pH replica-exchange method based on discrete protonation states (Q28728601)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

CHARMM: the biomolecular simulation program

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

The Amber biomolecular simulation programs

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Solution structure of cardiotoxin V from Naja naja atra

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Canonical dynamics: Equilibrium phase-space distributions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Very fast empirical prediction and rationalization of protein pKa values

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Predicting pKa values with continuous constant pH molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Conformational consequences of ionization of Lys, Asp, and Glu buried at position 66 in staphylococcal nuclease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Adaptations of proteins to cellular and subcellular pH

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Open science grid study of the coupling between conformation and water content in the interior of a protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Toward the accurate first-principles prediction of ionization equilibria in proteins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Coarse-grained normal mode analysis in structural biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Constant pH molecular dynamics with proton tautomerism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Biomolecular simulations at constant pH.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Normal-modes-based prediction of protein conformational changes guided by distance constraints

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Stabilization of internal charges in a protein: water penetration or conformational change?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Escaping free-energy minima

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Generalized-ensemble algorithms for molecular simulations of biopolymers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Molecular dynamics study of unbinding of the avidin-biotin complex

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Conformational change and inactivation of membrane phospholipid-related activity of cardiotoxin V from Taiwan cobra venom at acidic pH.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Comparison of the accuracy of protein solution structures derived from conventional and network-edited NOESY data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Prediction of pH-dependent properties of proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

pH, ionic strength, and temperature dependences of ionization equilibria for the carboxyl groups in turkey ovomucoid third domain.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3373023

Constant pH molecular dynamics in generalized Born implicit solvent

3 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Charges in the hydrophobic interior of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

The determinants of pKas in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Predicting slow structural transitions in macromolecular systems: Conformational flooding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Theoretical studies of transition states by the multioverlap molecular dynamics methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Effective sampling in the configurational space of a small peptide by the multicanonical-multioverlap algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Equation of State Calculations by Fast Computing Machines

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

NOTES ON BIAS IN ESTIMATION

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Theoretical and experimental analysis of ionization equilibria in ovomucoid third domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

Generalized-ensemble algorithms for molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.23176

The role of acidic amino acid residues in the structural stability of snake cardiotoxins

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22002801

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22002801

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22002801