OPM: Orientations of Proteins in Membranes database

By Mikhail A. Lomize, Andrei L. Lomize, Irina D. Pogozheva, Henry I. Mosberg. 2006

1,208 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

Computational Protein Design with Deep Learning Neural Networks (2018, methodology): “The resulting entries were cross-referenced with the OPM database 64 to remove membrane proteins.”
Methanotrophs and copper. (2010, methodology): “Membrane orientation was predicted using the methodology of Lomize et al. (2006) using structural information from Lieberman & Rosenzweig (2005) and Hakemian et al. (2008).”
All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences (2015, methodology): “T β-barrels (TMBs) constitute 2–3% of all genes in Gram-negative bacterial genomes (1) and are also found in eukaryotes (2).”
The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015, methodology): “For topology assignment, we combined different sources (PDBTM, OPM (35), TOPDB (36) and UniProt), along with manual inspection in some spurious cases.”
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning (2022, methodology): “OPM (86) Orientations of Proteins in Membranes database;”
MEDELLER: homology-based coordinate generation for membrane proteins (2010, methodology): “A list of MP structures was compiled by combining data from several publicly available databases: all PDB entries annotated with the SCOP class ‘membrane proteins’, the OPM database (Lomize et al., 2006), the PDB TM database (Tusnády et al., 2005) and the CGDB database (Scott et al., 2008).”
Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways (2013, methodology): “Membrane-aligned crystal structures for PDB IDs 2RH1 and 3P0G were extracted from the OPM database (29).”
The Physiology, Pathology, and Pharmacology of Voltage-Gated Calcium Channels and Their Future Therapeutic Potential (2015, neutral): “3-selective CCBs.”
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis (2012, background): “Considering that only 50 polytopic alpha-helical TMP superfamilies have been structurally characterized to date (45), applying FILM3 to these Pfam domains has the potential to expand our knowledge of TMP fold space significantly.”
An Integrated Framework Advancing Membrane Protein Modeling and Design (2015, methodology): “by using the PDBTM [39] or OPM [40] databases or the TMDET [41] or PPM [42] servers.”