ArticleComputational and structural biotechnology journal2023
CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking.
Article in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed, 14 citations in OpenAlex.
- Multi-state Structure Prediction of G Protein-Coupled Receptor Proteins via Prompting on AlphaFold.Computational and structural biotechnology journal · 2026Article
- Article
- Overcoming translational barriers in RNA-protein docking: enhancing computational accuracy for targeted drug discovery.Future medicinal chemistry · 2025Review
- RoseTTAFold diffusion-guided short peptide design: a case study of binders against Keap1/Nrf2.Computational and structural biotechnology journal · 2025Article
- CSearch: chemical space search via virtual synthesis and global optimization.Journal of cheminformatics · 2024Article
- Computational Strategies for Assessing Adverse Outcome Pathways: Hepatic Steatosis as a Case Study.International journal of molecular sciences · 2024Review
- Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.Biomolecules · 2023Article
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 at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structure prediction of protein-ligand complexes, called protein-ligand docking, is a critical computational technique that can be used to understand the underlying principle behind the protein functions at the atomic level and to design new molecules regulating the functions. Protein-ligand docking methods have been employed in structure-based drug discovery for hit discovery and lead optimization. One of the important technical challenges in protein-ligand docking is to account for protein conformational changes induced by ligand binding. A small change such as a single side-chain rotation upon ligand binding can hinder accurate docking. Here we report an increase in docking performance achieved by structure alignment to known complex structures. First, a fully flexible compound-to-compound alignment method CSAlign is developed by global optimization of a shape score. Next, the alignment method is combined with a docking algorithm to dock a new ligand to a target protein when a reference protein-ligand complex structure is available. This alignment-based docking method, called CSAlign-Dock, showed superior performance to
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.