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1. 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
Computational protein design aims to create proteins with novel properties. A key element is the energy or scoring function used to select the sequences and... 
MONTE-CARLO | GENERALIZED BORN SOLVENT | SURFACE-AREA | COMPUTATIONAL DESIGN | SEARCH ALGORITHMS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | DEAD-END ELIMINATION | FORCE-FIELDS | STRUCTURE PREDICTION | MOLECULAR-MECHANICS | CONTINUUM ELECTROSTATICS | Proteins | Proteus | Sequences | Energy use | Energy | Crystallography | Electrostatics | Redesign | Molecular chains | Life Sciences | Molecular biology | Cellular Biology | Quantitative Methods | Biochemistry, Molecular Biology | Cancer
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2. 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
Computational protein design (CPD) aims at predicting new proteins or modifying existing ones. The computational challenge is huge as it requires exploring an... 
surface area | Generalized Born | energy decomposition | molecular mechanics | Protein design | IMPLICIT SOLVENT MODELS | DEAD-END ELIMINATION | CHEMISTRY, MULTIDISCIPLINARY | MOLECULAR-MECHANICS | DIELECTRIC MEDIUM | GENERALIZED BORN MODEL | AMINO-ACID-SEQUENCE | BACKBONE FLEXIBILITY | TRANSFER-RNA SYNTHETASE | SIDE-CHAIN CONFORMATIONS | CONTINUUM ELECTROSTATICS | Thermodynamics | Protein Conformation | Proteins - chemistry | Computational Biology | Proteins | Chemistry | Decomposition | Matrix | Energy | Dielectric properties | Computation | Design modifications | Compounds | Surface area | Index Medicus | Life Sciences | Biochemistry, Molecular Biology
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3. Cerebral ischemia
by Simonson, Ernst, 1898 and McGavack, Thomas Hodge, 1898 and Gerontological Society
1964, American lecture series, publication no. 563. A monograph in American lecture series in geriatrics and gerontology, 299
Cerebral ischemia
Book
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4. Dictionary of banking terms
by Fitch, Thomas P
2000, 4th ed., Barron's business guides, ISBN 9780764112607, ix, 529
Banks and banking
Book
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5. 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
The prediction of protein side chain conformations from backbone coordinates is an important task in structural biology, with applications in structure... 
surface area | Generalized Born | computational protein design | side chain placement | molecular mechanics | Molecular mechanics | Computational protein design | Side chain placement | Surface area | HYDRATION FREE-ENERGIES | STRUCTURAL ENSEMBLES | BIOCHEMISTRY & MOLECULAR BIOLOGY | DEAD-END ELIMINATION | DEPENDENT ROTAMER LIBRARY | MOLECULAR-MECHANICS | GENERALIZED BORN SOLVENT | BIOPHYSICS | TRANSFER-RNA SYNTHETASE | MEAN-FIELD THEORY | COMPUTATIONAL DESIGN | ACCURATE PREDICTION | 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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6. Full Text Protein p Ka'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, 2018, Volume 14, Issue 12, pp. 6714 - 6721
Protein acid/base constants, or p Ka's are often computed from Monte Carlo or molecular dynamics simulations at a series of constant pH values. Instead, we... 
Index Medicus
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7. Full Text Using CSF biomarkers to replicate genetic associations in Alzheimer's disease
by Schott, Jonathan M and ADNI Investigators
Neurobiology of Aging, ISSN 0197-4580, 2012, Volume 33, Issue 7, pp. 1486.e9 - 1486.e15
Abstract Defining cases and controls on the basis of biomarkers rather than clinical diagnosis may reduce sample sizes required for genetic studies. The aim of... 
Neurology | Internal Medicine | Alzheimer's disease | Genome wide association studies | Cerebrospinal fluid | IDENTIFIES VARIANTS | CR-1 | CLU | SIGNATURE | NEUROSCIENCES | GENOME-WIDE ASSOCIATION | PICALM | GERIATRICS & GERONTOLOGY | Peptide Fragments - cerebrospinal fluid | Humans | Genetic Association Studies - methods | Male | Alzheimer Disease - cerebrospinal fluid | Alzheimer Disease - diagnosis | Aged, 80 and over | Amyloid beta-Peptides - cerebrospinal fluid | Polymorphism, Single Nucleotide - genetics | Female | Aged | Biomarkers - cerebrospinal fluid | Alzheimer Disease - genetics | Longitudinal Studies | Cohort Studies | Index Medicus | Neuroimaging | Gene frequency | Neurodegenerative diseases | Tau protein | Apolipoprotein E | biomarkers | Aging | Nervous system | Single-nucleotide polymorphism | Genome Wide Association Studies
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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 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
Protein acid/base constants, or pKa’s are often computed from Monte Carlo or molecular dynamics simulations at a series of constant pH values. Instead, we... 
Proteins | Flattening | Computer simulation | Bias | Molecular dynamics | Protonation | Titration | Free energy
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10. Full Text Protein side chain conformation predictions with an MMGBSA energy function
: Side Chain Predictions with MMGBSA
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
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11. Full Text Electrostatics and dynamics of proteins
by Simonson, Thomas
Reports on Progress in Physics, ISSN 0034-4885, 05/2003, Volume 66, Issue 5, pp. 737 - 787
Proteins are the working chemists of living cells. They are complex macromolecules, which display a rich and sometimes counterintuitive behaviour on many... 
HOLE-BURNING SPECTROSCOPY | LIGHT-HARVESTING COMPLEXES | FINITE-ELEMENT SOLUTION | DIELECTRIC SOLVATION DYNAMICS | ENZYME ACTIVE-SITE | PHYSICS, MULTIDISCIPLINARY | VIBRATIONAL STARK SPECTROSCOPY | BIOLOGICAL ELECTRON-TRANSFER | PHOTOSYNTHETIC REACTION-CENTER | POISSON-BOLTZMANN EQUATION | FREE-ENERGY SIMULATIONS | Life Sciences | Biochemistry, Molecular Biology
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