ArticleBioinformatics (Oxford, England)2011
Rigid substructure search.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Adaptation-proof SARS-CoV-2 vaccine design.Advanced functional materials · 2022Article
- Toward rational vaccine engineering.Advanced drug delivery reviews · 2022Review
- Whole proteome mapping of compound-protein interactions.Current research in chemical biology · 2022Article
- mRNA vaccines for cancer immunotherapy.Frontiers in immunology · 2022Review
- Motor neuron-derived induced pluripotent stem cells as a drug screening platform for amyotrophic lateral sclerosis.Frontiers in cell and developmental biology · 2022Review
- Searching for methyllysine-binding aromatic cages.The Biochemical journal · 2021Article
- Electrostatic regulation of blue copper sites.Chemical science · 2021Article
- Activating Sphingosine-1-phospahte signaling in endothelial cells increases myosin light chain phosphorylation to decrease endothelial permeability thereby inhibiting cancer metastasis.Cancer letters · 2021Article
- New computational protein design methods for de novo small molecule binding sites.PLoS computational biology · 2020Article
- Development of a Novel Multi-Isoform ALDH Inhibitor Effective as an Antimelanoma Agent.Molecular cancer therapeutics · 2020Article
- Rationally designed carbohydrate-occluded epitopes elicit HIV-1 Env-specific antibodies.Nature communications · 2019Article
- Harnessing Nature's Diversity: Discovering organophosphate bioscavenger characteristics among low molecular weight proteins.Scientific reports · 2016Article
- Artificial Diiron Enzymes with a De Novo Designed Four-Helix Bundle Structure.European journal of inorganic chemistry · 2015Article
- Rapid search for tertiary fragments reveals protein sequence-structure relationships.Protein science : a publication of the Protein Society · 2015Article
- A real-time all-atom structural search engine for proteins.PLoS computational biology · 2014Article
- ProBiS-2012: web server and web services for detection of structurally similar binding sites in proteins.Nucleic acids research · 2012Article
- ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.Journal of chemical information and modeling · 2012Article
- Crystal structure of a trapped catalytic intermediate suggests that forced atomic proximity drives the catalysis of mIPS.Biophysical journal · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
motivationIdentifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions. AVAILABILITY AND IMPLEMENTATION: We provide this service through a web server at http://erebus.dokhlab.org.
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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.