ArticleNucleic acids research2012
PSCDB: a database for protein structural change upon ligand binding.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Measuring and locating the changes in protein structure using MELO.Nature communications · 2026Article
- Exploration of questionable backbone conformations in crystallographic structure models using a structural alphabet.Acta crystallographica. Section D, Structural biology · 2025Article
- Natural Language Processing Methods for the Study of Protein-Ligand Interactions.Journal of chemical information and modeling · 2025Review
- Article
- Repurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids.Nature communications · 2023Article
- D3PM: a comprehensive database for protein motions ranging from residue to domain.BMC bioinformatics · 2022Article
- "Protein" no longer means what it used to.Current research in structural biology · 2021Review
- An intrinsic FRET sensor of protein-ligand interactions.Organic & biomolecular chemistry · 2020Article
- Structure dictates the mechanism of ligand recognition in the histidine and maltose binding proteins.Current research in structural biology · 2020Article
- ART-RRT: As-Rigid-As-Possible search for protein conformational transition paths.Journal of computer-aided molecular design · 2019Article
- Inherent versus induced protein flexibility: Comparisons within and between apo and holo structures.PLoS computational biology · 2019Article
- Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank.Biophysical reviews · 2017Review
- Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms.PloS one · 2016Article
- CCProf: exploring conformational change profile of proteins.Database : the journal of biological databases and curation · 2016Article
- The value of protein structure classification information-Surveying the scientific literature.Proteins · 2015Article
- ENCoM server: exploring protein conformational space and the effect of mutations on protein function and stability.Nucleic acids research · 2015Article
- ChSeq: A database of chameleon sequences.Protein science : a publication of the Protein Society · 2015Review
- sc-PDB: a 3D-database of ligandable binding sites--10 years on.Nucleic acids research · 2015Article
- Principles of allosteric interactions in cell signaling.Journal of the American Chemical Society · 2014Review
- Ligand-induced protein responses and mechanical signal propagation described by linear response theories.Biophysical journal · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. PSCDB is available at http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/.
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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.