المؤلفون: Gregory L. Dignon, Ken A. Dill

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Cancer, Inorganic Chemistry, Plant Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Information Systems not elsewhere classified, thermodynamic perturbation theory, resolution md simulations, particular monoclonal antibody, method successfully ranks, many biological processes, formulating biological drugs, different excipient molecules, computationally efficient model, approach appears useful, e ., excipients, mitigating protein association, predicting excipient effects, protein association, use small, reducing effect, phase separation, molecule additives, four types, excipients known

العلاقة: https://figshare.com/articles/journal_contribution/Computational_Procedure_for_Predicting_Excipient_Effects_on_Protein_Protein_Affinities/25119306Test

الإتاحة: https://doi.org/10.1021/acs.jctc.3c01197.s001Test
https://figshare.com/articles/journal_contribution/Computational_Procedure_for_Predicting_Excipient_Effects_on_Protein_Protein_Affinities/25119306Test

المؤلفون: Jeremy Schmit, Ken A. Dill

المصدر: Annual Review of Biophysics. 52:v-viii

مصطلحات موضوعية: Structural Biology, Biophysics, Bioengineering, Cell Biology, Biochemistry

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::43099ad063a30b3baa265996d929f0deTest
https://doi.org/10.1146/annurev-bb-52-030923-100001Test

المؤلفون: Ajeet Kumar Yadav (10099324), Pradipta Bandyopadhyay (473114), Tomaz Urbic (6034649), Ken A. Dill (154060)

مصطلحات موضوعية: Biophysics, Biochemistry, Plant Biology, Computational Biology, Biological Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Physical Sciences not elsewhere classified, Information Systems not elsewhere classified, Ionic Solvation, water molecule, nonpolar, function, solute radius, ion radius, gas series Ne, charge interactions, dipolar hydrogen-bonding disk, model

العلاقة: https://figshare.com/articles/journal_contribution/Analytical_2_Dimensional_Model_of_Nonpolar_and_Ionic_Solvation_in_Water/13717372Test

الإتاحة: https://doi.org/10.1021/acs.jpcb.0c10329.s001Test

المؤلفون: Cong Liu (66219), Emiliano Brini (1512898), Ken A. Dill (154060)

مصطلحات موضوعية: Biophysics, Biochemistry, Genetics, Molecular Biology, Pharmacology, Biotechnology, Cancer, Computational Biology, Biological Sciences not elsewhere classified, Mathematical Sciences not elsewhere classified, Chemical Sciences not elsewhere classified, Information Systems not elsewhere classified, accurate physical potentials, bracket finds best, compete different ligands, bracket <, well separated, molecular dynamics, method called, computationally expensive, binding affinities, binders rapidly, affinity ligands, active compounds

العلاقة: https://figshare.com/articles/journal_contribution/Accelerating_Molecular_Dynamics_Enrichments_of_High-Affinity_Ligands_for_Proteins/17143270Test

الإتاحة: https://doi.org/10.1021/acs.jctc.1c00855.s001Test

المؤلفون: Sandor Vajda, Ora Schueler-Furman, Orly Shimony, Emiliano Brini, Nawsad Alam, Dima Kozakov, Ken A. Dill, Orly Marcu, Alisa Khramushin, Dzmitry Padhorny

المصدر: Proteins, vol 88, iss 8
Proteins

مصطلحات موضوعية: Protein Conformation, alpha-Helical, Protein Conformation, Beta sheet, Peptide, Ligands, Biochemistry, Mathematical Sciences, Mice, Structural Biology, Protein Interaction Mapping, Rosetta, Side chain, chemistry.chemical_classification, 0303 health sciences, Hydrogen bond, 030302 biochemistry & molecular biology, Biological Sciences, peptide-protein interactions, Molecular Docking Simulation, Complementation, Myelin-Associated Glycoprotein, Research Design, peptide docking, Thermodynamics, CAPRI, Protein Binding, beta sheet interactions, high-resolution modeling, Bioinformatics, Protein domain, Computational biology, Article, Protein–protein interaction, 03 medical and health sciences, Information and Computing Sciences, Animals, Humans, Protein Interaction Domains and Motifs, Amino Acid Sequence, Molecular Biology, Structural Homology, 030304 developmental biology, Binding Sites, Protein, alpha-Helical, Proteins, Dyneins, Hydrogen Bonding, FlexPepDock, chemistry, Structural Homology, Protein, Docking (molecular), Protein Conformation, beta-Strand, beta-Strand, Generic health relevance, Protein Multimerization, Peptides, Software

