المؤلفون: Albin Joy, Rajib Biswas

مصطلحات موضوعية: Biophysics, Biochemistry, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, perform essential functions, incorporate metal ions, free energy surfaces, 35 k decrease, copper metal ion, 420 k ), high thermal stability, exceptional thermal stability, unfolding process revealed, form also started, native holo <, unfolding process, native <, remd ), copper cofactor, open <, thermodynamic analysis, sheet strands, opposite end, nonbonded forms, nonbonded form, nonbonded (<, microscopic origin

Relation: https://figshare.com/articles/journal_contribution/Significance_of_the_Disulfide_Bridge_in_the_Structure_and_Stability_of_Metalloprotein_Azurin/25020753

الاتاحة: https://doi.org/10.1021/acs.jpcb.3c07089.s001
https://figshare.com/articles/journal_contribution/Significance_of_the_Disulfide_Bridge_in_the_Structure_and_Stability_of_Metalloprotein_Azurin/25020753

المؤلفون: Fusheng Zhang, Baihao Huang, Xiaolan Huang, Huowen Chen, Lijuan Zhang

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Genetics, Pharmacology, Biotechnology, Cancer, Mental Health, Computational Biology, Space Science, Information Systems not elsewhere classified, tumor therapeutic platforms, stable polymeric micelles, potential therapeutic benefit, immobilizing micellar nanoreactors, immobilizing micellar nanoreactor, hydrogen bonding ), cooperating nonbonded interactions, contradictory requirements remains, stable drug delivery, controllable rapid release, term stability, simultaneously required, reversible cross, new prospect, linking strategy, formidable challenge, drug release, driven self, achieve long

Relation: https://figshare.com/articles/journal_contribution/Drug-Immobilizing_Micellar_Nanoreactor_An_Intriguing_Drug_Stable_Delivery_Strategy/25199784

الاتاحة: https://doi.org/10.1021/acsmaterialslett.4c00083.s001
https://figshare.com/articles/journal_contribution/Drug-Immobilizing_Micellar_Nanoreactor_An_Intriguing_Drug_Stable_Delivery_Strategy/25199784

المؤلفون: Sergei Izvekov, Matthew P. Kroonblawd, James P. Larentzos, John K. Brennan, Betsy M. Rice

مصطلحات موضوعية: Biophysics, Cell Biology, Cancer, Computational Biology, Physical Sciences not elsewhere classified, extended ensemble described, constant strain ensemble, applied external fields, graining via force, graining anisotropic media, proposed pme formulation, maximum entropy theory, maximum entropy, theory views, theory based, system coordinates, submolecular resolution, stress tensor, starting point, special case, nonequilibrium conditions, nonbonded interactions, molecular crystal, crystalline 1, better suited

Relation: https://figshare.com/articles/journal_contribution/Maximum_Entropy_Theory_of_Multiscale_Coarse-Graining_via_Matching_Thermodynamic_Forces_Application_to_a_Molecular_Crystal_TATB_/25421273

الاتاحة: https://doi.org/10.1021/acs.jpcb.3c07078.s001

المؤلفون: Yan Zhu, Saad Alqahtani, Xiche Hu

المصدر: Molecules, Vol 29, Iss 2, p 304 (2024)

مصطلحات موضوعية: dispersion-corrected DFTs, benchmarking, protein kinase inhibitors, motifs of nonbonded interactions, CCSD(T)/CBS reference, molecular recognition, Organic chemistry, QD241-441

Relation: https://www.mdpi.com/1420-3049/29/2/304; https://doaj.org/toc/1420-3049; https://doaj.org/article/2d1a86044d754b828874f7d6cd96cdd1

الاتاحة: https://doi.org/10.3390/molecules29020304
https://doaj.org/article/2d1a86044d754b828874f7d6cd96cdd1

المؤلفون: Hermansen, Christian¹, Mauro, John C.², Yuanzheng Yue^1,3 yy@bio.aau.dk

المصدر: Journal of Chemical Physics. 4/20/2014, Vol. 140 Issue 15, p154501-1-154501-8. 8p. 2 Diagrams, 4 Graphs.

