ArticleExpert opinion on drug discovery2011
X-ray crystallography: Assessment and validation of protein-small molecule complexes for drug discovery.
Article in Expert opinion on drug discovery, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed.
- Optimal 1TEL-target protein linker character is target protein-dependent.Acta crystallographica. Section D, Structural biology · 2026Article
- Optimal TELSAM-Target Protein Linker Character is Target Protein-Dependent.bioRxiv : the preprint server for biology · 2025Article
- Generalized open-source workflows for atomistic molecular dynamics simulations of viral helicases.GigaScience · 2024Article
- Increasing the bulk of the 1TEL-target linker and retaining the 10×His tag in a 1TEL-CMG2-vWa construct improves crystal order and diffraction limits.Acta crystallographica. Section D, Structural biology · 2023Article
- A Single-Entity Method for Actively Controlled Nucleation and High-Quality Protein Crystal Synthesis.Analytical chemistry · 2023Article
- CMM-An enhanced platform for interactive validation of metal binding sites.Protein science : a publication of the Protein Society · 2023Article
- Discovery of novel anti-tumor compounds targeting PARP-1 with induction of autophagy throughFrontiers in pharmacology · 2022Article
- Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy.RSC chemical biology · 2021Review
- 'International journal of molecular sciences · 2021Article
- Synergizing the potential of bacterial genomics and metabolomics to find novel antibiotics.Chemical science · 2021Review
- Development of a Raltegravir-based Photoaffinity-Labeled Probe for Human Immunodeficiency Virus-1 Integrase Capture.ACS medicinal chemistry letters · 2020Article
- In Situ Proteolysis Condition-Induced Crystallization of the XcpVWX Complex in Different Lattices.International journal of molecular sciences · 2020Article
- Review
- Nucleobase carbonyl groups are poor MgRNA (New York, N.Y.) · 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
- Characterization of Glycoproteins with the Immunoglobulin Fold by X-Ray Crystallography and Biophysical Techniques.Journal of visualized experiments : JoVE · 2018Article
- Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.Nucleic acids research · 2018Article
- Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.Protein science : a publication of the Protein Society · 2018Article
- Assigning crystallographic electron densities with free energy calculations-The case of the fluoride channel Fluc.PloS one · 2018Article
- Conformational energy range of ligands in protein crystal structures: The difficult quest for accurate understanding.Journal of molecular recognition : JMR · 2017Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
introductionCrystallography is the key initial component for structure-based and fragment-based drug design and can often generate leads that can be developed into high potency drugs. Therefore, huge sums of money are committed based on the outcome of crystallography experiments and their interpretation. AREAS COVERED: This review discusses how to evaluate the correctness of an X-ray structure, focusing on the validation of small molecule-protein complexes. Various types of inaccuracies found within the PDB are identified and the ramifications of these errors are discussed. The reader will gain an understanding of the key parameters that need to be inspected before a structure can be used in drug discovery efforts, as well as an appreciation of the difficulties of correctly interpreting electron density for small molecules. The reader will also be introduced to methods for validating small molecules within the context of a macromolecular structure. EXPERT OPINION: One of the reasons that ligand identification and positioning, within a macromolecular crystal structure, is so difficult is that the quality of small molecules widely varies in the PDB. For this reason, the PDB can not always be considered a reliable repository of structural information pertaining to small molecules, and this makes the derivation of general principles that govern small molecule-protein interactions more difficult.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.