المؤلفون: Metab Alharbi, Abdulrahman Alshammari, Jawza F. Alsabhan, Sami I. Alzarea, Talal Alshammari, Fawaz Alasmari, Abdullah F. Alasmari

المصدر: Frontiers in Immunology, Vol 15 (2024)

مصطلحات موضوعية: epitopes base vaccine construct, molecular docking, molecular dynamic simulation, Zika virus, binding free energies, Immunologic diseases. Allergy, RC581-607

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1426496/full; https://doaj.org/toc/1664-3224

URL الوصول: https://doaj.org/article/ecea8f03a0104724beca71fba57d39c3

المؤلفون: Muhammad Suleman, Chiara Moltrasio, Paola Maura Tricarico, Angelo Valerio Marzano, Sergio Crovella

المصدر: Biomolecules, Vol 14, Iss 12, p 1521 (2024)

مصطلحات موضوعية: atopic dermatitis, TSLP, molecular docking, MD simulation, binding free energies, Microbiology, QR1-502

وصف الملف: electronic resource

Relation: https://www.mdpi.com/2218-273X/14/12/1521; https://doaj.org/toc/2218-273X

URL الوصول: https://doaj.org/article/f6697d6702cc4b8e872d2440a814ed5b

المؤلفون: Nur Fathiah Rosilan, Muhamad Arif Mohamad Jamali, Siti Aishah Sufira, Khor Waiho, Hanafiah Fazhan, Noraznawati Ismail, Yeong Yik Sung, Zeti-Azura Mohamed-Hussein, Azzmer Azzar Abdul Hamid, Nor Afiqah-Aleng

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Immunology, Cancer, Inorganic Chemistry, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, pathogenesis remains unclear, global economic growth, complexes greatly contribute, binding free energies, several interacting residues, div >< p, protein kinase domain, chemotaxis chey protein, potential interaction sites, molecular binding sites, vibrio parahaemolyticus <, penaeus vannamei <, interaction sites, vibrio <, parahaemolyticus <, p <, binding affinity, several immune, molecular docking, protein interaction

Relation: https://figshare.com/articles/journal_contribution/Protein_structure_validation_using_ERRAT_PROCHECK_MolProbity_ProQ_and_ProSA_/25056253

الاتاحة: https://doi.org/10.1371/journal.pone.0297759.s004
https://figshare.com/articles/journal_contribution/Protein_structure_validation_using_ERRAT_PROCHECK_MolProbity_ProQ_and_ProSA_/25056253

المؤلفون: Nur Fathiah Rosilan, Muhamad Arif Mohamad Jamali, Siti Aishah Sufira, Khor Waiho, Hanafiah Fazhan, Noraznawati Ismail, Yeong Yik Sung, Zeti-Azura Mohamed-Hussein, Azzmer Azzar Abdul Hamid, Nor Afiqah-Aleng

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Immunology, Cancer, Inorganic Chemistry, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, pathogenesis remains unclear, global economic growth, complexes greatly contribute, binding free energies, several interacting residues, div >< p, protein kinase domain, chemotaxis chey protein, potential interaction sites, molecular binding sites, vibrio parahaemolyticus <, penaeus vannamei <, interaction sites, vibrio <, parahaemolyticus <, p <, binding affinity, several immune, molecular docking, protein interaction

Relation: https://figshare.com/articles/journal_contribution/Protein-protein_docking_score_using_the_HawkDock_server_/25056256

الاتاحة: https://doi.org/10.1371/journal.pone.0297759.s005
https://figshare.com/articles/journal_contribution/Protein-protein_docking_score_using_the_HawkDock_server_/25056256

المؤلفون: Nur Fathiah Rosilan, Muhamad Arif Mohamad Jamali, Siti Aishah Sufira, Khor Waiho, Hanafiah Fazhan, Noraznawati Ismail, Yeong Yik Sung, Zeti-Azura Mohamed-Hussein, Azzmer Azzar Abdul Hamid, Nor Afiqah-Aleng

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Genetics, Immunology, Cancer, Inorganic Chemistry, Infectious Diseases, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, pathogenesis remains unclear, global economic growth, complexes greatly contribute, binding free energies, several interacting residues, div >< p, protein kinase domain, chemotaxis chey protein, potential interaction sites, molecular binding sites, vibrio parahaemolyticus <, penaeus vannamei <, interaction sites, vibrio <, parahaemolyticus <, p <, binding affinity, several immune, molecular docking, protein interaction

Relation: https://figshare.com/articles/journal_contribution/Distance_of_non-bonded_contact_between_i_Penaeus_vannamei_i_and_i_V_i_i_parahaemolyticus_i_residues_/25056259

