ArticleProteins2009
Automated site preparation in physics-based rescoring of receptor ligand complexes.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed, 22 citations in OpenAlex.
- The Discovery of Potent SHP2 Inhibitors with Anti-Proliferative Activity in Breast Cancer Cell Lines.International journal of molecular sciences · 2022Article
- Dimorphite-DL: an open-source program for enumerating the ionization states of drug-like small molecules.Journal of cheminformatics · 2019Article
- Computational methods in drug discovery.Beilstein journal of organic chemistry · 2016Review
- On the energy components governing molecular recognition in the framework of continuum approaches.Frontiers in molecular biosciences · 2015Review
- Protonation and pK changes in protein-ligand binding.Quarterly reviews of biophysics · 2013Review
- The role of protonation states in ligand-receptor recognition and binding.Current pharmaceutical design · 2013Review
- Life beyond kinases: structure-based discovery of sorafenib as nanomolar antagonist of 5-HT receptors.Journal of medicinal chemistry · 2012Article
- Structure-based virtual screening for drug discovery: a problem-centric review.The AAPS journal · 2012Review
- A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series.Journal of chemical information and modeling · 2011Article
- Article
- Biased retrieval of chemical series in receptor-based virtual screening.Journal of computer-aided molecular design · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Hydrogen atoms are not typically observable in X-ray crystal structures, but inferring their locations is often important in structure-based drug design. In addition, protonation states of the protein can change in response to ligand binding, as can the orientations of OH groups, a subtle form of "induced fit." We implement and evaluate an automated procedure for optimizing polar hydrogens in protein-binding sites in complex with ligands. Specifically, we apply the previously described Independent Cluster Decomposition Algorithm (ICDA) algorithm (Li et al., Proteins 2007;66:824-837), which assigns the ionization states of titratable residues, the amide orientations of Asn/Gln side chains, the imidazole ring orientation in His, and the orientations of OH/SH groups, in a unified algorithm. We test the utility of this method for identifying nativelike ligand poses using 247 protein-ligand complexes from an established database of docked decoys. Pose selection is performed with a physics-based scoring function based on a molecular mechanics energy function and a Generalized Born implicit solvent model. The use of the ICDA receptor preparation protocol, implemented with no knowledge of the native ligand pose, increases the accuracy of pose selection significantly, with the average RMSD over all complexes decreasing from 2.7 to 1.5 A when applying ICDA. Large improvements are seen for specific classes of binding sites with titratable groups, such as aspartyl proteases.
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What OpenQuestion holds
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.