheimer’s, caspase-8, machine learning, molecular dynamics trajectories, descriptors

Relation: https://figshare.com/articles/dataset/DataSheet_1_Machine_Learning_From_Molecular_Dynamics_Trajectories_to_Predict_Caspase-8_Inhibitors_Against_Alzheimer_s_Disease_zip/8862617

الاتاحة: https://doi.org/10.3389/fphar.2019.00780.s001
https://figshare.com/articles/dataset/DataSheet_1_Machine_Learning_From_Molecular_Dynamics_Trajectories_to_Predict_Caspase-8_Inhibitors_Against_Alzheimer_s_Disease_zip/8862617

المؤلفون: Salma Jamal, Abhinav Grover, Sonam Grover

مصطلحات موضوعية: Pharmacology, Basic Pharmacology, Clinical Pharmacology and Therapeutics, Clinical Pharmacy and Pharmacy Practice, Pharmaceutical Sciences, Pharmacogenomics, Toxicology (incl. Clinical Toxicology), Pharmacology and Pharmaceutical Sciences not elsewhere classified, Alzheimer’s, caspase-8, machine learning, molecular dynamics trajectories, descriptors

Relation: https://figshare.com/articles/dataset/Table_1_Machine_Learning_From_Molecular_Dynamics_Trajectories_to_Predict_Caspase-8_Inhibitors_Against_Alzheimer_s_Disease_xlsx/8862620

الاتاحة: https://doi.org/10.3389/fphar.2019.00780.s002
https://figshare.com/articles/dataset/Table_1_Machine_Learning_From_Molecular_Dynamics_Trajectories_to_Predict_Caspase-8_Inhibitors_Against_Alzheimer_s_Disease_xlsx/8862620

المؤلفون: Mudedla, S. K., Singam, E. R. Azhagiya, Sundar, J. Vijay, Pedersen, Morten N., Murugan, N. Arul, Kongsted, Jacob, Ågren, Hans, Subramanian, V.

المصدر: The Journal of Physical Chemistry C. 119(1):653-664

مصطلحات موضوعية: Density functional theory, Enzymes, Gold, Gold compounds, Molecular dynamics, Motion analysis, Multilayers, Optical image storage, Optical properties, Principal component analysis, Classical molecular dynamics, Complex polarization propagator, Gold nanocluster, Molecular dynamics trajectories, Molecular Probes, Optical imaging, Specific optical properties, Time dependent density functional theory

وصف الملف: print

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-160751

المؤلفون: Ines Primožič, Maja Majerić Elenkov, Tomica Hrenar, Domagoj Fijan

المصدر: Physical chemistry chemical physics : PCCP. 19(47)

مصطلحات موضوعية: Conformational analysis, spiro-epoxides, principal component analysis, molecular dynamics trajectories, 010405 organic chemistry, Chemistry, Substituent, General Physics and Astronomy, 010402 general chemistry, Ring (chemistry), Energy minimization, 01 natural sciences, 0104 chemical sciences, chemistry.chemical_compound, Molecular dynamics, Computational chemistry, Position (vector), Physical and Theoretical Chemistry, Coordinate space, Conformational isomerism, Curse of dimensionality

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d88775f66d295534206988bfd568f304
https://pubmed.ncbi.nlm.nih.gov/29165452

المؤلفون: Maria Stepanova

المصدر: Molecular Simulation. 37:729-732

مصطلحات موضوعية: Differential equations, Protein G, Bioinformatics, Computer science, General Chemical Engineering, Drug design, Structural analysis, Molecular dynamics, Langevin dynamics, Domain (software engineering), Interpretation (model theory), Langevin equation, Projection Operator, Structural domains, Multi-scale approaches, General Materials Science, Statistical physics, Mathematical operators, Local flexibility, Multi-scale modelling, Nuclear magnetic resonance spectroscopy, Flexibility (engineering), Quantitative Biology::Biomolecules, Characterisation, Coarse Graining, Proteins, General Chemistry, Covariance analysis, Molecular dynamics trajectories, Condensed Matter Physics, interpretation of NMR measurements, Identification (information), Stable region, Prion protein, Structural biology, Drug Design, Modeling and Simulation, Prion Proteins, Experiments, Biological system, Information Systems

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c635f760fef1afcc7be6b5ecef5302f5
https://doi.org/10.1080/08927020903260843

المؤلفون: Heck, A., Woiczikowski, P. B., Kubař, T., Welke, K., Niehaus, T., Giese, B., Skourtis, Spiros S., Elstner, M., Steinbrecher, T. B.

المساهمون: Skourtis, Spiros S. 0000-0002-5834-248X

المصدر: Journal of Physical Chemistry B ; https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899488088&doi=10.1021%2fjp408907g&partnerID=40&md5=0cdb149665577e9d4730bce9c9593ccc ; J Phys Chem B

مصطلحات موضوعية: chemistry, Acetamides, Peptides, analogs and derivatives, Hamiltonians, Quantum chemistry, Molecular dynamics, electron, Electrons, Charge transfer, peptide, solvent, Solvents, Orders of magnitude, quantum theory, Molecular Dynamics Simulation, toluene, Ab initio and density functional calculations, acetamide, acetamide derivative, Charge transfer properties, dimethoxytoluene, Dimethylformamide, Electronic coupling, formamide, formamide derivative, Formamides, Importance sampling, Molecular dynamics trajectories, Molecular fragments

Relation: http://gnosis.library.ucy.ac.cy/handle/7/58719

الاتاحة: http://gnosis.library.ucy.ac.cy/handle/7/58719
https://doi.org/10.1021/jp408907g

المؤلفون: Potapov, A., Stepanova, M.

مصطلحات موضوعية: biomolecular dynamics, coarse-grained structure, conformational change, conformational dynamics, dimensionality reduction, dynamical properties, human prion protein, invariant properties, molecular dynamics simulations, molecular dynamics trajectories, multi-scale approaches, perturbation theory, physical mechanism, soft matter, subnanosecond, theoretical framework, time-dependent, biomolecules, molecular dynamics, statistical mechanics, dynamics

وصف الملف: text

Relation: Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics, Volume: 85, Issue: 2, Publication date: 2012

الاتاحة: https://doi.org/10.1103/PhysRevE.85.020901
https://nrc-publications.canada.ca/eng/view/object/?id=d23b9364-1662-45b9-8b52-89ed3009a399
https://nrc-publications.canada.ca/fra/voir/objet/?id=d23b9364-1662-45b9-8b52-89ed3009a399