الاتاحة: https://doi.org/10.1371/journal.pone.0297759.s006
https://figshare.com/articles/journal_contribution/Distance_of_non-bonded_contact_between_i_Penaeus_vannamei_i_and_i_V_i_i_parahaemolyticus_i_residues_/25056259

المؤلفون: Lee, Ju Yong, Seok, Chaok

المساهمون: Lee, Ju Yong, Seok, Chaok

مصطلحات موضوعية: BINDING FREE-ENERGIES, MOLECULAR-DYNAMICS, GENETIC ALGORITHM, SCORING FUNCTIONS, FLEXIBLE DOCKING, LAMBDA-DYNAMICS, AFFINITIES, EFFICIENT, SIMULATIONS, PREDICTION, protein-ligand binding mode, AutoDock, entropy, rescoring, scoring function

Relation: PROTEINS : Structure, Function, and Bioinformatics, Vol.70 No.3, pp.1074-1083; https://hdl.handle.net/10371/201549; 000252836300040; 2-s2.0-38549178026; 212414

الاتاحة: https://hdl.handle.net/10371/201549
https://doi.org/10.1002/prot.21844

المؤلفون: Martin Vögele, Bin W. Zhang, Jonas Kaindl, Lingle Wang

مصطلحات موضوعية: Biophysics, Biochemistry, Pharmacology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, thermodynamic principles suggest, proteins ’ functions, carefully designed restraints, eight g protein, corresponding conformational ensembles, binding free energy, binding free energies, various investigated receptors, important drug targets, protein conformational changes, particular functional response, binding thermodynamics provides, functional response, conformational equilibrium, strong binding, effective drug, coupled receptors, target protein, ligand binding, thoroughly validated, strong predictor, routinely calculated, receptor determined, prohibitively long

Relation: https://figshare.com/articles/journal_contribution/Is_the_Functional_Response_of_a_Receptor_Determined_by_the_Thermodynamics_of_Ligand_Binding_/24534663

الاتاحة: https://doi.org/10.1021/acs.jctc.3c00899.s001
https://figshare.com/articles/journal_contribution/Is_the_Functional_Response_of_a_Receptor_Determined_by_the_Thermodynamics_of_Ligand_Binding_/24534663

المؤلفون: Haide Wu, Morten Engsvang, Yosef Knattrup, Jakub Kubečka, Jonas Elm

مصطلحات موضوعية: Biophysics, Cell Biology, Genetics, 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, one long exploration, nucleation process leading, methodology allows us, around 1 nm, chosen computational method, bridge computational studies, approximately 2 nm, highly improved accuracy, binding free energies, clusters containing dimethylamine, 2 nm, binding energies, containing clusters, computational cost, experimental studies, 3c method, molecular clusters, large clusters, typically reach, quantum chemical, large systems

Relation: https://figshare.com/articles/journal_contribution/Improved_Configurational_Sampling_Protocol_for_Large_Atmospheric_Molecular_Clusters/24552577

الاتاحة: https://doi.org/10.1021/acsomega.3c06794.s001
https://figshare.com/articles/journal_contribution/Improved_Configurational_Sampling_Protocol_for_Large_Atmospheric_Molecular_Clusters/24552577

المؤلفون: Nuno M. S. Almeida, Semiha Kevser Bali, Deepak James, Cong Wang, Angela K. Wilson

مصطلحات موضوعية: Biophysics, Biochemistry, Microbiology, Cell Biology, Molecular Biology, Pharmacology, Cancer, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, significant health conditions, many drug targets, global structural effects, gene expression regulation, fundamental building blocks, dlpno – ccsd, density functional theory, activator receptor γ, binding free energies, replacing smaller pfas, nuclear receptors act, carnitine shows promise, different binding pockets, dna binding domain, investigated pockets, pfas binding, vivo <, unique properties, transcription factors, residue decomposition, remediation strategy

Relation: https://figshare.com/articles/journal_contribution/Binding_of_Per-_and_Polyfluoroalkyl_Substances_PFAS_to_the_PPAR_RXR_DNA_Complex/24604330

الاتاحة: https://doi.org/10.1021/acs.jcim.3c01384.s001
https://figshare.com/articles/journal_contribution/Binding_of_Per-_and_Polyfluoroalkyl_Substances_PFAS_to_the_PPAR_RXR_DNA_Complex/24604330

المؤلفون: Jacqueline C. Calderón, Eva Plut, Max Keller, Chiara Cabrele, Oliver Reiser, Francesco L. Gervasio, Timothy Clark

