(Q37036966)

17 August 2017

Induced fit docking, and the use of QM/MM methods in docking (English)

1 reference

17 August 2017

Mengang Xu

1

1 reference

PMC publication ID

3719877

17 August 2017

Markus A Lill

series ordinal

2

1 reference

17 August 2017

1 September 2013

1 reference

Drug discovery today. Technologies

17 August 2017

1 reference

17 August 2017

10

1 reference

17 August 2017

3

1 reference

17 August 2017

e411-8

1 reference

Tackling the challenges posed by target flexibility in drug design

17 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Potential and limitations of ensemble docking

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

On the applicability of elastic network normal modes in small-molecule docking

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

CSAR benchmark exercise of 2010: combined evaluation across all submitted scoring functions.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Efficient incorporation of protein flexibility and dynamics into molecular docking simulations

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Systematic exploitation of multiple receptor conformations for virtual ligand screening

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Significant enhancement of docking sensitivity using implicit ligand sampling

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Accommodating protein flexibility for structure-based drug design

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Accounting for induced-fit effects in docking: what is possible and what is not?

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

High-throughput virtual screening using quantum mechanical probes: discovery of selective kinase inhibitors

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Quantum mechanical pairwise decomposition analysis of protein kinase B inhibitors: validating a new tool for guiding drug design

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Managing protein flexibility in docking and its applications

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Flexible ligand docking to multiple receptor conformations: a practical alternative

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Conformational flexibility models for the receptor in structure based drug design.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Ligand Affinities Estimated by Quantum Chemical Calculations

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Efficient inclusion of receptor flexibility in grid-based protein-ligand docking.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Role of the key mutation in the selective binding of avian and human influenza hemagglutinin to sialosides revealed by quantum-mechanical calculations

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Flexible ligand recognition of peroxisome proliferator-activated receptor-gamma (PPARgamma).

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Interactions between 1alpha,25(OH)2D3 and residues in the ligand-binding pocket of the vitamin D receptor: a correlated fragment molecular orbital study

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Assessment of QM/MM scoring functions for molecular docking to HIV-1 protease.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Is quantum mechanics necessary for predicting binding free energy?

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

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

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in CytochromecPeroxidase

4 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands

4 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3719877

Accuracy of typical approximations in classical models of intermolecular polarization

4 December 2018

1 reference

12 December 2020

A QM/MM study of the binding of RAPTA ligands to cathepsin B

1 reference

12 December 2020

CSAR scoring challenge reveals the need for new concepts in estimating protein-ligand binding affinity

1 reference

12 December 2020

Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects

1 reference

12 December 2020

Elastic potential grids: accurate and efficient representation of intermolecular interactions for fully flexible docking

1 reference

12 December 2020

10.1016/J.DDTEC.2013.02.003

Identifiers

DOI

1 reference

17 August 2017

1 reference

PMC publication ID

3719877

17 August 2017

PubMed publication ID

24050138

1 reference

PMC publication ID

3719877