مصطلحات موضوعية: *PHOSPHATE glass, *NONBONDED molecular interactions, *MOLECULAR dynamics, *NUCLEAR magnetic resonance, *CATIONS

المؤلفون: Bernardi, Austen, Faller, Roland, Reith, Dirk, Kirschner, Karl N

مصطلحات موضوعية: Chemical Sciences, Physical Chemistry, ACPYPE, Glycam06, Force field, Nonbonded scaling factor, Carbohydrate, Gromacs, Computer Software

URL الوصول: https://escholarship.org/uc/item/9r9714c7

المؤلفون: Chaofu Wu

مصطلحات موضوعية: Biophysics, Medicine, Evolutionary Biology, Ecology, Immunology, Inorganic Chemistry, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, reproduce thermal expansion, proposed multiscale scheme, volumetric expansive coefficients, simulated bulk moduli, derived cg potentials, also satisfactorily restored, nonbonded cg potentials, nonbonded potentials, volumetric properties, transferable coarse, strain energies, referenced data, one bead, new coarse, molecular dynamics, melt densities, mechanical properties, little modifications, lactic acid, independent factors

Relation: https://figshare.com/articles/journal_contribution/Temperature-Transferable_Coarse-Grained_Models_for_Volumetric_Properties_of_Poly_lactic_Acid_/24913806

الاتاحة: https://doi.org/10.1021/acs.jpcb.3c07026.s001
https://figshare.com/articles/journal_contribution/Temperature-Transferable_Coarse-Grained_Models_for_Volumetric_Properties_of_Poly_lactic_Acid_/24913806

المؤلفون: Mst. Farhana Afrin, Emranul Kabir, M.R.O. Khan Noyon, Md Mosharef H. Bhuiyan, Mst Sharmin Sultana Shimu, Md Jahangir Alam, Monir Uzzaman, Md Walid Hossain Talukder

المصدر: Informatics in Medicine Unlocked, Vol 43, Iss , Pp 101399- (2023)

مصطلحات موضوعية: Ketoprofen, Cyclooxygenase, Molecular docking and dynamics simulation, Nonbonded interactions, ADMET and PASS prediction, Computer applications to medicine. Medical informatics, R858-859.7

وصف الملف: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352914823002459; https://doaj.org/toc/2352-9148

URL الوصول: https://doaj.org/article/35af58a1d968448fa7c07194d74d4e21

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: Utkarsh Kapoor, Young C. Kim, Jeetain Mittal

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Genetics, Molecular Biology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, predict various aspects, phase transition properties, including melting thermodynamics, findings shed light, experimental binding affinity, define nonbonded interactions, complex multiscale systems, molecular information may, complex molecular framework, microsecond time scale, atom hydropathy scale, generating conformational ensembles, provide molecular insights, without histone tails, dna model compatible, cg protein models, histone tails, enabled molecular, scale studies, level insights, conformational ensemble

Relation: https://figshare.com/articles/journal_contribution/Coarse-Grained_Models_to_Study_Protein_DNA_Interactions_and_Liquid_Liquid_Phase_Separation/24601802

الاتاحة: https://doi.org/10.1021/acs.jctc.3c00525.s001
https://figshare.com/articles/journal_contribution/Coarse-Grained_Models_to_Study_Protein_DNA_Interactions_and_Liquid_Liquid_Phase_Separation/24601802

المؤلفون: Hyuntae Kim, Balázs Fábián, Gerhard Hummer

مصطلحات موضوعية: Biophysics, Medicine, Cell Biology, Neuroscience, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, time steps nstlist, neighbor list updates, neighbor list artifacts, isotropically coupled barostat, found large membranes, dual pair list, apparent pressure tensor, anisotropic pressure coupling, aid nonexpert users, key input parameters, missed nonbonded interactions, l , md simulations using, missed interactions, r <, default parameters, >< sub, widely used, systematic imbalances, similar effects, primary cause

Relation: https://figshare.com/articles/journal_contribution/Neighbor_List_Artifacts_in_Molecular_Dynamics_Simulations/24707318

