المؤلفون: San Fabián Maroto, Jesús, García de la Vega, José Manuel, Omar, Salama

المساهمون: UAM. Departamento de Química Física Aplicada

مصطلحات موضوعية: computational protocol, side-chain vicinal spin–spin coupling constants, Karplus equation, amino acids, Alanine Dipeptide Model, the side-chain conformation, spin–spin coupling constants, Fourier coefficients, function and density functional methods, Química

وصف الملف: application/pdf

Relation: Journal of Chemical Theory and Computation; https://doi.org/10.1021/acs.jctc.9b00131; Comunidad de Madrid. S2013/MAE-2800; Journal of Chemical Theory and Computation 15.7 (2019): 4252-4263; http://hdl.handle.net/10486/714224; 4252; 4263

الاتاحة: http://hdl.handle.net/10486/714224
https://doi.org/10.1021/acs.jctc.9b00131

المؤلفون: Yao, Songyuan, Van, Richard, Pan, Xiaoliang, Park, Ji Hwan, Mao, Yuezhi, Pu, Jingzhi, Mei, Ye, Shao, Yihan

المساهمون: Chemistry and Chemical Biology, School of Science

المصدر: PMC

مصطلحات موضوعية: Machine learning (ML), Molecular dynamics, Alanine dipeptide

وصف الملف: application/pdf

Relation: RSC Advances; Yao S, Van R, Pan X, et al. Machine learning based implicit solvent model for aqueous-solution alanine dipeptide molecular dynamics simulations. RSC Adv. 2023;13(7):4565-4577. Published 2023 Feb 3. doi:10.1039/d2ra08180f; https://hdl.handle.net/1805/36617

الاتاحة: https://hdl.handle.net/1805/36617

المؤلفون: Ru-Huei Fu, Hui-Jye Chen, Syuan-Yu Hong

المصدر: Antioxidants, Vol 12, Iss 1896, p 1896 (2023)

مصطلحات موضوعية: amyotrophic lateral sclerosis (ALS), C9ORF72, glycine-alanine dipeptide repeat proteins (GA-DPRs), NLRP3 inflammasome, sulfide quinone oxidoreductase (SQOR), ROS, Therapeutics. Pharmacology, RM1-950

Relation: https://www.mdpi.com/2076-3921/12/10/1896; https://doaj.org/toc/2076-3921; https://doaj.org/article/ec474a281755450a84be402278f36109

الاتاحة: https://doi.org/10.3390/antiox12101896
https://doaj.org/article/ec474a281755450a84be402278f36109

المؤلفون: JaeHwan Shim, Juyong Lee, Jaejun Yu

المصدر: Journal of Physics Communications, Vol 7, Iss 2, p 025004 (2023)

مصطلحات موضوعية: Onsager-Machlup action, Gaussian process, chemical reaction pathway, action-CSA, surrogative machine learning, alanine dipeptide, Science, Physics, QC1-999

Relation: https://doi.org/10.1088/2399-6528/acba83; https://doaj.org/toc/2399-6528; https://doaj.org/article/c32504f57d61456c9b437ab3c1bf71b3

الاتاحة: https://doi.org/10.1088/2399-6528/acba83
https://doaj.org/article/c32504f57d61456c9b437ab3c1bf71b3

المؤلفون: Zineb Belkacemi (11886233), Paraskevi Gkeka (650340), Tony Lelièvre (1351011), Gabriel Stoltz (3602246)

مصطلحات موضوعية: Biochemistry, Sociology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, solvated chignolin mini, important conformational changes, free energy biasing, dimensionality reduction algorithms, dimensional slow degrees, learning model optimizes, generate new data, alanine dipeptide system, achieves cv convergence, new cv, protein system, iterative learning, sampling measure, reweighting scheme, prior knowledge, present results, powerful tools, methods rely, method includes, febilae )

Relation: https://figshare.com/articles/journal_contribution/Chasing_Collective_Variables_Using_Autoencoders_and_Biased_Trajectories/17703260

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00415.s001

المؤلفون: Ferry Hooft (10233020), Alberto Pérez de Alba Ortíz (8740281), Bernd Ensing (1354056)

