(Q38737287)

6 September 2017

title

Estimation of kinetic and thermodynamic ligand-binding parameters using computational strategies (English)

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6 September 2017

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Giuseppe Deganutti

1

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Stefano Moro

object named as

Stefano Moro

series ordinal

2

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publication date

31 March 2017

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Future Medicinal Chemistry

6 September 2017

published in

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6 September 2017

volume

9

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6 September 2017

issue

5

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6 September 2017

page(s)

507-523

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Origin of life: The RNA world

6 September 2017

cites work

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

From "simple" DNA-protein interactions to the macromolecular machines of gene expression

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

How enzymes work: analysis by modern rate theory and computer simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Electrostatic aspects of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

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

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Why continuum electrostatics theories cannot explain biological structure, polyelectrolytes or ionic strength effects in ion-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Beyond induced-fit receptor-ligand interactions: structural changes that can significantly extend bond lifetimes

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Shielded hydrogen bonds as structural determinants of binding kinetics: application in drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Recent progress in understanding hydrophobic interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The maximal affinity of ligands

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Aromatic rings in chemical and biological recognition: energetics and structures

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Stacking with No Planarity?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Water as an active constituent in cell biology

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The role of water molecules in computational drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The Entropic Cost of Bound Water in Crystals and Biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Hydration Site Thermodynamics Explain SARs for Triazolylpurines Analogues Binding to the A2A Receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Water networks contribute to enthalpy/entropy compensation in protein-ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Profound methyl effects in drug discovery and a call for new C-H methylation reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Methyl effects on protein-ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Virtual ligand screening: strategies, perspectives and limitations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Utilising structural knowledge in drug design strategies: applications using Relibase.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Water, water, everywhere… It's time to stop and think

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Rapid and accurate prediction and scoring of water molecules in protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Sampling protein motion and solvent effect during ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Decoding the Role of Water Dynamics in Ligand-Protein Unbinding: CRF1R as a Test Case.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Optimization of potent DFG-in inhibitors of platelet derived growth factor receptorβ (PDGF-Rβ) guided by water thermodynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Pathway and mechanism of drug binding to G-protein-coupled receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Molecular determinants of drug-receptor binding kinetics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

From Levinthal to pathways to funnels

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Folding and binding cascades: dynamic landscapes and population shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Essential role of conformational selection in ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Conformational selection or induced fit: a flux description of reaction mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Conformational selection or induced fit? A critical appraisal of the kinetic mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Conformational entropy in molecular recognition by proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Designing peptide receptor agonists and antagonists

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Predicting bioactive conformations and binding modes of macrocycles.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The consequences of translational and rotational entropy lost by small molecules on binding to proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Calculating kinetics and pathways of protein-ligand association

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The drug-target residence time model: a 10-year retrospective

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Drug-target residence time and its implications for lead optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Can residence time offer a useful strategy to target agonist drugs for sustained GPCR responses?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Pharmacokinetics and the drug-target residence time concept

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Clozapine, atypical antipsychotics, and the benefits of fast-off D2 dopamine receptor antagonism

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Ligand binding assays at equilibrium: validation and interpretation

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The Activated Complex in Chemical Reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Spectral gap optimization of order parameters for sampling complex molecular systems

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Reaction coordinates and rates from transition paths

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

How wet should be the reaction coordinate for ligand unbinding?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Ligand Binding Thermodynamics in Drug Discovery: Still a Hot Tip?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Thermodynamics of ligand binding and efficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The pathway of ligand entry from the membrane bilayer to a lipid G protein-coupled receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Molecular Basis of Ligand Dissociation from the Adenosine A2A Receptor.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Drug-target residence time: critical information for lead optimization.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Ligand Residence Time at G-protein-Coupled Receptors-Why We Should Take Our Time To Study It.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Structure of haemoglobin: a three-dimensional Fourier synthesis at 5.5-A. resolution, obtained by X-ray analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Docking and scoring in virtual screening for drug discovery: methods and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Alchemical free energy methods for drug discovery: progress and challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

A combined QM/MM approach to protein--ligand interactions: polarization effects of the HIV-1 protease on selected high affinity inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the Lck SH2 domain

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Computational and experimental studies of the interaction between phospho-peptides and the C-terminal domain of BRCA1.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Impact, determination and prediction of drug-receptor residence times for GPCRs

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Multiscale methods for macromolecular simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Millisecond-scale molecular dynamics simulations on Anton

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Bridging molecular docking to membrane molecular dynamics to investigate GPCR-ligand recognition: the human A₂A adenosine receptor as a key study.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Combining docking and molecular dynamic simulations in drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

How many drug targets are there?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Markov state models of biomolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Everything you wanted to know about Markov State Models but were afraid to ask

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Deciphering the Complexity of Ligand-Protein Recognition Pathways Using Supervised Molecular Dynamics (SuMD) Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Towards the prediction of order parameters from molecular dynamics simulations in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Escaping free-energy minima

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Flexible docking in solution using metadynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Metadynamics with Adaptive Gaussians.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Funnel metadynamics as accurate binding free-energy method

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

From metadynamics to dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

A bias-exchange approach to protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Substrate binding mechanism of HIV-1 protease from explicit-solvent atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Steered molecular dynamics and mechanical functions of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Steered molecular dynamics simulation on the binding of NNRTI to HIV-1 RT.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Substrate binding process and mechanistic functioning of type 1 11β-hydroxysteroid dehydrogenase from enhanced sampling methods

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

The dynamics of ligand barrier crossing inside the acetylcholinesterase gorge

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Population based reweighting of scaled molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Molecular Dynamics Simulations and Kinetic Measurements to Estimate and Predict Protein-Ligand Residence Times.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Kinetics of protein-ligand unbinding via smoothed potential molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

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

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Accelerated molecular dynamics simulations of the octopamine receptor using GPUs: discovery of an alternate agonist-binding position.

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Replica-exchange molecular dynamics method for protein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

QM/MM Methods for Biological Systems

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

QM/MM: what have we learned, where are we, and where do we go from here?

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Exploring the recognition pathway at the human A2A adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Assessing the Accuracy of Metadynamics†

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

21 January 2018

1 reference

https://api.crossref.org/works/10.4155%2FFMC-2016-0224

21 January 2018

Identifiers

DOI

10.4155/FMC-2016-0224

1 reference

6 September 2017

1 reference