(Q36627431)

15 August 2017

1 reference

title

Modeling electrostatic effects in proteins (English)

1 reference

15 August 2017

1

Arieh Warshel

1 reference

15 August 2017

Pankaz K Sharma

2

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15 August 2017

Mitsunori Kato

series ordinal

3

1 reference

15 August 2017

William W Parson

series ordinal

4

1 reference

15 August 2017

language of work or name

English

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publication date

25 August 2006

1 reference

Biochimica et Biophysica Acta

15 August 2017

published in

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15 August 2017

volume

1764

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15 August 2017

issue

11

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15 August 2017

page(s)

1647-1676

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Optimized Monte Carlo data analysis

15 August 2017

cites work

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Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

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On the energetics of conformational changes and pH dependent redox behaviour of electron transfer proteins

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Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin

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Electrostatic Energy and Macromolecular Function

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High yield of M-side electron transfer in mutants of Rhodobacter capsulatus reaction centers lacking the L-side bacteriopheophytin

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Semianalytical treatment of solvation for molecular mechanics and dynamics

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Quantum Mechanical Dynamical Effects in an Enzyme-Catalyzed Proton Transfer Reaction

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Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

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11 October 2022

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Computer simulation of the triosephosphate isomerase catalyzed reaction

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11 October 2022

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The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design?

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11 October 2022

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Electrostatic interactions in macromolecules: theory and applications

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How important are entropic contributions to enzyme catalysis?

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Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

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Computer modelling of enzyme catalysed reaction mechanisms.

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Absolute comparison of simulated and experimental protein-folding dynamics

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Impact of distal mutations on the network of coupled motions correlated to hydride transfer in dihydrofolate reductase

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11 October 2022

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Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase

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11 October 2022

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Electrostatic effects in macromolecules: fundamental concepts and practical modeling

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11 October 2022

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Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Realistic simulations of proton transport along the gramicidin channel: demonstrating the importance of solvation effects

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Molecular dynamics effects on protein electrostatics

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The catalytic power of ketosteroid isomerase investigated by computer simulation

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Generalized born models of macromolecular solvation effects

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the Ewald artifacts in computer simulations. The test-case of the octaalanine peptide with charged termini

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Why ion pair reversal by protein engineering is unlikely to succeed

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Effects of Nonpolar Environments on the Redox Potentials of Heme Complexes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

What about protein polarity?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Buried, charged, non-ion-paired aspartic acid 76 contributes favorably to the conformational stability of ribonuclease T1

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Voltage-gated proton channels and other proton transfer pathways

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Internal and interfacial dielectric properties of cytochrome c from molecular dynamics in aqueous solution

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Characterization of cspB, a Bacillus subtilis inducible cold shock gene affecting cell viability at low temperatures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Microscopic formulation of Marcus’ theory of electron transfer

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Studies of proton translocations in biological systems: simulating proton transport in carbonic anhydrase by EVB-based models

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Conformational substates modulate hydride transfer in dihydrofolate reductase.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Alternative view of enzyme reactions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Direct evidence for the exploitation of an alpha-helix in the catalytic mechanism of triosephosphate isomerase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic effects in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The Mechanism of Proton Exclusion in the Aquaporin-1 Water Channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Free Energy of Ionic Hydration

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Effective Born radii in the generalized Born approximation: the importance of being perfect

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Charge stabilization mechanism in the visual and purple membrane pigments

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Nonequilibrium Equality for Free Energy Differences

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The statistical-thermodynamic basis for computation of binding affinities: a critical review

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

What are the roles of substrate-assisted catalysis and proximity effects in peptide bond formation by the ribosome?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Why does the Ras switch "break" by oncogenic mutations?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Dielectric properties of proteins from simulation: the effects of solvent, ligands, pH, and temperature

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Water and ion permeation in bAQP1 and GlpF channels: a kinetic Monte Carlo study

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

What are the dielectric "constants" of proteins and how to validate electrostatic models?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

How optimal are the binding energetics of barnase and barstar?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

