Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". (Q37372747)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

review article

1 reference

title

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

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

publication date

1 April 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

volume

17

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

issue

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

page(s)

489-498

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

26 January 2020

cites work

1 reference

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Target flexibility: an emerging consideration in drug discovery and design

6 September 2017

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Calculation of protein-ligand binding free energy by using a polarizable potential

6 September 2017

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MM-GB/SA rescoring of docking poses in structure-based lead optimization.

6 September 2017

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Comprehensive Mechanistic Analysis of Hits from High-Throughput and Docking Screens against β-Lactamase

6 September 2017

1 reference

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Rescoring Docking Hit Lists for Model Cavity Sites: Predictions and Experimental Testing

6 September 2017

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Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

6 September 2017

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Dynamic personalities of proteins

6 September 2017

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Intrinsic motions along an enzymatic reaction trajectory

6 September 2017

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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

6 September 2017

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Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

6 September 2017

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Tracing changes in protonation: a prerequisite to factorize thermodynamic data of inhibitor binding to aldose reductase

6 September 2017

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Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?

6 September 2017

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Predicting absolute ligand binding free energies to a simple model site

6 September 2017

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Physics-based methods for studying protein-ligand interactions

6 September 2017

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Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP)

6 September 2017

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Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins

6 September 2017

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Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia

6 September 2017

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Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor

6 September 2017

1 reference

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Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers?

6 September 2017

1 reference

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A semiempirical free energy force field with charge-based desolvation

6 September 2017

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Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind beta-secretase in a N-terminal 10s-loop down conformation

6 September 2017

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Ligand configurational entropy and protein binding

6 September 2017

1 reference

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Molecular mechanics methods for predicting protein-ligand binding.

6 September 2017

1 reference

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Calculation of protein-ligand binding affinities.

6 September 2017

1 reference

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"Four-dimensional" protein structures: examples from metalloproteins.

6 September 2017

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Intrinsic disorder and functional proteomics

6 September 2017

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A critical assessment of docking programs and scoring functions

6 September 2017

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Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic

6 September 2017

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The dynamic energy landscape of dihydrofolate reductase catalysis

6 September 2017

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Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics

6 September 2017

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Protein-ligand docking: current status and future challenges

6 September 2017

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Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials

6 September 2017

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The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution

6 September 2017

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Probing molecular docking in a charged model binding site

6 September 2017

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Novel procedure for modeling ligand/receptor induced fit effects.

6 September 2017

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Fluctuating enzymes: lessons from single-molecule studies.

6 September 2017

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Intrinsic dynamics of an enzyme underlies catalysis

6 September 2017

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Direct calculation of the binding free energies of FKBP ligands

6 September 2017

1 reference

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Observation of a Power-Law Memory Kernel for Fluctuations within a Single Protein Molecule

6 September 2017

1 reference

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ERbeta ligands. 3. Exploiting two binding orientations of the 2-phenylnaphthalene scaffold to achieve ERbeta selectivity

6 September 2017

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6 September 2017

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Conformational changes observed in enzyme crystal structures upon substrate binding

6 September 2017

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Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design

6 September 2017

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A naphthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase

6 September 2017

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Discovery of a novel binding trench in HIV integrase.

6 September 2017

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

6 September 2017

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The many roles of computation in drug discovery

6 September 2017

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Protein kinase inhibitors: insights into drug design from structure.

