ArticleJournal of chemical theory and computation2019
Protein Docking Using a Single Representation for Protein Surface, Electrostatics, and Local Dynamics.
Article in Journal of chemical theory and computation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 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
8 citing papers in PubMed.
- ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles.Database : the journal of biological databases and curation · 2024Article
- Functional antibody characterization via direct structural analysis and information-driven protein-protein docking.Proteins · 2022Article
- Cleaning of Wastewater Using Crosslinked Poly(Acrylamide-Gels (Basel, Switzerland) · 2022Article
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Transmembrane Protein Docking with JabberDock.Journal of chemical information and modeling · 2021Article
- Mass Photometry of Membrane Proteins.Chem · 2021Article
- Structure-based molecular modeling in SAR analysis and lead optimization.Computational and structural biotechnology journal · 2021Review
- Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking.Journal of chemical theory and computation · 2020Article
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
No grant is acknowledged in the PubMed record.
Abstract
Predicting the assembly of multiple proteins into specific complexes is critical to understanding their biological function in an organism and thus the design of drugs to address their malfunction. Proteins are flexible molecules, which inherently pose a problem to any protein docking computational method, where even a simple rearrangement of the side chain and backbone atoms at the interface of binding partners complicates the successful determination of the correct docked pose. Herein, we present a means of representing protein surface, electrostatics, and local dynamics within a single volumetric descriptor. We show that our representations can be physically related to the surface-accessible solvent area and mass of the protein. We then demonstrate that the application of this representation into a protein-protein docking scenario bypasses the need to compensate for, and predict, specific side chain packing at the interface of binding partners. This representation is leveraged in our de novo protein docking software, JabberDock, which can accurately and robustly predict difficult target complexes with an average success rate of >54%, which is comparable to or greater than the currently available methods.
Indexed as
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.