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1. Full Text Pairwise decomposition of an MMGBSA energy function for computational protein design
by Gaillard, Thomas and Simonson, Thomas
Journal of computational chemistry, ISSN 0192-8651, 07/2014, Volume 35, Issue 18, pp. 1371 - 1387
surface area | Generalized Born | energy decomposition | molecular mechanics | Protein design | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology | Thermodynamics | Protein Conformation | Proteins - chemistry | Computational Biology | Proteins | Decomposition | Matrix | Energy | Dielectric properties | Compounds | Surface area | Computation | Design modifications | Index Medicus | Life Sciences | Biochemistry, Molecular Biology
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2. Full Text Full Protein Sequence Redesign with an MMGBSA Energy Function
by Gaillard, Thomas and Simonson, Thomas
Journal of chemical theory and computation, ISSN 1549-9618, 10/2017, Volume 13, Issue 10, pp. 4932 - 4943
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Proteins | Energy consumption | Sequences | Energy | Crystallography | Electrostatics | Redesign | Molecular chains | Life Sciences | Molecular biology | Cellular Biology | Quantitative Methods | Biochemistry, Molecular Biology | Cancer
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3. Full Text RECENT RESEARCH IN SINGING
by Simonson, Donald
Journal of singing, ISSN 1086-7732, 01/2019, Volume 75, Issue 3, p. 367
Singing | Singers | Handbooks | Repertoire | Research | Dvorak, Antonin (1841-1904) | Lewis, Megan | Musical performances | Hardy, Thomas (1840-1928) | Composers | Learning | Contemporary art | Vocal music | Teachers | Students | Physiology | Dissertations & theses | Opera
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4. Full Text Protein side chain conformation predictions with an MMGBSA energy function
by Gaillard, Thomas and Panel, Nicolas and Simonson, Thomas
Proteins, structure, function, and bioinformatics, ISSN 0887-3585, 06/2016, Volume 84, Issue 6, pp. 803 - 819
surface area | Generalized Born | computational protein design | side chain placement | molecular mechanics | Molecular mechanics | Computational protein design | Side chain placement | Surface area | Biochemistry & Molecular Biology | Biophysics | Life Sciences & Biomedicine | Science & Technology | Thermodynamics | Animals | Databases, Protein | Humans | Amino Acids - chemistry | Models, Molecular | Protein Conformation | Proteins - chemistry | Static Electricity | Proteins | Analysis | Force and energy | Electric properties | Index Medicus | Life Sciences | Biochemistry, Molecular Biology
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5. Protein: Ligand recognition: Simple models for electrostatic effects
by Simonson, Thomas
Current pharmaceutical design, ISSN 1381-6128, 2013, Volume 19, Issue 23, pp. 4241 - 4256
Continuum electrostatics | Molecular dynamics | Free energy simulations | Linear response | Life Sciences & Biomedicine | Pharmacology & Pharmacy | Science & Technology | Aspartic Acid Proteases - chemistry | Protease Inhibitors - pharmacology | Catalytic Domain | Drug Design | Models, Molecular | Protease Inhibitors - chemistry | Ligands | Aspartic Acid Proteases - antagonists & inhibitors | Catalysis | Static Electricity | Aspartic Acid Proteases - metabolism
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6. Full Text What Is the Dielectric Constant of a Protein When Its Backbone Is Fixed?
by Simonson, Thomas
Journal of chemical theory and computation, ISSN 1549-9618, 10/2013, Volume 9, Issue 10, pp. 4603 - 4608
Physical Sciences | Chemistry | Physics, Atomic, Molecular & Chemical | Chemistry, Physical | Physics | Science & Technology | Life Sciences | Biochemistry, Molecular Biology
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7. Full Text Protein pK^sub a^’s from Adaptive Landscape Flattening Instead of Constant-pH Simulations
by Francesco Villa and Thomas Simonson
Journal of chemical theory and computation, ISSN 1549-9618, 12/2018, Volume 14, Issue 12, p. 6714
Proteins | Flattening | Computer simulation | Bias | Molecular dynamics | Protonation | Titration | Free energy
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8. Full Text Protein pKa’s from Adaptive Landscape Flattening Instead of Constant-pH Simulations
by Villa, Francesco and Simonson, Thomas
Journal of chemical theory and computation, ISSN 1549-9618, 12/2018, Volume 14, Issue 12, pp. 6714 - 6721
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9. Full Text Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases
by Aleksandrov, Alexey and Simonson, Thomas
The Journal of biological chemistry, ISSN 0021-9258, 04/2010, Volume 285, Issue 18, pp. 13807 - 13815
Life Sciences & Biomedicine | Biochemistry & Molecular Biology | Science & Technology | Protein Structure, Secondary | Protein-Tyrosine Kinases - metabolism | Humans | Models, Molecular | Neoplasms - enzymology | Piperazines - chemistry | Piperazines - therapeutic use | Imatinib Mesylate | Pyrimidines - chemistry | Neoplasms - drug therapy | Protein Kinase Inhibitors - chemistry | Animals | Protein Kinase Inhibitors - therapeutic use | Pyrimidines - therapeutic use | Chickens | Computer Simulation | Protein-Tyrosine Kinases - chemistry | Protein Binding | Benzamides | Protein-Tyrosine Kinases - antagonists & inhibitors | Index Medicus | Piperazines | Biochemistry, Molecular Biology | Neoplasms | Life Sciences | Pyrimidines | Protein Kinase Inhibitors | Protein-Tyrosine Kinases | Enzyme Inhibitors | Molecular Dynamics | Mathematical Modeling | Molecular Biophysics | Computer Modeling | Protein Drug Interactions | Computational Biology | Tyrosine-protein Kinase (Tyrosine Kinase) | Drug Action | Phosphotyrosine Signaling | Anticancer Drug
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10. Full Text Variable Neighborhood Search with Cost Function Networks To Solve Large Computational Protein Design Problems
by Charpentier, Antoine and Mignon, David and Barbe, Sophie and Cortes, Juan and Schiex, Thomas and Simonson, Thomas and Allouche, David
Journal of chemical information and modeling, ISSN 1549-9596, 01/2019, Volume 59, Issue 1, pp. 127 - 136
Computer Science, Information Systems | Physical Sciences | Computer Science, Interdisciplinary Applications | Chemistry | Life Sciences & Biomedicine | Technology | Computer Science | Pharmacology & Pharmacy | Chemistry, Medicinal | Chemistry, Multidisciplinary | Science & Technology | Solution space | Neighborhoods | Amino acids | Compounds | Redesign | Proteins | Algorithms | Computation | Upper bounds | Searching | Energy conservation | Cost function | Heuristic | Index Medicus | Life Sciences | Modeling and Simulation | Artificial Intelligence | Biochemistry, Molecular Biology | Biomolecules | Bioinformatics
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11. Full Text Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest‐descent heuristic
by Mignon, David and Simonson, Thomas
Journal of computational chemistry, ISSN 0192-8651, 07/2016, Volume 37, Issue 19, pp. 1781 - 1793
force field | inverse protein folding problem | molecular modeling | Proteus package | Force field | Inverse protein folding problem | Molecular modeling | Physical Sciences | Chemistry | Chemistry, Multidisciplinary | Science & Technology | Thermodynamics | Algorithms | Stochastic Processes | Heuristics | Protein Conformation | Proteins - chemistry | Proteins - chemical synthesis | Monte Carlo Method | Proteins | Monte Carlo method | Analysis | Amino acids | Comparative analysis | Monte Carlo simulation | Heuristic | Index Medicus | Life Sciences | Biochemistry, Molecular Biology
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