(Q44096745)

29 November 2017

Docking and scoring: applications to drug discovery in the interactomics era. (English)

1 reference

29 November 2017

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2

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29 November 2017

Solène Grosdidier

1

1 reference

PubMed ID

23489159

29 November 2017

language of work or name

English

0 references

publication date

1 June 2009

1 reference

Expert Opinion on Drug Discovery

29 November 2017

1 reference

29 November 2017

4

1 reference

29 November 2017

6

1 reference

29 November 2017

673-686

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Inhibition of protein-protein association by small molecules: approaches and progress

29 November 2017

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

What has virtual screening ever done for drug discovery?

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Reaching for high-hanging fruit in drug discovery at protein-protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes?

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Comparing protein-ligand docking programs is difficult.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Virtual screening of chemical libraries for drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Community benchmarks for virtual screening

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Modulation of protein-protein interactions with small organic molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Synthetic peptide GRGDS induces dissociation of alpha-actinin and vinculin from the sites of focal contacts

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Lipopeptides as dimerization inhibitors of HIV-1 protease

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Design of a peptide inhibitor that blocks the cell fusion mediated by glycoprotein 41 of human immunodeficiency virus type 1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

A beta-sheet peptide inhibitor of E47 dimerization and DNA binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of the CD8 DE loop as a surface functional epitope. Implications for major histocompatibility complex class I binding and CD8 inhibitor design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

The thumb domain of the P51-subunit is essential for activation of HIV reverse transcriptase

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Disruption of the HIV-1 protease dimer with interface peptides: structural studies using NMR spectroscopy combined with [2-(13)C]-Trp selective labeling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

PocketPicker: analysis of ligand binding-sites with shape descriptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Pocketome via comprehensive identification and classification of ligand binding envelopes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Fast prediction and visualization of protein binding pockets with PASS.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Prediction of protein-protein interactions by docking methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Flexible protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Recent Progress and Future Directions in Protein-Protein Docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

High-resolution protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Modelling protein docking using shape complementarity, electrostatics and biochemical information

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Docking unbound proteins using shape complementarity, desolvation, and electrostatics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

ZDOCK: an initial-stage protein-docking algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

A novel shape complementarity scoring function for protein‐protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Integrating statistical pair potentials into protein complex prediction.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

GRAMM-X public web server for protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

PatchDock and SymmDock: servers for rigid and symmetric docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Soft protein-protein docking in internal coordinates

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

HADDOCK: a protein-protein docking approach based on biochemical or biophysical information

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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%2F17460440903002067

ATTRACT: protein-protein docking in CAPRI using a reduced protein model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Successful discrimination of protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Using protein binding site prediction to improve protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Improved prediction of protein-protein binding sites using a support vector machines approach.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Prediction of protein interaction sites from sequence profile and residue neighbor list.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Protein binding site prediction using an empirical scoring function

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

ProMate: a structure based prediction program to identify the location of protein-protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Prediction-based fingerprints of protein-protein interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of protein-protein interaction sites from docking energy landscapes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Optimal docking area: a new method for predicting protein-protein interaction sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

PRISM: protein interactions by structural matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

PRISM: protein-protein interaction prediction by structural matching

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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%2F17460440903002067

A hot spot of binding energy in a hormone-receptor interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Anatomy of hot spots in protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Hot spots--a review of the protein-protein interface determinant amino-acid residues

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Unraveling hot spots in binding interfaces: progress and challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Fast transient cytokine-receptor interactions monitored in real time by reflectometric interference spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Rapid mapping of protein functional epitopes by combinatorial alanine scanning

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Site-directed ligand discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Spatial chemical conservation of hot spot interactions in protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

A simple physical model for binding energy hot spots in protein-protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of hot spot residues at protein-protein interface

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of hot-spot residues in protein-protein interactions by computational docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Protein-protein interaction hotspots carved into sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

The atomic structure of protein-protein recognition sites

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Hematopoietic receptor complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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%2F17460440903002067

Is allostery an intrinsic property of all dynamic proteins?

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Subtype-selective allosteric modulators of muscarinic receptors for the treatment of CNS disorders

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Allosteric modulators of GPCRs: a novel approach for the treatment of CNS disorders

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Small-molecule inhibition of TNF-alpha

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Inhibiting HIV-1 integrase by shifting its oligomerization equilibrium

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Simulation of the diffusional association of barnase and barstar.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Computer simulation of protein-protein association kinetics: acetylcholinesterase-fasciculin

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

On the protein-protein diffusional encounter complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

The courtship of proteins: understanding the encounter complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Visualization of transient encounter complexes in protein-protein association.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Cell biology: brief encounters bolster contacts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Hot-spot mimicry of a cytokine receptor by a small molecule

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

An inhibitor of Bcl-2 family proteins induces regression of solid tumours

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Allosteric Inhibition of the Protein-Protein Interaction between the Leukemia-Associated Proteins Runx1 and CBFβ

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Shape shifting leads to small-molecule allosteric drug discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of a specific inhibitor of the dishevelled PDZ domain

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Optimizing Dvl PDZ domain inhibitor by exploring chemical space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of tripeptides recognized by the PDZ domain of Dishevelled

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

The SH2 domain: versatile signaling module and pharmaceutical target

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Identification of novel fragment compounds targeted against the pY pocket of v-Src SH2 by computational and NMR screening and thermodynamic evaluation

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Flexible ligand docking using a genetic algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Gaussian docking functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Improved protein-ligand docking using GOLD

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

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%2F17460440903002067

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Computational alanine scanning mutagenesis--an improved methodological approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

Transient Pockets on Protein Surfaces Involved in Protein−Protein Interaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1517%2F17460440903002067

10.1517/17460440903002067

21 January 2018

Identifiers

DOI

1 reference

29 November 2017

1 reference

PubMed ID

23489159