High apparent dielectric constants in the interior of a protein reflect water penetration

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatics of nanosystems: application to microtubules and the ribosome

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A simple physical model for binding energy hot spots in protein-protein complexes

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Experimental pK(a) values of buried residues: analysis with continuum methods and role of water penetration

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Progress in modeling of protein structures and interactions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Dipoles localized at helix termini of proteins stabilize charges

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Improved side-chain modeling for protein-protein docking

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computer simulation of protein folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A computational study of ion binding and protonation states in the KcsA potassium channel.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Comparative study of generalized Born models: protein dynamics

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Ions and blockers in potassium channels: insights from free energy simulations.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Probing protein electrostatics with a synthetic fluorescent amino acid.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Using a charging coordinate in studies of ionization induced partial unfolding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Exploring the origin of the ion selectivity of the KcsA potassium channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Modeling of protein conformational fluctuations in pKa predictions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electric fields at the active site of an enzyme: direct comparison of experiment with theory.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Control of reduction potential by protein matrix: lesson from a spherical protein model

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic interactions in an integral membrane protein

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Are unit charges always negligible?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Increasing protein stability by altering long-range coulombic interactions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Molecular dynamics studies of a DNA‐binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Are acidic and basic groups in buried proteins predicted to be ionized?

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculated protein and proton motions coupled to electron transfer: electron transfer from QA- to QB in bacterial photosynthetic reaction centers.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic Tuning of Permeation and Selectivity in Aquaporin Water Channels

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic models for computing protonation and redox equilibria in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the calculation of electrostatic interactions in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic origin of the catalytic power of enzymes and the role of preorganized active sites

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Intrinsic pKas of ionizable residues in proteins: an explicit solvent calculation for lysozyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulations of ion current in realistic models of ion channels: the KcsA potassium channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the origin of the electrostatic barrier for proton transport in aquaporin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Roles of electrostatic interaction in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The mechanism of proton exclusion in aquaporin channels

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Molecular dynamics study of the KcsA potassium channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structure and function of channels and channelogs as studied by computational chemistry

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The impact of protein flexibility on protein-protein docking

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Probing ion-channel pores one proton at a time

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Energetics of charge-charge interactions in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Through the channel and around the channel: Validating and comparing microscopic approaches for the evaluation of free energy profiles for ion penetration through ion channels

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Control of the redox potential of cytochrome c and microscopic dielectric effects in proteins.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The modelling of electrostatic interactions in the function of globular proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the calculation of pKas in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The barrier for proton transport in aquaporins as a challenge for electrostatic models: the role of protein relaxation in mutational calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Characterization of the denaturation of human alpha-lactalbumin in urea by molecular dynamics simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structure of bovine mitochondrial F(1)-ATPase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The 2.2 A crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Theoretical Studies of Protein Folding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Experimental measurement of the effective dielectric in the hydrophobic core of a protein.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Small Molecule Docking and Scoring

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11 October 2022

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Electrostatic contributions to the stability of hyperthermophilic proteins.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Protein disk of tobacco mosaic virus at 2.8 Å resolution showing the interactions within and between subunits

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Relationship between ion pair geometries and electrostatic strengths in proteins

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computer simulations with explicit solvent: recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Microscopic theory of the dielectric properties of proteins

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Comparative study of generalized born models: Born radii and peptide folding

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

How do serine proteases really work?

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Prediction of pH-dependent properties of proteins

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Protein Control of Redox Potentials of Ironminus signSulfur Proteins

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

How does GAP catalyze the GTPase reaction of Ras? A computer simulation study

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computer simulation and analysis of the reaction pathway of triosephosphate isomerase

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

General parameterized SCF model for free energies of solvation in aqueous solution

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computer simulation studies of the fidelity of DNA polymerases

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase

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11 October 2022

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Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The dielectric constant of a folded protein

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structural determinants of water permeation through aquaporin-1

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computer simulations of enzyme catalysis: methods, progress, and insights

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

COMPUTING: Screen Savers of the World Unite!

