(Q40139517)

17 September 2017

Molecular simulation of protein-surface interactions: benefits, problems, solutions, and future directions (English)

1 reference

17 September 2017

Robert A Latour

1

1 reference

PMC publication ID

2756768

17 September 2017

language of work or name

1 reference

1 September 2008

1 reference

17 September 2017

1 reference

17 September 2017

3

1 reference

17 September 2017

3

1 reference

17 September 2017

FC2-12

1 reference

Determination of the adsorption free energy for peptide-surface interactions by SPR spectroscopy

17 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Towards improving compound selection in structure-based virtual screening

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Polymer nanoparticles covered with phosphorylcholine groups and immobilized with antibody for high-affinity separation of proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Combining experiment and simulation in protein folding: closing the gap for small model systems

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Characterization of nanoparticles for therapeutics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Molecular docking and analysis of interactions between vascular endothelial growth factor (VEGF) and SPARC protein

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Carbon nanotube/polysulfone screen-printed electrochemical immunosensor

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Parallel tempering molecular dynamics folding simulation of a signal peptide in explicit water

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Coarse-grained peptide modeling using a systematic multiscale approach

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Hydrophobic interaction and hydrogen-bond network for a methane pair in liquid water

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Insertion and assembly of membrane proteins via simulation.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Empirical force fields for biological macromolecules: overview and issues.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Recent advances in the development and application of implicit solvent models in biomolecule simulations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Magnetite-containing spherical silica nanoparticles for biocatalysis and bioseparations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Peptide folding simulations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Selection criteria for drug-like compounds

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Single framework recombinant antibody fragments designed for protein chip applications

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Principles of docking: An overview of search algorithms and a guide to scoring functions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Protein folding and unfolding at atomic resolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Generalized-ensemble algorithms for molecular simulations of biopolymers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Changes in a phospholipid bilayer induced by the hydrolysis of a phospholipase A2 enzyme: a molecular dynamics simulation study.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Generalized born models of macromolecular solvation effects

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

A solvent model for simulations of peptides in bilayers. II. Membrane-spanning alpha-helices.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Protein adsorption on solid surfaces

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Molecular dynamics simulations of peptide-surface interactions

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

All-atom level direct folding simulation of a betabetaalpha miniprotein.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Infrared optical immunosensor: application to the measurement of the herbicide atrazine.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Ab initio molecular dynamics of hydrogen dissociation on metal surfaces using neural networks and novelty sampling.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Docking study and free energy simulation of the complex between p53 DNA-binding domain and azurin.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Passivating protein coatings for implantable glucose sensors: evaluation of protein retention.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Temperature weighted histogram analysis method, replica exchange, and transition paths.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Methods for molecular dynamics simulations of protein folding/unfolding in solution

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Study of the electrostatics treatment in molecular dynamics simulations.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Simulations of protein folding and unfolding

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

The impact of protein flexibility on protein-protein docking

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756768

Exploring the energy landscape of a beta hairpin in explicit solvent

2 December 2018

1 reference

12 December 2020

Platelet adhesion to polystyrene-based surfaces preadsorbed with plasmas selectively depleted in fibrinogen, fibronectin, vitronectin, or von Willebrand's factor

1 reference

12 December 2020

Characterization of the TIP4P-Ew water model: vapor pressure and boiling point

1 reference

12 December 2020

Accurate evaluation of the absorption maxima of retinal proteins based on a hybrid QM/MM method

1 reference

12 December 2020

Comparison of implicit solvent models for the simulation of protein-surface interactions

1 reference

12 December 2020

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

1 reference

12 December 2020

Dimerisation of urea in water solution: a quantum mechanical investigation

1 reference

12 December 2020

Simulation of conformational changes occurring when a protein interacts with its receptor

1 reference

12 December 2020

Quantum effects in liquid water from an ab initio-based polarizable force field

1 reference

12 December 2020

Empirical bond-order potential for hydrocarbons: adaptive treatment of van der Waals interactions

1 reference

12 December 2020

Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery

1 reference

12 December 2020

An improved replica-exchange sampling method: temperature intervals with global energy reassignment

1 reference

12 December 2020

Computational study of the binding mode of epidermal growth factor receptor kinase inhibitors

1 reference

12 December 2020

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

1 reference

12 December 2020

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

1 reference

12 December 2020

Polarizable Force Fields: History, Test Cases, and Prospects

1 reference

12 December 2020

Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir

1 reference

12 December 2020

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

1 reference

12 December 2020

Principles of docking: An overview of search algorithms and a guide to scoring functions

1 reference

12 December 2020

Identifiers

DOI

10.1116/1.2965132

1 reference

17 September 2017

1 reference

PMC publication ID

2756768

17 September 2017

PubMed publication ID

19809597

1 reference

PMC publication ID

2756768