مصطلحات موضوعية: Biophysics, Biochemistry, Medicine, Cell Biology, Molecular Biology, Pharmacology, Immunology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, 4 , 2 , 1 , binding free energies, alternative binding sites, unbinding free energies, one previously presented, extended metadynamics protocol, g ‑ protein, metadynamics protocol, protocol expands, vasopressin binding, oxytocin binding, unbinding small, peptide ligands, otr ), molecule ligands, exemplary simulations

Relation: https://figshare.com/articles/journal_contribution/Extended_Metadynamics_Protocol_for_Binding_Unbinding_Free_Energies_of_Peptide_Ligands_to_Class_A_G_Protein-Coupled_Receptors/24908651

الاتاحة: https://doi.org/10.1021/acs.jcim.3c01574.s001
https://figshare.com/articles/journal_contribution/Extended_Metadynamics_Protocol_for_Binding_Unbinding_Free_Energies_of_Peptide_Ligands_to_Class_A_G_Protein-Coupled_Receptors/24908651

المؤلفون: Fábio P. S. Souza (14321561), Germano Heinzelmann (177901), Giovanni F. Caramori (542883)

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Biotechnology, Ecology, Computational Biology, Space Science, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, polar protic ), methodology employed presents, hg supramolecular systems, − 20 kcal, results also reveal, nonpolar ), acetonitrile, experimental available δ, 4 +, binding free energies, pahs – exbox, free energies, − 5, results showed, also extensible, binding affinities, work investigates, widely dispersed, tetracationic box, solvent effects, soil washing

Relation: https://figshare.com/articles/journal_contribution/Investigating_the_Solvent_Effects_on_Binding_Affinity_of_PAHs_ExBox_sup_4_sup_Complexes_An_Alchemical_Approach/21806687

الاتاحة: https://doi.org/10.1021/acs.jpcb.2c06271.s001

المؤلفون: Akachukwu Ibezim, Emmanuel Onah, Ebubechukwu N. Dim, Fidele Ntie-Kang

المصدر: BMC Complementary Medicine and Therapies, Vol 21, Iss 1, Pp 1-8 (2021)

مصطلحات موضوعية: Binding free energies, Docking, Drug repositioning, Psoriasis, Other systems of medicine, RZ201-999

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2662-7671

URL الوصول: https://doaj.org/article/529accd2c7004afdb754a3fc5fd5970b

المؤلفون: Nahlah Makki Almansour

المصدر: Frontiers in Microbiology, Vol 13 (2022)

مصطلحات موضوعية: Merkel cell polyomavirus, multi-epitopes vaccine, molecular docking simulation, binding free energies, immunoinformatics, Microbiology, QR1-502

وصف الملف: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2022.929669/full; https://doaj.org/toc/1664-302X

URL الوصول: https://doaj.org/article/b2ea10c7e1294b1aaaaf500c0b2141b9

المؤلفون: Gary Tresadern (836509), Kanaka Tatikola (5677193), Javier Cabrera (690793), Lingle Wang (1441657), Robert Abel (1441678), Herman van Vlijmen (3537107), Helena Geys (5051510)

مصطلحات موضوعية: Biophysics, Biochemistry, Pharmacology, Chemical Sciences not elsewhere classified, work extends beyond, free energy methods, binding free energies, property prediction methods, calculated binding affinities, calculated error, accurate prediction, binding affinity, unexpected outcomes, statistical analysis, standard deviation, small molecules, remarkable achievement, recent years, plausible ratios, dramatic increase, deliver results, 1 kcal

Relation: https://figshare.com/articles/journal_contribution/The_Impact_of_Experimental_and_Calculated_Error_on_the_Performance_of_Affinity_Predictions/18864040

الاتاحة: https://doi.org/10.1021/acs.jcim.1c01214.s001

المؤلفون: Julie Aufort (9657817), Alicia Schuitemaker (8714586), Rebecca Green (4351084), Raffaella Demichelis (1498630), Paolo Raiteri (1498624), Julian D. Gale (1498627)

مصطلحات موضوعية: Biophysics, Biochemistry, Physiology, Biotechnology, Ecology, Environmental Sciences not elsewhere classified, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, force field developed, exhibit moderate binding, contains static multipoles, binding free energies, 101 ̅ 4, small species studied, small organic molecules, one growth site, strong hydration layers, fixed charge rigid, consistent induced dipoles, adsorption free energies, calcium carbonate based, carbonate ions within, including polarization allows, hydration layers, calcium carbonate, calcium ions, species bearing, organic additives, carbonate groups