مصطلحات موضوعية: Medicine, Genetics, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, Neural Networks, case studies, Collective Variables, Genetic Algorithms, atom coordinates, simulation data sets, CV selection, network performance, transition, alternative Hoogsteen pairing, autoencoder network, input CVs, network input, simulation data, CV values, network architecture, time-correlation functions, B-DNA, Molecular Transitions, Key advantages, hyperparameter optimization, base pair, alanine dipeptide molecule

Relation: https://figshare.com/articles/journal_contribution/Discovering_Collective_Variables_of_Molecular_Transitions_via_Genetic_Algorithms_and_Neural_Networks/14167088

الاتاحة: https://doi.org/10.1021/acs.jctc.0c00981.s001

المؤلفون: Ankita Katiyar (10305117), Ward H. Thompson (1388418)

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Ecology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, calculation, Peptide Conformational Equilibria, Single Temperature, energy surface, dihedral angles, function, alanine dipeptide, Temperature Dependence, single-temperature simulations, fluctuation theory, sampling methods, canonical test system

Relation: https://figshare.com/articles/journal_contribution/Temperature_Dependence_of_Peptide_Conformational_Equilibria_from_Simulations_at_a_Single_Temperature/14217264

الاتاحة: https://doi.org/10.1021/acs.jpca.1c00150.s001

المؤلفون: Bittracher, Andreas, Klus, Stefan, Hamzi, Boumediene, Koltai, Péter, Schütte, Christof

مصطلحات موضوعية: alanine dipeptide, diffusion maps, dynamics, kinetics, models, rates, ddc:510

وصف الملف: 41 Seiten; application/pdf

Relation: https://refubium.fu-berlin.de/handle/fub188/29403; http://dx.doi.org/10.17169/refubium-29149

الاتاحة: https://refubium.fu-berlin.de/handle/fub188/29403
https://doi.org/10.17169/refubium-29149
https://doi.org/10.1007/s00332-020-09668-z

المؤلفون: Stimper, Vincent

مصطلحات موضوعية: Alanine Dipeptide, Boltzmann Generators, Equivariance, Generative Modelling, Hamiltonian Monte Carlo, Machine Learning, Normalising Flows, normflows, Sampling

وصف الملف: application/pdf

Relation: https://www.repository.cam.ac.uk/handle/1810/370465; https://doi.org/10.17863/CAM.109883

الاتاحة: https://www.repository.cam.ac.uk/handle/1810/370465
https://doi.org/10.17863/CAM.109883

المؤلفون: Rubio Martínez, Jaime, Tomás Belenguer, María Santos, Pérez González, Juan Jesús

المساهمون: Universitat Politècnica de Catalunya. Departament de Tecnologia de l'Arquitectura, Universitat Politècnica de Catalunya. Departament d'Enginyeria Química, Universitat Politècnica de Catalunya. GBMI - Grup de Biotecnologia Molecular i Industrial

مصطلحات موضوعية: Àrees temàtiques de la UPC::Enginyeria química::Química física, Peptides, Alanine dipeptide, Amino acid conformations, Chloroform, Dimethyl sulfoxide, Intermolecular interactions, Intramolecular interactions, MD simulations, Methanol, N-methylacetamide, Solvent effects, Pèptids

وصف الملف: 11 p.

Relation: http://www.sciencedirect.com/science/article/pii/S1093326317306101?via%3Dihub; Rubio, J., Tomas, M., Perez, J. Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations. "Journal of Molecular Graphics and Modelling", 1 Novembre 2017, vol. 78, núm. November, p. 1-11.; 1873-4243 10933263; http://hdl.handle.net/2117/110882

الاتاحة: http://hdl.handle.net/2117/110882
https://doi.org/10.1016/j.jmgm.2017.10.005

المؤلفون: Burkoff, NS, Baldock, RJN, Várnai, C, Wild, DL, Csányi, G

مصطلحات موضوعية: Nested Sampling, Alanine dipeptide, Molecular dynamics, Potential energy surface, Heat capacity

