(Q26864013)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

title

Protein flexibility in docking and surface mapping (English)

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

author name string

Katrina W Lexa

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

language of work or name

1 reference

9 May 2012

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

Quarterly Reviews of Biophysics

31 January 2020

published in

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

volume

45

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

issue

3

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

page(s)

301-343

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

Flexible ligand docking to multiple receptor conformations: a practical alternative

31 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Multiple solvent crystal structures of ribonuclease A: an assessment of the method

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Fragment-based discovery of the pyrazol-4-yl urea (AT9283), a multitargeted kinase inhibitor with potent aurora kinase activity

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Design of annulated pyrazoles as inhibitors of HIV-1 reverse transcriptase

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Organic solvents order the dynamic switch II in Ras crystals

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Experimental and computational mapping of the binding surface of a crystalline protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Locating interaction sites on proteins: the crystal structure of thermolysin soaked in 2% to 100% isopropanol

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

X-ray studies on cross-linked lysozyme crystals in acetonitrile-water mixture

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The crystal structure of subtilisin Carlsberg in anhydrous dioxane and its comparison with those in water and acetonitrile

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Ionic interactions in crystalline bovine pancreatic ribonuclease A

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Enzyme crystal structure in a neat organic solvent

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Comparative protein structure modeling of genes and genomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Backbone-dependent rotamer library for proteins. Application to side-chain prediction

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Computational identification of uncharacterized cruzain binding sites

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Computational fragment-based binding site identification by ligand competitive saturation

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

21 March 2017

1 reference

https://api.crossref.org/works/10.1017/S0033583512000066

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

22 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

A critical assessment of docking programs and scoring functions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Discovering high-affinity ligands for proteins: SAR by NMR

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Computational analysis of protein hotspots

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

28 September 2017

Protein-ligand docking.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Predictive power of molecular dynamics receptor structures in virtual screening

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The rise of fragment-based drug discovery

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Full protein flexibility is essential for proper hot-spot mapping.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Docking validation resources: protein family and ligand flexibility experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Computer-aided drug-discovery techniques that account for receptor flexibility

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Mining protein dynamics from sets of crystal structures using "consensus structures".

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Ensemble-based virtual screening reveals dual-inhibitors for the p53-MDM2/MDMX interactions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Successful applications of computer aided drug discovery: moving drugs from concept to the clinic

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The multi-copy simultaneous search methodology: a fundamental tool for structure-based drug design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Binding site detection and druggability index from first principles.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Managing protein flexibility in docking and its applications

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Solvent dramatically affects protein structure refinement.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Target flexibility: an emerging consideration in drug discovery and design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

A poke in the eye: inhibiting HIV-1 protease through its flap-recognition pocket

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Docking ligands into flexible and solvated macromolecules. 2. Development and application of fitted 1.5 to the virtual screening of potential HCV polymerase inhibitors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Current topics in computer-aided drug design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Protein-ligand docking with multiple flexible side chains

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

A flexible approach to induced fit docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Discovery of antiandrogen activity of nonsteroidal scaffolds of marketed drugs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Insights into equilibrium dynamics of proteins from comparison of NMR and X-ray data with computational predictions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Exploring experimental sources of multiple protein conformations in structure-based drug design.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Towards in silico lead optimization: scores from ensembles of protein/ligand conformations reliably correlate with biological activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Prediction of protein-ligand interactions. Docking and scoring: successes and gaps

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Protein-ligand docking: current status and future challenges

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Virtual ligand screening: strategies, perspectives and limitations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Combining docking and molecular dynamic simulations in drug design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Effective handling of induced-fit motion in flexible docking.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Novel procedure for modeling ligand/receptor induced fit effects.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Receptor flexibility in de novo ligand design and docking.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Accounting for global protein deformability during protein-protein and protein-ligand docking

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Target flexibility in molecular recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The limit of accuracy of protein modeling: influence of crystal packing on protein structure.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Maximizing discovery efficiency with a computationally driven fragment approach

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Is allostery an intrinsic property of all dynamic proteins?