الاتاحة: https://doi.org/10.1021/acs.jctc.3c00777.s001
https://figshare.com/articles/journal_contribution/Neighbor_List_Artifacts_in_Molecular_Dynamics_Simulations/24707318

المؤلفون: Julian M. Delgado, Péter R. Nagy, Sameer Varma

مصطلحات موضوعية: Biophysics, Biochemistry, Ecology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, recommend critical changes, proteins remain large, nonpolarizable force fields, high field response, experimental structural data, polarizable amoeba model, amoeba protein model, provides new insights, revised polarization parameters, provide detailed insights, modeling divalent cations, mean absolute error, dramatically improves mg, fix )” corrections, enzymes also require, 2 +, new model, divalent cations, fix corrections, explicit polarization, dihedral parameters, also present, “ nonbonded, utilize nucleotides, systematic assessment

Relation: https://figshare.com/articles/journal_contribution/Polarizable_AMOEBA_Model_for_Simulating_Mg_sup_2_sup_Protein_Nucleotide_Complexes/24747592

الاتاحة: https://doi.org/10.1021/acs.jcim.3c01513.s001
https://figshare.com/articles/journal_contribution/Polarizable_AMOEBA_Model_for_Simulating_Mg_sup_2_sup_Protein_Nucleotide_Complexes/24747592

المؤلفون: Weiwen Zhuang, Yujian Liu, Ziqi Deng, Yu Guo, Philip C. Y. Chow, David Lee Phillips, Wei Jiang, Zhaohui Wang, Junzhi Liu

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Pharmacology, Biotechnology, Computational Biology, Chemical Sciences not elsewhere classified, topologically defined length, strong circular dichroism, stranded carbon helix, specific heteroatomic perturbation, rationally designed precursors, highly regioselective one, bn -[ 6, nitrogen atoms resulted, improved optical properties, helically chiral small, h , chiroptical properties, boron atoms, chiral sensors, chiral materials, theoretical studies, promising candidate, programmable routes, pot borylation, nonbonded boron, membered rings, inner rims, fused six

Relation: https://figshare.com/articles/journal_contribution/Synthesis_Structures_and_Chiroptical_Properties_of_NBN-Doped_Helicenes_with_Boron_Atoms_in_the_Inner_Rims/24849395

الاتاحة: https://doi.org/10.1021/prechem.3c00097.s001
https://figshare.com/articles/journal_contribution/Synthesis_Structures_and_Chiroptical_Properties_of_NBN-Doped_Helicenes_with_Boron_Atoms_in_the_Inner_Rims/24849395

المؤلفون: Qiao Xue, Zhiyue Jiao, Xian Liu, Wenxiao Pan, Jianjie Fu, Aiqian Zhang

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Ecology, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, soil organic matter, leonardite humic acid, declining structural amphiphilicity, analysis revealed component, amphiphilic lipids formed, including diverse components, constitute som ’, lha ), lipids, carbohydrates facilitated diffusion, water systems, som system, som components, nonbonded interactions, mesoscopic scale, layered phase, interaction mechanism, hydrophobic core, embedded within, effective approach, dynamic behavior, despite forming

Relation: https://figshare.com/articles/journal_contribution/Dynamic_Behavior_and_Interaction_Mechanism_of_Soil_Organic_Matter_in_Water_Systems_A_Coarse-Grained_Molecular_Dynamics_Study/24881639

الاتاحة: https://doi.org/10.1021/acs.est.3c05966.s001
https://figshare.com/articles/journal_contribution/Dynamic_Behavior_and_Interaction_Mechanism_of_Soil_Organic_Matter_in_Water_Systems_A_Coarse-Grained_Molecular_Dynamics_Study/24881639

المؤلفون: Hsu-Chun Tsai (9088101), Tai-Sung Lee (345944), Abir Ganguly (1281624), Timothy J. Giese (1314369), Maximilian CCJC Ebert (14351961), Paul Labute (1270920), Kenneth M. Merz (1311057), Darrin M. York (58145)