وصف الملف: application/pdf

Relation: https://www.repository.cam.ac.uk/handle/1810/255810

الاتاحة: https://www.repository.cam.ac.uk/handle/1810/255810

المؤلفون: Jerry Y. Y. Heng, Ling Zhou, Qiuxiang Yin, Chin W. Yong, Lina Zhou, Ethan Errington, Mingxia Guo, Ilian T. Todorov, Ian Rosbottom

المساهمون: Engineering & Physical Science Research Council (EPSRC)

مصطلحات موضوعية: Technology, PROTEINS, Materials Science, PROPENSITIES, Molecular Conformation, Peptide, Materials Science, Multidisciplinary, Physics, Atomic, Molecular & Chemical, law.invention, AMINO-ACID-RESIDUES, Molecular dynamics, RAMAN, X-RAY-DIFFRACTION, law, TRIALANINE, General Materials Science, Physical and Theoretical Chemistry, Crystallization, Nanoscience & Nanotechnology, Protein secondary structure, Polyproline helix, chemistry.chemical_classification, SOLVENT, Aqueous solution, Science & Technology, 02 Physical Sciences, Chemistry, Physical, Physics, Water, NMR, HELIX, Crystallography, Chemistry, ALANINE DIPEPTIDE, chemistry, Homopeptide, Physical Sciences, Science & Technology - Other Topics, Peptides, 03 Chemical Sciences, Single crystal, Oligopeptides

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2a8190c93e52e839aa838e8afa8a701e
http://hdl.handle.net/10044/1/91822

المؤلفون: Guo, M, Rosbottom, I, Zhou, L, Yong, CW, Yin, Q, Todorov, IT, Errington, E, Heng, JYY

المساهمون: Engineering & Physical Science Research Council (EPSRC)

المصدر: 8422 ; 8416

مصطلحات موضوعية: Science & Technology, Physical Sciences, Technology, Chemistry, Physical, Nanoscience & Nanotechnology, Materials Science, Multidisciplinary, Physics, Atomic, Molecular & Chemical, Science & Technology - Other Topics, AMINO-ACID-RESIDUES, X-RAY-DIFFRACTION, ALANINE DIPEPTIDE, RAMAN, TRIALANINE, SOLVENT, HELIX, PROTEINS, NMR, PROPENSITIES, Crystallization, Molecular Conformation, Oligopeptides, Peptides, Water

Relation: Journal of Physical Chemistry Letters; http://hdl.handle.net/10044/1/91822; EP/N015916/1

الاتاحة: http://hdl.handle.net/10044/1/91822
https://doi.org/10.1021/acs.jpclett.1c01622

المؤلفون: Fadda, Elisa, Woods, Robert J.

مصطلحات موضوعية: alanine dipeptide, short polyalanine peptides, ab initio and dft calculations, empirical dispersion-corrected dft, peptides structure and stability, ramachandran plot, density-functional theory, molecular-dynamics simulations, ion mobility spectrometry, der-waals interactions, quantum-mechanics, force-fields, ab-initio, noncovalent interactions, mass-spectrometry, aqueous-solution

Relation: Canadian Journal of Chemistry; Fadda, Elisa; Woods, Robert J. (2013). Contribution of the empirical dispersion correction on the conformation of short alanine peptides obtained by gas-phase qm calculations. Canadian Journal of Chemistry 91 (9), 859-865; 0008-4042,1480-3291; http://hdl.handle.net/10379/11391

الاتاحة: http://hdl.handle.net/10379/11391
https://doi.org/10.1139/cjc-2012-0542

المؤلفون: Andreas Bittracher, Péter Koltai, Stefan Klus, Christof Schütte, Boumediene Hamzi

المساهمون: Universitätsbibliothek Der FU Berlin

المصدر: Journal of Nonlinear Science

مصطلحات موضوعية: FOS: Computer and information sciences, Function space, Computer science, Computation, 500 Naturwissenschaften und Mathematik::510 Mathematik::510 Mathematik, rates, Machine Learning (stat.ML), Dynamical Systems (math.DS), Topology, 01 natural sciences, 010305 fluids & plasmas, models, Statistics - Machine Learning, 0103 physical sciences, FOS: Mathematics, diffusion maps, Mathematics - Dynamical Systems, 010304 chemical physics, Applied Mathematics, Dimensionality reduction, alanine dipeptide, General Engineering, dynamics, Manifold, Distortion (mathematics), kinetics, Modeling and Simulation, Kernel (statistics), Embedding, Reproducing kernel Hilbert space

