ArticleNucleic acids research2006
The Database of Macromolecular Motions: new features added at the decade mark.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed, 148 citations in OpenAlex.
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- A new polymodal gating model of the proton-activated chloride channel.PLoS biology · 2023Article
- D3PM: a comprehensive database for protein motions ranging from residue to domain.BMC bioinformatics · 2022Article
- Macrophages show higher levels of engulfment after disruption ofJournal of cell science · 2020Article
- Normal Mode Analysis as a Routine Part of a Structural Investigation.Molecules (Basel, Switzerland) · 2019Review
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- Conformational Transitions and Alternating-Access Mechanism in the Sarcoplasmic Reticulum Calcium Pump.Journal of molecular biology · 2017Article
- Molecular mechanisms of substrate-controlled ring dynamics and substepping in a nucleic acid-dependent hexameric motor.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations.Nature communications · 2016Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.Nucleic acids research · 2016Article
- PDB-Explorer: a web-based interactive map of the protein data bank in shape space.BMC bioinformatics · 2015Article
- Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.PLoS computational biology · 2015Article
- Pathways of allosteric regulation in Hsp70 chaperones.Nature communications · 2015Article
- ChSeq: A database of chameleon sequences.Protein science : a publication of the Protein Society · 2015Review
- Molecular dynamics simulations: advances and applications.Advances and applications in bioinformatics and chemistry : AABC · 2015Review
- Insights into the molecular mechanism of allostery in Hsp70s.Frontiers in molecular biosciences · 2015Review
- A local average distance descriptor for flexible protein structure comparison.BMC bioinformatics · 2014Article
- The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation.Journal of the American Chemical Society · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered on MolMovDB. In particular, we further developed the Morph Server to produce improved interpolations between two submitted structures. We added support for multiple chains to the original adiabatic mapping interpolation, allowing the analysis of subunit motions. We also added the option of using FRODA interpolation, which allows for more complex pathways, potentially overcoming steric barriers. We added an interface to a hinge prediction service, which acts on single structures and predicts likely residue points for flexibility. We developed tools to relate such points of flexibility in a structure to particular key residue positions, i.e. active sites or highly conserved positions. Lastly, we began relating our motion classification scheme to function using descriptions from the Gene Ontology Consortium.
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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.