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c1fcd05d50a8ba4e99c3dedfe33bc02dTest
https://doi.org/10.1002/prot.25871Test

المؤلفون: James C. Robertson, Ken A. Dill, Emiliano Brini, Cong Liu, Roy Nassar, Alberto Perez

المصدر: Proteins

مصطلحات موضوعية: Physics, 0303 health sciences, Magnetic Resonance Spectroscopy, Protein Conformation, 030302 biochemistry & molecular biology, Computational Biology, Proteins, Reproducibility of Results, Molecular Dynamics Simulation, Protein structure prediction, Space (mathematics), Residual, Biochemistry, Nmr data, Article, 03 medical and health sciences, Molecular dynamics, Protein structure, Structural Biology, Limit (mathematics), Statistical physics, Molecular Biology, Algorithms, 030304 developmental biology

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d698ddda6e3fddfc22f8b484614cf43eTest
https://doi.org/10.1002/prot.25788Test

المؤلفون: Martyn Winn, Maxim Igaev, Bohdan Monastyrskyy, Genki Terashi, Catherine L. Lawson, Mark A. Herzik, Jianlin Cheng, Michael F. Schmid, Renzhi Cao, Kevin Cowtan, Mateusz Olek, Dilip Kumar, Jonas Pfab, Stephanie A. Wankowicz, Wah Chiu, Luisa U. Schäfer, Paul D. Adams, Grigore D. Pintilie, Daipayan Sarkar, Sumit Mittal, Daisuke Kihara, Frank DiMaio, Zhe Wang, Tianqi Wu, Andriy Kryshtafovych, Tom Burnley, Mrinal Shekhar, Paul S. Bond, Gunnar F. Schröder, Li-Wei Hung, Andrea C. Vaiana, Ardan Patwardhan, Daniel P. Farrell, Liguo Wang, Ken A. Dill, Pavel V. Afonine, Jane S. Richardson, Agnel Praveen Joseph, Xiaodi Yu, Helen M. Berman, Singharoy A, Alberto Perez, Thomas C. Terwilliger, Kaiming Zhang, Jie Hou, Soon Wen Hoh, James S. Fraser, Dong Si, Peter B. Rosenthal, Colin M. Palmer, Benjamin A Barad, Matthew L. Baker, Grzegorz Chojnowski, Christopher J. Williams

المصدر: Nature Methods
Nature methods 18(2), 156-164 (2021). doi:10.1038/s41592-020-01051-w
Nature methods, vol 18, iss 2

مصطلحات موضوعية: Models, Molecular, Technology, Statistical methods, Computer science, Protein Conformation, computer.software_genre, Crystallography, X-Ray, Biochemistry, Medical and Health Sciences, Model validation, 0302 clinical medicine, Software, Models, media_common, 0303 health sciences, Crystallography, Protein databases, Biological Sciences, Networking and Information Technology R&D, Biotechnology, Validation study, Modeling software, media_common.quotation_subject, Context (language use), Bioengineering, Machine learning, 03 medical and health sciences, Benchmark (surveying), Quality (business), ddc:610, Molecular Biology, 030304 developmental biology, Structure (mathematical logic), business.industry, Cryoelectron Microscopy, Molecular, Proteins, Cell Biology, X-Ray, Artificial intelligence, Generic health relevance, business, computer, 030217 neurology & neurosurgery, Analysis, Developmental Biology

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::86f62d2baaf785b72bd94d370b444153Test
https://hdl.handle.net/21.11116/0000-000B-3152-121.11116/0000-000B-3145-021.11116/0000-000B-3147-ETest

