المؤلفون: Cong Liu, Evangelos A. Coutsias, Ken A. Dill, Sergei Kotelnikov, Andrey Alekseenko, Mikhail Ignatov, Dzmitry Padhorny, Dima Kozakov, Emiliano Brini, Mark Lukin

المصدر: J Comput Aided Mol Des

مصطلحات موضوعية: Macrocyclic Compounds, Design data, Computer science, Molecular Dynamics Simulation, Ligands, Energy minimization, 01 natural sciences, Article, Computational science, Molecular dynamics, 0103 physical sciences, Drug Discovery, Aspartic Acid Endopeptidases, Humans, Physical and Theoretical Chemistry, Binding Sites, 010304 chemical physics, 0104 chemical sciences, Computer Science Applications, Molecular Docking Simulation, 010404 medicinal & biomolecular chemistry, Protein–ligand docking, Docking (molecular), Drug Design, Thermodynamics, Template based, Amyloid Precursor Protein Secretases, Monte Carlo Method, Protein Binding

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::106e6931dd1404c95e61783f6d35abdfTest
https://doi.org/10.1007/s10822-019-00257-1Test

المؤلفون: Gaspard Debussche, Emad Tajkhorshid, Mrinal Shekhar, Chitrak Gupta, Jonathan Nguyen, Wade D. Van Horn, Alberto Perez, Abhishek Singharoy, Daisuke Kihara, John Vant, Nicholas J. Sisco, Arup Mondal, Genki Terashi, Ken A. Dill, Daipayan Sarkar, Petra Fromme

المصدر: Matter, vol 4, iss 10
Matter

مصطلحات موضوعية: Quantitative Biology::Biomolecules, Ensemble forecasting, Computer science, Cryo-electron microscopy, 1.1 Normal biological development and functioning, Resolution (electron density), Bioengineering, Folding (DSP implementation), Python (programming language), 1.4 Methodologies and measurements, Article, Molecular dynamics, Protein structure, Underpinning research, 2.1 Biological and endogenous factors, General Materials Science, Protein folding, Generic health relevance, Aetiology, Biological system, computer, computer.programming_language

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d117e55b540adeb16485a4911581afaTest
https://escholarship.org/uc/item/9ns981p8Test

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: Jason A. Wagoner, Ken A. Dill

المصدر: Proceedings of the National Academy of Sciences of the United States of America, vol 116, iss 13

مصطلحات موضوعية: Multidisciplinary, Molecular Structure, free-energy landscape, Computer science, Molecular Motor Proteins, Work (physics), Molecular Conformation, Bioengineering, Control engineering, Models, Theoretical, Molecular machine, nonequilibrium steady state, Chemical energy, Energy Transfer, Theoretical, Affordable and Clean Energy, Models, Physical Sciences, evolution, kinetic optimization, molecular machines, Nonequilibrium steady state, Energy Metabolism, Energy (signal processing)

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8ecefe8c88025ccc83ff50dcfef25942Test
https://doi.org/10.1073/pnas.1812149116Test

المؤلفون: Dzmitry Padhorny, Zhuyezi Sun, Sergei Kotelnikov, Yaroslav Kholodov, Istvan Kolosvari, Andrey Alekseenko, Cong Liu, Dima Kozakov, Ivan V Grebenkin, Ken A. Dill, Alberto Perez, Mikhail Ignatov, Andrey Kazennov

المصدر: Journal of computer-aided molecular design, vol 33, iss 1

مصطلحات موضوعية: Computer science, Medicinal & Biomolecular Chemistry, Monte Carlo method, Molecular Conformation, Molecular Dynamics Simulation, Crystallography, X-Ray, Ligands, Energy minimization, 01 natural sciences, Article, Databases, Medicinal and Biomolecular Chemistry, Theoretical and Computational Chemistry, 0103 physical sciences, Drug Discovery, Physical and Theoretical Chemistry, Databases, Protein, Monte Carlo, Quantitative Biology::Biomolecules, Crystallography, Binding Sites, 010304 chemical physics, Protein, MD, Translational motion, Cathepsins, Manifold, Minimization, 0104 chemical sciences, Computer Science Applications, Molecular Docking Simulation, 010404 medicinal & biomolecular chemistry, Docking (molecular), Drug Design, X-Ray, Thermodynamics, Computer-Aided Design, Pose prediction, Minification, Monte Carlo Method, Algorithm, Cathepsin S, D3R, Protein Binding, Protein ligand

