(Q38428430)

3 September 2017

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title

Protein Flexibility in Drug Discovery: From Theory to Computation (English)

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3 September 2017

main subject

computational biology

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Matteo Masetti

3

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author name string

Rosa Buonfiglio

series ordinal

1

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3 September 2017

Maurizio Recanatini

series ordinal

2

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3 September 2017

publication date

17 April 2015

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3 September 2017

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3 September 2017

volume

10

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3 September 2017

issue

7

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3 September 2017

page(s)

1141-1148

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Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

3 September 2017

cites work

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Perspective: Alchemical free energy calculations for drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Implicit solvent methods for free energy estimation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Exploring the role of receptor flexibility in structure-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Einfluss der Configuration auf die Wirkung der Enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Essential role of conformational selection in ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

The Key–Lock Theory and the Induced Fit Theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Conformational substates in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

The dynamic energy landscape of dihydrofolate reductase catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Enzymatic detoxication, conformational selection, and the role of molten globule active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Distinct States of Methionyl-tRNA Synthetase Indicate Inhibitor Binding by Conformational Selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Large conformational changes in proteins: signaling and other functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Protein folding: binding of conformationally fluctuating building blocks via population selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

The role of dynamic conformational ensembles in biomolecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Folding and binding cascades: dynamic landscapes and population shifts

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

The Energy Landscapes and Motions of Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Contacting the protein folding funnel with NMR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Protein conformational substates from X-ray crystallography

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Implications of protein flexibility for drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Molecular mechanics and dynamics: numerical tools to sample the configuration space

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

"Soft docking": matching of molecular surface cubes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Soft docking and multiple receptor conformations in virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Novel procedure for modeling ligand/receptor induced fit effects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Rosetta Ligand docking with flexible XML protocols

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Incorporating protein flexibility into docking and structure-based drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Unveiling the full potential of flexible receptor docking using multiple crystallographic structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Recipes for the selection of experimental protein conformations for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Molecular docking to ensembles of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

FlexE: efficient molecular docking considering protein structure variations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Significant enhancement of docking sensitivity using implicit ligand sampling

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Utilizing experimental data for reducing ensemble size in flexible-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Protein flexibility and drug design: how to hit a moving target.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Developing a dynamic pharmacophore model for HIV-1 integrase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Representing receptor flexibility in ligand docking through relevant normal modes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

ALiBERO: evolving a team of complementary pocket conformations rather than a single leader

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Protein flexibility in ligand docking and virtual screening to protein kinases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Complementarity of Structure Ensembles in Protein-Protein Binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Conformational selection of syn -cAMP upon binding to the cAMP receptor protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

On the Role of the Crystal Environment in Determining Protein Side-chain Conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Collecting and assessing human lactate dehydrogenase-A conformations for structure-based virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

Synergistic folding of two intrinsically disordered proteins: searching for conformational selection

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

The use of saturation transfer NMR experiments to monitor the conformational selection accompanying ligand-protein interactions

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

Statistical thermodynamic linkage between conformational and binding equilibria.

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https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

Use of an induced fit receptor structure in virtual screening

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https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

Chapter 11. Enhanced Sampling Methods in Drug Design

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https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to Ligand Docking

1 reference

https://api.crossref.org/works/10.1002%2FCMDC.201500086

7 January 2021

Identifiers

DOI

10.1002/CMDC.201500086

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3 September 2017

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