ArticleNucleic acids research2007
eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 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
31 citing papers in PubMed.
- Computational approaches to druggable site identification: Current status and future perspective.Acta pharmaceutica Sinica. B · 2026Review
- Deciphering the language of mingling lipids and proteins.Current opinion in structural biology · 2025Review
- Article
- Exploring Ligand Binding Domain Dynamics in the NRs Superfamily.International journal of molecular sciences · 2022Article
- What Makes GPCRs from Different Families Bind to the Same Ligand?Biomolecules · 2022Article
- Precise parallel volumetric comparison of molecular surfaces and electrostatic isopotentials.Algorithms for molecular biology : AMB · 2020Article
- Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors.RSC advances · 2019Article
- Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.BMC bioinformatics · 2018Article
- Discovery of Potent Disheveled/Dvl Inhibitors Using Virtual Screening Optimized With NMR-Based Docking Performance Index.Frontiers in pharmacology · 2018Article
- Landscape of protein-small ligand binding modes.Protein science : a publication of the Protein Society · 2016Article
- PatchSurfers: Two methods for local molecular property-based binding ligand prediction.Methods (San Diego, Calif.) · 2016Article
- PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.Nucleic acids research · 2015Article
- PL-PatchSurfer: a novel molecular local surface-based method for exploring protein-ligand interactions.International journal of molecular sciences · 2014Article
- Exhaustive comparison and classification of ligand-binding surfaces in proteins.Protein science : a publication of the Protein Society · 2013Article
- Accidental interaction between PDZ domains and diclofenac revealed by NMR-assisted virtual screening.Molecules (Basel, Switzerland) · 2013Article
- DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.Communications in computational physics · 2013Article
- ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.Nucleic acids research · 2012Article
- Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.Proteins · 2012Article
- PoSSuM: a database of similar protein-ligand binding and putative pockets.Nucleic acids research · 2012Article
- Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format.Nucleic acids research · 2012Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed a method to predict ligand-binding sites in a new protein structure by searching for similar binding sites in the Protein Data Bank (PDB). The similarities are measured according to the shapes of the molecular surfaces and their electrostatic potentials. A new web server, eF-seek, provides an interface to our search method. It simply requires a coordinate file in the PDB format, and generates a prediction result as a virtual complex structure, with the putative ligands in a PDB format file as the output. In addition, the predicted interacting interface is displayed to facilitate the examination of the virtual complex structure on our own applet viewer with the web browser (URL: http://eF-site.hgc.jp/eF-seek).
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.