6 September 2017

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Tautomerism in computer-aided drug design

6 September 2017

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Implications of protein flexibility for drug discovery

6 September 2017

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A review of protein-small molecule docking methods

6 September 2017

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Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors

6 September 2017

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Lead discovery using molecular docking

6 September 2017

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Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)

6 September 2017

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pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design

6 September 2017

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Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design

6 September 2017

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Enzyme dynamics during catalysis

6 September 2017

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Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations

6 September 2017

1 reference

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Structure-based design and protein X-ray analysis of a protein kinase inhibitor

6 September 2017

1 reference

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Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition

6 September 2017

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Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase

6 September 2017

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

6 September 2017

1 reference

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The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core

6 September 2017

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Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models

6 September 2017

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Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm

6 September 2017

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Structure-based design of inhibitors specific for bacterial thymidylate synthase

6 September 2017

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Ligand binding to proteins: The binding landscape model

6 September 2017

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Structures of Competitive Inhibitor Complexes of Protocatechuate 3,4-Dioxygenase: Multiple Exogenous Ligand Binding Orientations within the Active Site,

6 September 2017

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Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4

6 September 2017

1 reference

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Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study

6 September 2017

1 reference

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Rational design of potent sialidase-based inhibitors of influenza virus replication

6 September 2017

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Structural mechanisms for domain movements in proteins

6 September 2017

1 reference

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Application of the three-dimensional structures of protein target molecules in structure-based drug design

6 September 2017

1 reference

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X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites

6 September 2017

1 reference

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

6 September 2017

1 reference

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The mobile flavin of 4-OH benzoate hydroxylase

6 September 2017

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Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease

6 September 2017

1 reference

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Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme

6 September 2017

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Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: linkage of dynamics and structural plasticity

6 September 2017

1 reference

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A geometric approach to macromolecule-ligand interactions

6 September 2017

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Structural analysis of a series of antiviral agents complexed with human rhinovirus 14.

6 September 2017

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Structure, multiple site binding, and segmental accommodation in thymidylate synthase on binding dUMP and an anti-folate

6 September 2017

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Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation

6 September 2017

1 reference

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The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations

6 September 2017

1 reference

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Treating entropy and conformational changes in implicit solvent simulations of small molecules

6 September 2017

1 reference

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On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

26 June 2018

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Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study

26 June 2018

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Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects

26 June 2018

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Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib

2 September 2018

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Molecular modeling based approach to potent P2-P4 macrocyclic inhibitors of hepatitis C NS3/4A protease

2 September 2018

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Classification of water molecules in protein binding sites.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

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

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Calculation of absolute protein-ligand binding affinity using path and endpoint approaches

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Hydration free energies and entropies for water in protein interiors

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Assessing scoring functions for protein-ligand interactions

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Specific empirical free energy function for automated docking of carbohydrates to proteins

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Contributions to the binding free energy of ligands to avidin and streptavidin.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Protein side-chain rotamers from dipolar couplings in a liquid crystalline phase

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Interpreting trends in the binding of cyclic ureas to HIV-1 protease.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Side-chain flexibility in proteins upon ligand binding

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Ligand solvation in molecular docking.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Ligand docking to proteins with discrete side-chain flexibility.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2756098

Two-state allosteric behavior in a single-domain signaling protein

2 September 2018

1 reference

12 December 2020

Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?

1 reference

12 December 2020

Predicting the product specificity and coupling of cytochrome P450cam

1 reference

12 December 2020

Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase

1 reference

12 December 2020

A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase

1 reference

12 December 2020

Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes

1 reference

12 December 2020

Do structurally similar ligands bind in a similar fashion?

1 reference

12 December 2020

Atypical protonation states in the active site of HIV-1 protease: a computational study

1 reference

12 December 2020

Torsion angle preference and energetics of small-molecule ligands bound to proteins

1 reference

12 December 2020

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

12 December 2020

Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding

1 reference

12 December 2020

Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant.

1 reference

12 December 2020

Calculation of the relative change in binding free energy of a protein-inhibitor complex

1 reference

12 December 2020

Hydrophilicity of cavities in proteins

1 reference

12 December 2020

Hydration energy landscape of the active site cavity in cytochrome P450cam

1 reference

12 December 2020

10.1016/J.STR.2009.02.010

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19368882%20AND%20SRC:MED&resulttype=core&format=json

26 January 2020

PubMed publication ID

19368882

1 reference