Relation: https://figshare.com/articles/journal_contribution/Determining_the_Adsorption_Free_Energies_of_Small_Organic_Molecules_and_Intrinsic_Ions_at_the_Terrace_and_Steps_of_Calcite/18651049

الاتاحة: https://doi.org/10.1021/acs.cgd.1c01414.s001

المؤلفون: Wafa Abdullah I. Al-Megrin, Alaa Karkashan, Abdullah M. Alnuqaydan, Faris F. Aba Alkhayl, Faris Alrumaihi, Ahmad Almatroudi, Khaled S. Allemailem

المصدر: Vaccines; Volume 10; Issue 6; Pages: 886

مصطلحات موضوعية: Enterobacter cloaca, pangenome subtractive proteomics, immunoinformatic, molecular docking, molecular dynamic simulations, binding free energies

وصف الملف: application/pdf

Relation: Innate and Adaptive Immunity in Vaccination; https://dx.doi.org/10.3390/vaccines10060886

الاتاحة: https://doi.org/10.3390/vaccines10060886

المؤلفون: Saba Ismail, Sumra Wajid Abbasi, Maha Yousaf, Sajjad Ahmad, Khalid Muhammad, Yasir Waheed

المصدر: Vaccines; Volume 10; Issue 3; Pages: 378

مصطلحات موضوعية: hantaviruses, ViPR database, multi-epitope database, molecular dynamics simulations, binding free energies

وصف الملف: application/pdf

Relation: Cellular/Molecular Immunology; https://dx.doi.org/10.3390/vaccines10030378

الاتاحة: https://doi.org/10.3390/vaccines10030378

المؤلفون: Nahlah Makki Almansour

المصدر: Saudi Journal of Biological Sciences, Vol 29, Iss 7, Pp 103335- (2022)

مصطلحات موضوعية: Maternal embryonic leucine zipper kinase, Virtual screening, Molecular dynamics simulations, Binding free energies, Pharmacokinetics, Biology (General), QH301-705.5

Relation: http://www.sciencedirect.com/science/article/pii/S1319562X22002510; https://doaj.org/toc/1319-562X; https://doaj.org/article/a79b375c57c947a7880536c0c68cb5c9

الاتاحة: https://doi.org/10.1016/j.sjbs.2022.103335
https://doaj.org/article/a79b375c57c947a7880536c0c68cb5c9

المؤلفون: Damas, Giane B.

المساهمون: Araujo, Carlos Moyses, Docent, Ahuja, Rajeev, Professor, 1965, Persson, Clas, Professor

المصدر: Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology.

مصطلحات موضوعية: Photocatalytic hydrogen production, polymeric materials, donor-acceptor architecture, small molecules, density functional theory, hydrogen binding free energies, exciton binding energies, electrocatalysis, carbon dioxide conversion, formic acid production, Sn-based electrodes, Tin oxides, Ru-complexes, Metal Organic Frameworks, carbon dioxide capture.

وصف الملف: electronic

URL الوصول: https://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-398175
https://uu.diva-portal.org/smash/get/diva2:1374802/FULLTEXT01.pdf
https://uu.diva-portal.org/smash/get/diva2:1374802/PREVIEW01.jpg

المؤلفون: Yudong Qiu (1906885), Daniel G. A. Smith (11468128), Simon Boothroyd (11468131), Hyesu Jang (11468134), David F. Hahn (9681119), Jeffrey Wagner (2108986), Caitlin C. Bannan (5908607), Trevor Gokey (2008708), Victoria T. Lim (5908610), Chaya D. Stern (4278925), Andrea Rizzi (1845439), Bryon Tjanaka (11468137), Gary Tresadern (836509), Xavier Lucas (400968), Michael R. Shirts (141621), Michael K. Gilson (673405), John D. Chodera (1323594), Christopher I. Bayly (1515103), David L. Mobley (1323615), Lee-Ping Wang (1279797)

مصطلحات موضوعية: Biophysics, Biotechnology, Evolutionary Biology, Computational Biology, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, resulting force field, quantum reference data, parameter assignment formalism, molecule force field, minimal human intervention, general force fields, general force field, database software ecosystem, data types outside, classical molecular simulations, binding free energies, tests show improvements, report tests, vibrational frequencies, training set, rapidly optimize, phase structures, parsley ’, parsley small, liquid properties, initial application, handles increases, full optimization

Relation: https://figshare.com/articles/journal_contribution/Development_and_Benchmarking_of_Open_Force_Field_v1_0_0_the_Parsley_Small-Molecule_Force_Field/16663714

الاتاحة: https://doi.org/10.1021/acs.jctc.1c00571.s001