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1. Full Text Improved Generalized Born Solvent Model Parameters for Protein Simulations
by Nguyen, Hai and Roe, Daniel R and Simmerling, Carlos
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2013, Volume 9, Issue 4, pp. 2020 - 2034
The generalized Born (GB) model is one of the fastest implicit solvent models, and it has become widely adopted for Molecular Dynamics (MD) simulations. This... 
GENETIC ALGORITHMS | CONFORMATIONAL ENSEMBLES | IMPLICIT SOLVATION | HEADPIECE HELICAL SUBDOMAIN | FREE-ENERGY LANDSCAPE | TRP-CAGE MINIPROTEIN | MECHANICS FORCE-FIELDS | RAY CRYSTAL-STRUCTURES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SECONDARY STRUCTURE BIAS | MOLECULAR-DYNAMICS SIMULATIONS | GBSA | Generalized Born | Implicit solvent | solvation energy | protein folding | perfect radii
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2. Full Text Generalized Born Implicit Solvent Models for Biomolecules
by Onufriev, Alexey V and Case, David A
Annual Review of Biophysics, ISSN 1936-122X, 5/2019, Volume 48, Issue 1, pp. 275 - 296
It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent... 
implicit solvation | biomolecular simulations | electrostatics | generalized Born | dielectric | ELECTROSTATIC INTERACTIONS | SOLVATION FREE-ENERGIES | NONPOLAR SOLVATION | NUCLEIC-ACIDS | BIOPHYSICS | CONTINUUM SOLVENT | PROTEIN TITRATION CURVES | DIELECTRIC POLARIZATION | CHARGE HYDRATION ASYMMETRY | MOLECULAR-DYNAMICS SIMULATIONS | MEMBRANE-PROTEINS | Molecular dynamics | Biotechnology | Models | Biochemistry | Analysis | bio-molecular simulations
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3. Full Text Effective Born radii in the generalized Born approximation: The importance of being perfect
by Onufriev, Alexey and Case, David A and Bashford, Donald
Journal of Computational Chemistry, ISSN 0192-8651, 11/2002, Volume 23, Issue 14, pp. 1297 - 1304
Generalized Born (GB) models provide, for many applications, an accurate and computationally facile estimate of the electrostatic contribution to aqueous... 
macromolecules | Poisson equation | effective Born radii | molecular dynamics | generalized Born approximation | Generalized Born approximation | Molecular dynamics | Effective Born radii | Macromolecules | MOLECULAR-DYNAMICS | SOLVATION MODELS | FREE-ENERGIES | CHEMISTRY, MULTIDISCIPLINARY | NUCLEIC-ACIDS | DYNAMICS SIMULATIONS | ELECTROSTATICS | PROTEINS | Thermodynamics | Models, Chemical | Molecular Conformation | Myoglobin - chemistry | Static Electricity | Mathematical Computing | Macromolecular Substances
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4. Full Text Exploring protein native states and large‐scale conformational changes with a modified generalized born model
by Onufriev, Alexey and Bashford, Donald and Case, David A
Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, 05/2004, Volume 55, Issue 2, pp. 383 - 394
Implicit solvation models provide, for many applications, a reasonably accurate and computationally effective way to describe the electrostatics of aqueous... 
macromolecules | Generalized Born approximation | molecular dynamics | Molecular dynamics | Macromolecules | MOLECULAR-DYNAMICS | BIOCHEMISTRY & MOLECULAR BIOLOGY | ENERGETICS | FREE-ENERGIES | generalized Born approximation | NUCLEIC-ACIDS | SOLVENT MODELS | GENETICS & HEREDITY | SOLVATION ENERGIES | SIMULATIONS | ELECTROSTATICS | POISSON-BOLTZMANN EQUATION | Ribonucleases - chemistry | Solvents - chemistry | Ubiquitin - chemistry | Models, Molecular | Static Electricity | Protein Folding | Ribonucleases - metabolism | Bacterial Proteins | Staphylococcal Protein A - chemistry | Thermodynamics | Proteins - metabolism | Computer Simulation | Poisson Distribution | Protein Conformation | Software | Proteins - chemistry | Thioredoxins - chemistry
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5. Full Text An approximate inverse to the extended Born modeling operator
by Hou, Jie and Symes, William W
Geophysics, ISSN 0016-8033, 09/2015, Volume 80, Issue 6, pp. R331 - R349
Given a correct (data-consistent) velocity model, reverse time migration (RTM) correctly positions reflectors but generally with incorrect amplitudes and... 
