ArticleNucleic acids research2019
The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed.
- Deep learning-driven de novo discovery of binders targeting the transmembrane domain of BamA.Archives of microbiology · 2026Article
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- Functional role of a structural water in the elevator domain of dicarboxylate transporter VcINDY.PNAS nexus · 2026Article
- A dataset of small protein conformational ensembles from all-atom molecular dynamics simulations.Scientific data · 2026Article
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- Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction.bioRxiv : the preprint server for biology · 2026Article
- Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction.Proteins · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
- TMEM63 proteins act as mechanically activated cholesterol modulated lipid scramblases contributing to membrane mechano-resilience.Nature communications · 2026Article
- MPLID (Membrane Protein-Lipid Interaction Database): A Large-Scale Experimental Resource of Residue-Level Protein-Lipid Contacts.GigaScience · 2026Article
- Structural basis of outer membrane biogenesis by the TamAB translocase.Nature communications · 2026Article
- MemPrO: A Predictive Tool for Membrane Protein Orientation.Journal of chemical theory and computation · 2026Article
- MetaMP Ecosystem for Unified, Auditable, and Benchmark-Ready Data for Reliable Membrane Protein Annotation.Computational and structural biotechnology journal · 2026Article
- Structural basis of undecaprenyl phosphate glycosylation leading to polymyxin resistance in Gram-negative bacteria.Nature communications · 2025Article
- Mechanistic basis of antimicrobial resistance mediated by the phosphoethanolamine transferase MCR-1.Nature communications · 2025Article
- Lipid bilayer thinning near a ubiquitin ligase selects ER membrane proteins for degradation.bioRxiv : the preprint server for biology · 2025Article
- Article
- Beyond static structures: protein dynamic conformations modeling in the post-AlphaFold era.Briefings in bioinformatics · 2025Review
- An integrative modelling approach to the mitochondrial cristae.Communications biology · 2025Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Integral membrane proteins fulfil important roles in many crucial biological processes, including cell signalling, molecular transport and bioenergetic processes. Advancements in experimental techniques are revealing high resolution structures for an increasing number of membrane proteins. Yet, these structures are rarely resolved in complex with membrane lipids. In 2015, the MemProtMD pipeline was developed to allow the automated lipid bilayer assembly around new membrane protein structures, released from the Protein Data Bank (PDB). To make these data available to the scientific community, a web database (http://memprotmd.bioch.ox.ac.uk) has been developed. Simulations and the results of subsequent analysis can be viewed using a web browser, including interactive 3D visualizations of the assembled bilayer and 2D visualizations of lipid contact data and membrane protein topology. In addition, ensemble analyses are performed to detail conserved lipid interaction information across proteins, families and for the entire database of 3506 PDB entries. Proteins may be searched using keywords, PDB or Uniprot identifier, or browsed using classification systems, such as Pfam, Gene Ontology annotation, mpstruc or the Transporter Classification Database. All files required to run further molecular simulations of proteins in the database are provided.
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