ArticleJournal of cheminformatics2013
MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
Article in Journal of cheminformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 165 papers.
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Who cites it
165 citing papers in PubMed.
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- Structural insights into PSL polysaccharide assembly and export to the cell surface via the Wzx/Wzy-dependent pathway.Nature communications · 2026Article
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- Interaction of Staphylococcus aureus di-iron Repair of Iron Centers protein with the iron-sulfur cluster assembly SUF system.Protein science : a publication of the Protein Society · 2026Article
- Dynamic structures of a membrane transporter in native cellular membranes.Science advances · 2025Article
- From AI-AssistedPharmaceuticals (Basel, Switzerland) · 2025Review
- Structural basis of ClC-3 transporter inhibition by TMEM9 and PtdIns(3,5)PNature structural & molecular biology · 2025Article
- Identification and classification of ion-channels across the tree of life provide functional insights into understudied CALHM channels.bioRxiv : the preprint server for biology · 2025Article
- MOLEonline: a web-based tool for analysing channels, tunnels, and pores (2025 update).Bioinformatics (Oxford, England) · 2025Article
- Identification and Structural Characterization of Viroporins from Deadly Hemorrhagic Viruses.Viruses · 2025Article
- A porin-like protein used by bacterial predators defines a wider lipid-trapping superfamily.Nature communications · 2025Article
- Structural dynamics and permeability of the TRPV3 pentamer.Nature communications · 2025Article
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Structure of the yeast ceramide synthase.Nature structural & molecular biology · 2025Article
105 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChannels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity.
resultsWe present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily.
conclusionEstimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
Identifiers
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Registered trials
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