ArticleACS medicinal chemistry letters2014
Protein-ligand cocrystal structures: we can do better.
Article in ACS medicinal chemistry letters, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design.Journal of computer-aided molecular design · 2023Article
- A systematic pipeline of protein structure selection for computer-aided drug discovery: A case study on T790M/L858R mutant EGFR structures.Protein science : a publication of the Protein Society · 2023Article
- A Distributional Model of Bound Ligand Conformational Strain: From Small Molecules up to Large Peptidic Macrocycles.Journal of medicinal chemistry · 2023Article
- Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality.Structure (London, England : 1993) · 2021Article
- Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics.Journal of chemical information and modeling · 2020Article
- Refinement of protein structures using a combination of quantum-mechanical calculations with neutron and X-ray crystallographic data.Acta crystallographica. Section D, Structural biology · 2019Article
- Tetrahydroisoquinoline CXCR4 Antagonists Adopt a Hybrid Binding Mode within the Peptide Subpocket of the CXCR4 Receptor.ACS medicinal chemistry letters · 2019Article
- High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement with PHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure.Acta crystallographica. Section D, Structural biology · 2018Article
- Conformational investigation of the structure-activity relationship of GdFFD and its analogues on an achatin-like neuropeptide receptor of Aplysia californica involved in the feeding circuit.Physical chemistry chemical physics : PCCP · 2018Article
- How Diverse Are the Protein-Bound Conformations of Small-Molecule Drugs and Cofactors?Frontiers in chemistry · 2018Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
- Strategies for carbohydrate model building, refinement and validation.Acta crystallographica. Section D, Structural biology · 2017Article
- Ligand fitting with CCP4.Acta crystallographica. Section D, Structural biology · 2017Article
- AceDRG: a stereochemical description generator for ligands.Acta crystallographica. Section D, Structural biology · 2017Article
- Validation and extraction of molecular-geometry information from small-molecule databases.Acta crystallographica. Section D, Structural biology · 2017Article
- When Does Chemical Elaboration Induce a Ligand To Change Its Binding Mode?Journal of medicinal chemistry · 2017Article
- Molecular-interaction and signaling profiles of AM3677, a novel covalent agonist selective for the cannabinoid 1 receptor.ACS chemical neuroscience · 2015Article
- Carbohydrate anomalies in the PDB.Nature chemical biology · 2015Article
- Targeting human central nervous system protein kinases: An isoform selective p38αMAPK inhibitor that attenuates disease progression in Alzheimer's disease mouse models.ACS chemical neuroscience · 2015Article
- Comparing pharmacophore models derived from crystal structures and from molecular dynamics simulations.Monatshefte fur chemieArticle
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is a large body of evidence that many protein-ligand cocrystal structures contain poorly refined ligand geometries. These errors result in bound structures that have nonideal bond lengths and angles, are strained, contain improbable conformations, and have bad protein-ligand contacts. Many of these problems can be greatly reduced with better refinement models.
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Registered trials
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