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Testing a flexible-receptor docking algorithm in a model binding site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The many roles of computation in drug discovery

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Implications of protein flexibility for drug discovery

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Structure-based ligand design for flexible proteins: application of new F-DycoBlock.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Structured disorder and conformational selection

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

FlexE: efficient molecular docking considering protein structure variations.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Docking ligands onto binding site representations derived from proteins built by homology modelling.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

The Protein Data Bank and the challenge of structural genomics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Developing a dynamic pharmacophore model for HIV-1 integrase.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Folding and binding cascades: dynamic landscapes and population shifts

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Folding and binding cascades: shifts in energy landscapes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Folding funnels, binding funnels, and protein function

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Locating and characterizing binding sites on proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Conformational isomerism and the diversity of antibodies

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Comparison of four independently determined structures of human recombinant interleukin-4.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Reproducing crystal binding modes of ligand functional groups using Site-Identification by Ligand Competitive Saturation (SILCS) simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Recipes for the selection of experimental protein conformations for virtual screening

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Blind docking of pharmaceutically relevant compounds using RosettaLigand

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

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

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Soft docking and multiple receptor conformations in virtual screening

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Molecular docking to ensembles of protein structures

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

"Soft docking": matching of molecular surface cubes

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

Conformational selection in silico: loop latching motions and ligand binding in enzymes.

31 May 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Allosteric inhibition of protein tyrosine phosphatase 1B.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Protein-ligand docking against non-native protein conformers

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Modeling and selection of flexible proteins for structure-based drug design: backbone and side chain movements in p38 MAPK.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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/10.1017%2FS0033583512000066

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/10.1017%2FS0033583512000066

Computational drug design accommodating receptor flexibility: the relaxed complex scheme

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Development of a new predictive model for interactions with human cytochrome P450 2A6 using pharmacophore ensemble/support vector machine (PhE/SVM) approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Prediction of cytochrome P450 2B6-substrate interactions using pharmacophore ensemble/support vector machine (PhE/SVM) approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Optimization and computational evaluation of a series of potential active site inhibitors of the V82F/I84V drug-resistant mutant of HIV-1 protease: an application of the relaxed complex method of structure-based drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

A novel approach using pharmacophore ensemble/support vector machine (PhE/SVM) for prediction of hERG liability

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Molecular dynamics studies of alanine racemase: a structural model for drug design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

GRID/CPCA: a new computational tool to design selective ligands.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Efficient conformational sampling of local side-chain flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Enhanced docking with the mining minima optimizer: acceleration and side-chain flexibility

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Functionality maps of binding sites: a multiple copy simultaneous search method

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Diverse, high-quality test set for the validation of protein-ligand docking performance.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Synthese des Traubenzuckers

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Generation and selection of novel estrogen receptor ligands using the de novo structure-based design tool, SkelGen.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Fragment-Based Drug Discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

RosettaLigand docking with full ligand and receptor flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Docking ligands into flexible and solvated macromolecules. 3. Impact of input ligand conformation, protein flexibility, and water molecules on the accuracy of docking programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Grand canonical free-energy calculations of protein-ligand binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Grand canonical Monte Carlo simulation of ligand-protein binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Representing receptor flexibility in ligand docking through relevant normal modes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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/10.1017%2FS0033583512000066

A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE).

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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/10.1017%2FS0033583512000066

FLIPDock: docking flexible ligands into flexible receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

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/10.1017%2FS0033583512000066

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Docking Ligands on Protein Surfaces: The Case Study of Prion Protein

21 January 2018

2 references

https://api.crossref.org/works/10.1017%2FS0033583512000066

21 January 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

COCO: A simple tool to enrich the representation of conformational variability in NMR structures

28 November 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Side-chain flexibility in proteins upon ligand binding.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

MCSS functionality maps for a flexible protein.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272345

How Reliable Are Current Docking Approaches for Structure-Based Drug Design? Lessons from Aldose Reductase

28 November 2018

1 reference

https://api.crossref.org/works/10.1017%2FS0033583512000066

Antigen recognition by conformational selection

21 January 2018

1 reference

12 December 2020

Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI

1 reference

12 December 2020

The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase

1 reference

12 December 2020

A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening

1 reference

12 December 2020

Use of an induced fit receptor structure in virtual screening

1 reference

12 December 2020

Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase

1 reference

12 December 2020

A novel computational analysis of ligand-induced conformational changes in the ATP binding sites of cyclin dependent kinases

1 reference

12 December 2020

Addressing protein flexibility and ligand selectivity by "in situ cross-docking"

1 reference

12 December 2020

High-resolution structure of the p53 core domain: implications for binding small-molecule stabilizing compounds

1 reference

12 December 2020

Comparison of experimental and computational functional group mapping of an RNase A structure: implications for computer-aided drug design

1 reference

12 December 2020

10.1017/S0033583512000066

Identifiers

DOI

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22569329%20AND%20SRC:MED&resulttype=core&format=json

31 January 2020

PubMed publication ID

22569329

2 references