VELOCITY ANALYSIS | ONE-WAY | GEOCHEMISTRY & GEOPHYSICS | DOMAIN | 3D ANGLE GATHERS | REVERSE-TIME MIGRATION | GENERALIZED RADON-TRANSFORM | WAVE-FORM INVERSION | GRADIENT | Operators | Approximation | Amplitudes | Migration | Inversions | Ray tracing | Modelling | Offsets
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6. Full Text Heterogeneous dielectric generalized Born model with a van der Waals term provides improved association energetics of membrane‐embedded transmembrane helices
by Dutagaci, Bercem and Sayadi, Maryam and Feig, Michael
Journal of Computational Chemistry, ISSN 0192-8651, 06/2017, Volume 38, Issue 16, pp. 1308 - 1320
The heterogeneous dielectric generalized Born (HDGB) implicit membrane formalism is extended by the addition of a van der Waals dispersion term to better... 
transmembrane helix dimers | generalized Born formalism | implicit membrane model | HYDRATION FREE-ENERGY | ADDITIVE FORCE-FIELD | ACID SIDE-CHAINS | IMPLICIT SOLVENT MODEL | CHEMISTRY, MULTIDISCIPLINARY | HYDROPHOBIC MISMATCH | LIPID-BILAYERS | COMPUTER-SIMULATIONS | MOLECULAR-DYNAMICS SIMULATIONS | POISSON-BOLTZMANN EQUATION | SIMPLE COMPUTATIONAL MODEL | Implicit membrane model
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7. Full Text Born Pupils? Natural Pedagogy and Cultural Pedagogy
by Heyes, Cecilia
Perspectives on Psychological Science, ISSN 1745-6916, 3/2016, Volume 11, Issue 2, pp. 280 - 295
The theory of natural pedagogy is an important focus of research on the evolution and development of cultural learning. It proposes that we are born pupils;... 
imitation | pedagogy | evolution of cognition | teaching | cultural evolution | infant development | SOCIAL CUES | INFANT-DIRECTED SPEECH | FACE RECOGNITION | 1ST YEAR | COMMUNICATIVE SIGNALS | GENERALIZED IMITATION | PSYCHOLOGY, MULTIDISCIPLINARY | AUDITORY PREFERENCES | EYE CONTACT | RATIONAL IMITATION | YOUNG-CHILDREN | Biological Evolution | Learning | Imitative Behavior | Students | Eye Movements | Humans | Models, Psychological | Infant | Culture | Cognitive change | Sociocultural factors | Contingencies | Eye contact | Inheritance | Social learning | Teaching | Pedagogy | Eye fixation | Social bonding | Cuing | Imitation | Speech | Receptivity
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8. Full Text Constant pH molecular dynamics in generalized Born implicit solvent
by Mongan, John and Case, David A and McCammon, J. Andrew
Journal of Computational Chemistry, ISSN 0192-8651, 12/2004, Volume 25, Issue 16, pp. 2038 - 2048
A new method is proposed for constant pH molecular dynamics (MD), employing generalized Born (GB) electrostatics. Protonation states are modeled with different... 
pKa prediction | lysozyme | Monte Carlo | constant pH molecular dynamics | generalized Born | Constant pH molecular dynamics | Generalized Born | Lysozyme | APPROXIMATION | CONFORMATIONAL FLEXIBILITY | MODEL | CALCULATING PK(A)S | SIMULATION | CHEMISTRY, MULTIDISCIPLINARY | CONSISTENT | PROTEIN STRUCTURES | TITRATION | ENERGIES | EXPLICIT | Solvents | Thermodynamics | Algorithms | Muramidase - chemistry | Models, Molecular | Monte Carlo Method | Hydrogen-Ion Concentration
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9. Full Text Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
by Hou, Tingjun and Wang, Junmei and Li, Youyong and Wang, Wei
Journal of Computational Chemistry, ISSN 0192-8651, 04/2011, Volume 32, Issue 5, pp. 866 - 877
In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high‐throughput screenings. Most scoring functions... 