المؤلفون: Ken A. Dill, Tomaz Urbic

المصدر: Journal of the American Chemical Society, vol 140, iss 49

مصطلحات موضوعية: Phase transition, Liquid water, Static Electricity, Chemical, 010402 general chemistry, 01 natural sciences, Biochemistry, Phase Transition, Article, Catalysis, Colloid and Surface Chemistry, Models, 0103 physical sciences, Static electricity, Pressure, Molecule, Supercooling, Physics::Atmospheric and Oceanic Physics, 010304 chemical physics, Chemistry, Hydrogen bond, Temperature, Water, Hydrogen Bonding, General Chemistry, 0104 chemical sciences, Temperature and pressure, Models, Chemical, Chemical physics, Chemical Sciences, Thermodynamics, Current (fluid)

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8291f78a2bb02c0726f82fafb2b8cb9cTest
https://doi.org/10.1021/jacs.8b08856Test

المؤلفون: Adam Mr de Graff, Tilly Sharp, David J. Grainger, David E. Mosedale, Ken A. Dill

المساهمون: Skolnick, Jeffrey

المصدر: PLoS computational biology, vol 16, iss 12
PLoS Computational Biology, Vol 16, Iss 12, p e1008460 (2020)
PLoS Computational Biology

مصطلحات موضوعية: 0301 basic medicine, Protein Folding, Nematoda, Proteomes, Computer science, Protein Synthesis, Biochemistry, Mathematical Sciences, 0302 clinical medicine, Theoretical, Models, Macromolecular Structure Analysis, Biology (General), Protein Metabolism, Flow Rate, Mammals, Ecology, biology, Physics, Chemical Synthesis, Eukaryota, Classical Mechanics, Animal Models, Biological Sciences, Experimental Organism Systems, Computational Theory and Mathematics, Caenorhabditis Elegans, Modeling and Simulation, Vertebrates, Physical Sciences, Proteome, Protein folding, Biological system, Research Article, Protein Binding, Protein Structure, Biosynthetic Techniques, QH301-705.5, Bioinformatics, 1.1 Normal biological development and functioning, Biophysics, Fluid Mechanics, Research and Analysis Methods, Continuum Mechanics, 03 medical and health sciences, Cellular and Molecular Neuroscience, Model Organisms, Underpinning research, Information and Computing Sciences, Genetics, Animals, Humans, Differential expression, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Organisms, Biology and Life Sciences, Proteins, Fluid Dynamics, Models, Theoretical, Invertebrates, Kinetics, Metabolism, 030104 developmental biology, Proteostasis, Chaperone (protein), Amniotes, Foldase, Animal Studies, Caenorhabditis, biology.protein, Energy cost, Generic health relevance, Zoology, 030217 neurology & neurosurgery, Molecular Chaperones

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::93aba04938b0770fda0c821ff7e9975bTest
https://escholarship.org/uc/item/4hr4g41rTest

المؤلفون: Nawsad Alam, Emiliano Brini, Dmitri Beglov, Israel Desta, Sergei Kotelnikov, Kathryn A. Porter, Dima Kozakov, Andrey Alekseenko, Ora Schueler-Furman, Sandor Vajda, Mikhail Ignatov, Dzmitry Padhorny, Zhuyezi Sun, Ryota Ashizawa, Ken A. Dill

المصدر: Proteins

مصطلحات موضوعية: Protein Conformation, alpha-Helical, Computer science, computer.software_genre, Ligands, Biochemistry, Article, 03 medical and health sciences, Structural Biology, DOCK, Protein Interaction Mapping, Humans, Macromolecular docking, Protein Interaction Domains and Motifs, Homology modeling, Amino Acid Sequence, Molecular Biology, 030304 developmental biology, 0303 health sciences, Binding Sites, 030302 biochemistry & molecular biology, Proteins, Molecular Docking Simulation, Benchmarking, Template, Fully automated, Docking (molecular), Research Design, Structural Homology, Protein, Thermodynamics, Critical assessment, Protein Conformation, beta-Strand, Data mining, Template based, Protein Multimerization, Peptides, computer, Software, Protein Binding

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6bb3f88f571951906d404ca9160b96a6Test
https://pubmed.ncbi.nlm.nih.gov/32142178Test