مصطلحات موضوعية: Biochemistry, Medicine, Genetics, Neuroscience, Pharmacology, Computational Biology, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, unitless control parameters, transformation end points, stabilize behavior near, pairwise form based, nonbonded cutoff boundary, free energy estimates, effective interaction distance, new functional form, consistent power scaling, lj contact radius, shifted scaling, new framework, traditional methods, smoothstep functions, scheduling features, rigorous smoothing, resulting pathways, numerical stability, minimal variance, maintain balance, important features

Relation: https://figshare.com/articles/journal_contribution/AMBER_Free_Energy_Tools_A_New_Framework_for_the_Design_of_Optimized_Alchemical_Transformation_Pathways/21842652

الاتاحة: https://doi.org/10.1021/acs.jctc.2c00725.s001

المؤلفون: Waro Nakanishi, Satoko Hayashi, Ryosuke Imanaka, Taro Nishide, Eiichiro Tanaka, Hikaru Matsuoka

المصدر: International Journal of Molecular Sciences; Volume 24; Issue 3; Pages: 2798

مصطلحات موضوعية: ab initio calculations, quantum theory of atoms-in-molecules (QTAIM), nonbonded interactions, inverse behavior of interactions, normal behavior of interactions

جغرافية الموضوع: agris

وصف الملف: application/pdf

Relation: Physical Chemistry and Chemical Physics; https://dx.doi.org/10.3390/ijms24032798

الاتاحة: https://doi.org/10.3390/ijms24032798

المؤلفون: Dr. Satoko Hayashi, Taro Nishide, Kengo Nagata, Prof. Waro Nakanishi

المصدر: ChemistryOpen, Vol 10, Iss 7, Pp 656-665 (2021)

مصطلحات موضوعية: ab initio calculations, natural bond orbital analysis, nonbonded interactions, QTAIM, selenides, Chemistry, QD1-999

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2191-1363

URL الوصول: https://doaj.org/article/5944007fba5446c28e53fb5952a25a7a

المؤلفون: Luo, Jinping¹, Liu, Lijun¹

المصدر: Molecular Simulation. Mar2017, Vol. 43 Issue 4, p284-290. 7p.

مصطلحات موضوعية: *PRINCIPLE of locality (Physics), *NONBONDED molecular interactions, *MOLECULAR dynamics, *ENERGY measurement, *COMPUTER architecture, *DATA structures

المؤلفون: Shuzhe Wang (4454710), Kajo Krummenacher (11949747), Gregory A. Landrum (1450801), Benjamin D. Sellers (2553409), Paola Di Lello (11949750), Sarah J. Robinson (2131063), Bryan Martin (11949753), Jeffrey K. Holden (11949756), Jeffrey Y. K. Tom (2950314), Anastasia C. Murthy (11949759), Nataliya Popovych (2100757), Sereina Riniker (1450804)

مصطلحات موضوعية: Biophysics, Biochemistry, Biotechnology, Infectious Diseases, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, various subselection techniques, unnatural amino acids, structural refinement techniques, intramolecular nonbonded interactions, resulting conformer bundles, based conformer generators, packages currently available, large macrocycles well, derived interproton distances, distance bounds matrix, derived distances, distance geometry, conformer generation, conformer bundle, small molecules, prior force, loose upper, fully open, field parametrization, especially useful, best reproduces, benchmarked using

Relation: https://figshare.com/articles/journal_contribution/Incorporating_NOE-Derived_Distances_in_Conformer_Generation_of_Cyclic_Peptides_with_Distance_Geometry/18428586

الاتاحة: https://doi.org/10.1021/acs.jcim.1c01165.s001

المؤلفون: Taro Nishide, Satoko Hayashi

المصدر: Nanomaterials, Vol 12, Iss 321, p 321 (2022)

مصطلحات موضوعية: ab initio calculations, quantum theory of atoms-in-molecules (QTAIM), nonbonded interactions, polycyclic aromatic hydrocarbon (PAH), Chemistry, QD1-999

Relation: https://www.mdpi.com/2079-4991/12/3/321; https://doaj.org/toc/2079-4991; https://doaj.org/article/53fefc5e6d474f6b87bf81245cf308b3

الاتاحة: https://doi.org/10.3390/nano12030321
https://doaj.org/article/53fefc5e6d474f6b87bf81245cf308b3