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e3254730a1ea75083b59e699000eb2ad
https://doi.org/10.1007/s00332-020-09668-z

المؤلفون: Leila Pujal, Maximilian van Zyl, Esteban Vöhringer-Martinez, Toon Verstraelen, Patrick Bultinck, Paul W. Ayers, Farnaz Heidar-Zadeh

المصدر: JOURNAL OF CHEMICAL PHYSICS

مصطلحات موضوعية: FRONTIER-ELECTRON THEORY, General Physics and Astronomy, DENSITY-FUNCTIONAL THEORY, AXIOMATIC APPROACH, ENERGY, Chemistry, ALANINE DIPEPTIDE, MOLECULES, NUMBER, Physics and Astronomy, SHAPE FUNCTION, INFORMATION-THEORY, Physical and Theoretical Chemistry, PARTICLE

وصف الملف: application/pdf

URL الوصول: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c6ae4a90c37629f781541b81d12c9fb4
https://doi.org/10.1063/5.0089466

المؤلفون: Echenique, Pablo, Alonso, José Luis

مصطلحات موضوعية: molecular coordinates, systematic, modular, separable, SASMIC, peptides, Constraints, Alanine dipeptide

Relation: http://hdl.handle.net/10261/36967

الاتاحة: http://hdl.handle.net/10261/36967
https://doi.org/10.1002/jcc.20424

المؤلفون: Rossmeisl, Jan, Hinnemann, Berit, Jacobsen, Karsten Wedel, Nørskov, Jens Kehlet, Olsen, Ole H., Pedersen, Jan T.

المصدر: Rossmeisl , J , Hinnemann , B , Jacobsen , K W , Nørskov , J K , Olsen , O H & Pedersen , J T 2003 , ' A simple and realistic model system for studying hydrogen bonds in beta-sheets ' , Journal of Chemical Physics , vol. 118 , no. 21 , pp. 9783-9794 . https://doi.org/10.1063/1.1570395

مصطلحات موضوعية: ALANINE DIPEPTIDE, DENSITY-FUNCTIONAL THEORY, CONFORMATIONAL BEHAVIOR, N-METHYLACETAMIDE, PROTEINS, POLYGLYCINE, CENTER-DOT-O=C, ENERGETICS, AB-INITIO, PERIODIC BOUNDARY-CONDITIONS

وصف الملف: application/pdf

Relation: https://orbit.dtu.dk/en/publications/16f1a488-57ab-4a79-89ea-4c1380ec4e69

الاتاحة: https://orbit.dtu.dk/en/publications/16f1a488-57ab-4a79-89ea-4c1380ec4e69
https://doi.org/10.1063/1.1570395
https://backend.orbit.dtu.dk/ws/files/4286252/Jan.pdf
http://link.aip.org/link/JCPSA6/v118/i21/p9783/s1

المؤلفون: Yang Su, Emilio Gallicchio

المساهمون: The Pennsylvania State University CiteSeerX Archives

المصدر: http://biomaps.rutgers.edu/Su_Gallicchio.pdf.

مصطلحات موضوعية: Potential of mean force, Implicit solvent model, Alanine dipeptide, Non-polar solvation, hydrophobicity, Free energy perturbation, Dimerization

وصف الملف: application/pdf

Relation: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.622.1617; http://biomaps.rutgers.edu/Su_Gallicchio.pdf

الاتاحة: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.622.1617
http://biomaps.rutgers.edu/Su_Gallicchio.pdf

المؤلفون: Echenique, Pablo, Chass, Gregory

مصطلحات موضوعية: Alanine dipeptide, model chemistries, B3LYP, Basis sets

Relation: Preprint; http://www.eilab.org/pn/v1i1/20090003.htm; http://hdl.handle.net/10261/35169

الاتاحة: http://hdl.handle.net/10261/35169