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::78e19b71fc0da1cb5535fe69a54936cfTest
https://doi.org/10.1007/s10822-018-0176-0Test

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

مصطلحات موضوعية: Structure (mathematical logic), Computer science, business.industry, media_common.quotation_subject, Context (language use), computer.file_format, Protein Data Bank, computer.software_genre, Software, Atomic resolution, Benchmark (surveying), Quality (business), Data mining, Focus (optics), business, computer, media_common

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::b8865de76a951abdceb7408e522b1f9dTest
https://doi.org/10.1101/2020.06.12.147033Test

المؤلفون: Kingshuk Ghosh, Purushottam D. Dixit, Ken A. Dill, Luca Agozzino

المصدر: Annu Rev Phys Chem

مصطلحات موضوعية: Computer science, Protein Conformation, Neuronal firing, Entropy, Complex system, Non-equilibrium thermodynamics, Molecular Dynamics Simulation, 01 natural sciences, Article, 03 medical and health sciences, symbols.namesake, Variational principle, 0103 physical sciences, Gene Regulatory Networks, Statistical physics, Physical and Theoretical Chemistry, 030304 developmental biology, Network model, 0303 health sciences, 010304 chemical physics, Models, Genetic, Proteins, Maximization, DNA, Models, Theoretical, Kinetics, Models, Chemical, Caliber, Boltzmann constant, symbols, Nucleic Acid Conformation

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d3bc02e51066800b340dceeca9860446Test
https://pubmed.ncbi.nlm.nih.gov/32075515Test

المؤلفون: Lilianne R. Mujica-Parodi, Luca Agozzino, Corey Weistuch, Ken A. Dill

المساهمون: You, Lingchong

المصدر: PLoS computational biology, vol 16, iss 11
PLoS Computational Biology, Vol 16, Iss 11, p e1008435 (2020)
PLoS Computational Biology

مصطلحات موضوعية: 0301 basic medicine, Computer science, Entropy, Action Potentials, Inference, Quantitative Biology - Quantitative Methods, 01 natural sciences, Mathematical Sciences, Electronics Engineering, Animal Cells, Gene Regulatory Networks, Biology (General), Quantitative Methods (q-bio.QM), Data Management, Neurons, Ecology, Artificial neural network, Approximation Methods, Physics, Brain, Biological Sciences, Inverse problem, Computational Theory and Mathematics, Biological Physics (physics.bio-ph), Modeling and Simulation, Physical Sciences, Neurological, Engineering and Technology, Thermodynamics, Neurons and Cognition (q-bio.NC), Cellular Types, Algorithm, Neuronal Tuning, Algorithms, Research Article, Computer and Information Sciences, Neural Networks, QH301-705.5, Bioinformatics, FOS: Physical sciences, Topology (electrical circuits), Mathematical proof, Proof of Concept Study, Measure (mathematics), Computer, 03 medical and health sciences, Cellular and Molecular Neuroscience, Information and Computing Sciences, 0103 physical sciences, Toggle Switches, Genetics, Phase Diagrams, Physics - Biological Physics, 010306 general physics, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Data Visualization, Neurosciences, Biology and Life Sciences, Cell Biology, Nonlinear system, 030104 developmental biology, Cellular Neuroscience, Physics - Data Analysis, Statistics and Probability, Quantitative Biology - Neurons and Cognition, FOS: Biological sciences, Pairwise comparison, Neural Networks, Computer, Mathematics, Data Analysis, Statistics and Probability (physics.data-an), Neuroscience

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::361ab0eda7d7b873a1270e03b39977caTest

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

مصطلحات موضوعية: Docking (molecular), Computer science, Computational biology, Template based

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::91089c08f46b63cc46bb57025cd68d0cTest
https://doi.org/10.1002/prot.25887/v2/response1Test