molecular docking | MM/GBSA | Poisson Boltzmann | generalized Born | binding free energy | MM/PBSA | DRUG DISCOVERY | EMPIRICAL SCORING FUNCTIONS | ATOMIC CHARGES | FREE-ENERGIES | CHEMISTRY, MULTIDISCIPLINARY | DIELECTRIC MEDIUM | BINDING-AFFINITY | FORCE-FIELD | PROTEIN-LIGAND INTERACTIONS | SH3 DOMAIN | RAS-RAF | Thermodynamics | Catalytic Domain | Surface Properties | Models, Molecular | Ligands | Proteins - chemistry | Molecular Dynamics Simulation
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10. Full Text Explicit ions/implicit water generalized Born model for nucleic acids
by Tolokh, Igor S and Thomas, Dennis G and Onufriev, Alexey V and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
The Journal of Chemical Physics, ISSN 0021-9606, 05/2018, Volume 148, Issue 19, p. 195101
The ion atmosphere around highly charged nucleic acid molecules plays a significant role in their dynamics, structure, and interactions. Here we utilized the... 
HYDRATION FREE-ENERGIES | MOLECULAR-DYNAMICS | IMPLICIT SOLVATION | ELECTROSTATICS CALCULATIONS | SMOOTH DIELECTRIC FUNCTION | HISTONE TAILS | MEAN-FORCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | ENTHALPY-ENTROPY | ION INTERACTIONS | SOLVENT MODEL | DNA - chemistry | Ions - chemistry | Sodium - chemistry | Solvents - chemistry | Water - chemistry | Chlorides - chemistry | RNA - chemistry | Monte Carlo Method | Molecular Dynamics Simulation | Binding | Fluid dynamics | Computer simulation | Thymine | Ion pairs | Molecular dynamics | Dielectrics | Nucleic acids | Condensation | Simulation | Ribonucleic acids | Trivalent ions | Physical simulation | DNA methylation | Methylation | Deoxyribonucleic acid--DNA | explicit ion model | generalized born | nucleic acids | implicit water model | ARTICLES
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11. Full Text Comparing pairwise‐additive and many‐body generalized Born models for acid/base calculations and protein design
by Villa, Francesco and Mignon, David and Polydorides, Savvas and Simonson, Thomas
Journal of Computational Chemistry, ISSN 0192-8651, 10/2017, Volume 38, Issue 28, pp. 2396 - 2410
Generalized Born (GB) solvent models are common in acid/base calculations and protein design. With GB, the interaction between a pair of solute atoms depends... 
generalized Born model | Proteus program | molecular mechanics | implicit solvent | protein electrostatics | PK(A) VALUES | PH MOLECULAR-DYNAMICS | CONSTANT-PH | IMPLICIT SOLVENT MODELS | FREE-ENERGIES | CHEMISTRY, MULTIDISCIPLINARY | TRANSFER-RNA SYNTHETASE | PDZ DOMAINS | CONTINUUM ELECTROSTATIC MODEL | STAPHYLOCOCCAL NUCLEASE | POISSON-BOLTZMANN EQUATION | Models, Chemical | Acids - chemistry | Protein Unfolding | Solvents - chemistry | Humans | Static Electricity | Thermodynamics | Hemoglobins - chemistry | Algorithms | Alkalies - chemistry | Animals | Databases, Protein | PDZ Domains | Proteins - chemistry | Monte Carlo Method | Proteins | Monte Carlo method | Analysis | Life Sciences | Molecular biology | Cellular Biology | Quantitative Methods | Biochemistry, Molecular Biology | Cancer
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