ArticleJournal of chemical theory and computation2008
Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements.
Article in Journal of chemical theory and computation, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
26 citing papers in PubMed.
- Methotrexate Inhibits the Binding of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Receptor Binding Domain to the Host-Cell Angiotensin-Converting Enzyme-2 (ACE-2) Receptor.ACS pharmacology & translational science · 2024Article
- Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist.Journal of the American Chemical Society · 2023Article
- The dynamics of agonist-βNature chemistry · 2023Article
- Predicted structure and cell signaling of TAS2R14 reveal receptor hyper-flexibility for detecting diverse bitter tastes.iScience · 2023Article
- Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery.Nature communications · 2023Article
- The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- A Human Ribonuclease Variant and ERK-Pathway Inhibitors Exhibit Highly Synergistic Toxicity for Cancer Cells.Molecular cancer therapeutics · 2018Article
- Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structure and dynamics of a constitutively active neurotensin receptor.Scientific reports · 2016Article
- Computational Prediction and Biochemical Analyses of New Inverse Agonists for the CB1 Receptor.Journal of chemical information and modeling · 2016Article
- Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1.Journal of computer-aided molecular design · 2014Article
- Ligand- and mutation-induced conformational selection in the CCR5 chemokine G protein-coupled receptor.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Article
- Molecular basis for dramatic changes in cannabinoid CB1 G protein-coupled receptor activation upon single and double point mutations.Protein science : a publication of the Protein Society · 2013Article
- Predicted structure of agonist-bound glucagon-like peptide 1 receptor, a class B G protein-coupled receptor.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Molecular basis for the interplay of apoptosis and proliferation mediated by Bcl-xL:Bim interactions in pancreatic cancer cells.Biochemical and biophysical research communications · 2012Article
- Bihelix: Towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations.Proteins · 2012Article
- Structure-based prediction of subtype selectivity of histamine H3 receptor selective antagonists in clinical trials.Journal of chemical information and modeling · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
We present a new strategy for protein side-chain placement that uses flat-bottom potentials for rotamer scoring. The extent of the flat bottom depends on the coarseness of the rotamer library and is optimized for libraries ranging from diversities of 0.2 Å to 5.0 Å. The parameters reported here were optimized for forcefields using Lennard-Jones 12-6 van der Waals potential with DREIDING parameters but are expected to be similar for AMBER, CHARMM, and other forcefields. This Side-Chain Rotamer Excitation Analysis Method is implemented in the SCREAM software package. Similar scoring function strategies should be useful for ligand docking, virtual ligand screening, and protein folding applications.
Identifiers
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.