Tackling the challenges posed by target flexibility in drug design (Q30419540)

21 June 2017

Tackling the challenges posed by target flexibility in drug design (English)

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21 June 2017

2

Martin Zacharias

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21 June 2017

Christian Beier

1

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PubMed ID

22823087

21 June 2017

language of work or name

English

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publication date

1 April 2010

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Expert Opinion on Drug Discovery

21 June 2017

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21 June 2017

5

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21 June 2017

4

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21 June 2017

347-359

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Protein structure prediction and structural genomics

21 June 2017

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https://api.crossref.org/works/10.1517%2F17460441003713462

Modelling mutations and homologous proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

970 Million Druglike Small Molecules for Virtual Screening in the Chemical Universe Database GDB-13

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Managing protein flexibility in docking and its applications

21 January 2018

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https://api.crossref.org/works/10.1517%2F17460441003713462

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Structure and function of Rubisco

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Temperature-dependent equilibrium between the open and closed conformation of the p66 subunit of HIV-1 reverse transcriptase revealed by site-directed spin labelling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Mechanism of inhibition of HIV-1 reverse transcriptase by non-nucleoside inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Small-angle X-ray scattering from RNA, proteins, and protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

A structure-based simulation approach for electron paramagnetic resonance spectra using molecular and stochastic dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Identifying conformational changes with site-directed spin labeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Determination of protein-ligand binding modes using complexation-induced changes in (1)h NMR chemical shift.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Inter- and intra-molecular distances determined by EPR spectroscopy and site-directed spin labeling reveal protein-protein and protein-oligonucleotide interaction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Confocal FRET microscopy to measure clustering of ligand-receptor complexes in endocytic membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Pocketome via comprehensive identification and classification of ligand binding envelopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

On the nature of cavities on protein surfaces: application to the identification of drug-binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Binding site detection and druggability index from first principles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

An improved hydrogen bond potential: impact on medium resolution protein structures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Automated docking screens: a feasibility study

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Molecular recognition and docking algorithms

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Molecular docking to ensembles of protein structures

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Automatic generation of 3D-atomic coordinates for organic molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

A fast and efficient method to generate biologically relevant conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Automated docking of substrates to proteins by simulated annealing

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

SODOCK: swarm optimization for highly flexible protein-ligand docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Docking flexible ligands to macromolecular receptors by molecular shape

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Recent developments in fragment-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Fragment-based drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Protein-ligand docking: current status and future challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Development and testing of a general amber force field

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Automatic atom type and bond type perception in molecular mechanical calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

An improved method to predict the entropy term with the MM/PBSA approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

21 January 2018

Implicit solvent models

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Refinement of the primary hydration shell model for molecular dynamics simulations of large proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Molecular dynamics and free energy studies on the wild-type and mutated HIV-1 protease complexed with four approved drugs: mechanism of binding and drug resistance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Improved sampling methods for molecular simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Flexible protein-flexible ligand docking with disrupted velocity simulated annealing.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

M-score: a knowledge-based potential scoring function accounting for protein atom mobility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Protein-protein docking with a reduced protein model accounting for side-chain flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

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/10.1517%2F17460441003713462

Side-chain conformational space analysis (SCSA): a multi conformation-based QSAR approach for modeling and prediction of protein-peptide binding affinities

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Prediction of the binding sites of huperzine A in acetylcholinesterase by docking studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Essential dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Geometry-based sampling of conformational transitions in proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

What induces pocket openings on protein surface patches involved in protein-protein interactions?

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Analysis of domain motions by approximate normal mode calculations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Fully flexible low-mode docking: application to induced fit in HIV integrase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Association of putative concave protein-binding sites with the fluctuation behavior of residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

A method for biomolecular structural recognition and docking allowing conformational flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

FlexProt: alignment of flexible protein structures without a predefinition of hinge regions

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Flexibility of prolyl oligopeptidase: molecular dynamics and molecular framework analysis of the potential substrate pathways.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Protein flexibility predictions using graph theory

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Flexible ligand docking to multiple receptor conformations: a practical alternative

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

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/10.1517%2F17460441003713462

Improved prediction of protein side-chain conformations with SCWRL4

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

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/10.1517%2F17460441003713462

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

DOCK 6: combining techniques to model RNA-small molecule complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

FlexE: efficient molecular docking considering protein structure variations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Gaussian docking functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Novel procedure for modeling ligand/receptor induced fit effects.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

QXP: powerful, rapid computer algorithms for structure-based drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody Fab fragment at 2.8 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Structure of unliganded HIV-1 reverse transcriptase at 2.7 A resolution: implications of conformational changes for polymerization and inhibition mechanisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460441003713462

10.1517/17460441003713462

21 January 2018

Identifiers

DOI

1 reference

21 June 2017

1 reference

PubMed ID

22823087