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structural distribution of stability in a thermophilic enzyme

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Classical electrostatics in biology and chemistry

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11 October 2022

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Mechanisms of thiamine-catalyzed reactions. Decarboxylation of 2-(1-carboxy-l-hydroxyethyl)-3,4-dimethylthiazolium chloride

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A theoretical model for the effects of local nonpolar heme environments on the redox potentials in cytochromes

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Energetics of enzyme catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The pore helix dipole has a minor role in inward rectifier channel function

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulations of apo and holo-fatty acid binding protein: structure and dynamics of protein, ligand and internal water.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Dominant forces in protein folding

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Control of the selectivity of the aquaporin water channel family by global orientational tuning

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the calculation of absolute macromolecular binding free energies

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The Grotthuss mechanism

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Absolute and relative entropies from computer simulation with applications to ligand binding

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Comparing atomistic simulation data with the NMR experiment: how much can NOEs actually tell us?

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Continuum electrostatic analysis of irregular ionization and proton allocation in proteins

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

An electrostatic basis for the stability of thermophilic proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structural origins of redox potentials in Fe-S proteins: electrostatic potentials of crystal structures

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic contributions to T4 lysozyme stability: solvent-exposed charges versus semi-buried salt bridges

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Entropy calculations on a reversibly folding peptide: changes in solute free energy cannot explain folding behavior.

1 reference

11 October 2022

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AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulation of charge-mutant acetylcholinesterases

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The alpha-helix dipole and the properties of proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Probing the effect of point mutations at protein-protein interfaces with free energy calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins.

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Improving macromolecular electrostatics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Tuning heme redox potentials in the cytochrome C subunit of photosynthetic reaction centers.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Docking and electron transfer studies between rubredoxin and rubredoxin:oxygen oxidoreductase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structural determinants of proton blockage in aquaporins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Identification of residues contributing to the Bohr effect of human haemoglobin

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Calculations of electrostatic interactions in biological systems and in solutions

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Ion channels, permeation, and electrostatics: insight into the function of KcsA.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The Mechanisms of Hydrolysis of Glycosides and Their Revelance to Enzyme-Catalysed Reactions

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Conservation of polar residues as hot spots at protein interfaces

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the use of different dielectric constants for computing individual and pairwise terms in poisson-boltzmann studies of protein ionization equilibrium

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The dynamics and energetics of water permeation and proton exclusion in aquaporins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Reorganization energy of the initial electron-transfer step in photosynthetic bacterial reaction centers

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Aquaporin water channels: molecular mechanisms for human diseases

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions†

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Structural basis of water-specific transport through the AQP1 water channel

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic orientation during electron transfer between flavodoxin and cytochrome c

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Energetic optimization of ion conduction rate by the K+ selectivity filter

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Protein-protein docking of electron transfer complexes: Cytochromecoxidase and cytochromec

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Solvation, reorganization energy, and biological catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Ion permeation mechanism of the potassium channel

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

The contribution of electrostatic and van der Waals interactions to the stereospecificity of the reaction catalyzed by lactate dehydrogenase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

A new method for predicting binding affinity in computer-aided drug design

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11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Free energy calculations and ligand binding

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Dynamics of biochemical and biophysical reactions: insight from computer simulations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic control of GTP and GDP binding in the oncoprotein p21ras

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic control of charge separation in bacterial photosynthesis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Climatic impact of tropical lowland deforestation on nearby montane cloud forests

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

On the role of the active site helix in papain, an AB initio molecular orbital study

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Computational, pulse-radiolytic, and structural investigations of lysine-136 and its role in the electrostatic triad of human Cu,Zn superoxide dismutase

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Electrostatic basis for enzyme catalysis

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Do salt bridges stabilize proteins? A continuum electrostatic analysis.

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.BBAPAP.2006.08.007

Identifiers

DOI

10.1016/J.BBAPAP.2006.08.007

1 reference

15 August 2017

1 reference