ArticleNucleic acids research2012
Monte Carlo simulations of peptide-membrane interactions with the MCPep web server.
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 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
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- Localization and Dynamics of the Methionine Sulfoxide Reductases MsrB1 and MsrB2 in Beech Seeds.International journal of molecular sciences · 2021Article
- Design, Screening, and Testing of Non-Rational Peptide Libraries with Antimicrobial Activity: In Silico and Experimental Approaches.Antibiotics (Basel, Switzerland) · 2020Review
- Dual roles of the sterol recognition region in Hedgehog protein modification.Communications biology · 2020Article
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- Intracellular Delivery of DNA and Protein by a Novel Cell-Permeable Peptide Derived from DOT1L.Biomolecules · 2020Article
- Bacterial LPX motif-harboring virulence factors constitute a species-spanning family of cell-penetrating effectors.Cellular and molecular life sciences : CMLS · 2018Article
- Secondary structure of cell-penetrating peptides during interaction with fungal cells.Protein science : a publication of the Protein Society · 2018Article
- Novel Naja atra cardiotoxin 1 (CTX-1) derived antimicrobial peptides with broad spectrum activity.PloS one · 2018Article
- Membrane insertion of the BAX core, but not latch domain, drives apoptotic pore formation.Scientific reports · 2017Article
- Bacterium-Derived Cell-Penetrating Peptides Deliver Gentamicin To Kill Intracellular Pathogens.Antimicrobial agents and chemotherapy · 2017Article
- The role and significance of potential lipid-binding regions in the mitochondrial protein import motor: an in-depth in silico study.3 Biotech · 2015Article
- Identification and in silico analysis of helical lipid binding regions in proteins belonging to the amphitropic protein family.Journal of biosciences · 2014Article
- Herp coordinates compartmentalization and recruitment of HRD1 and misfolded proteins for ERAD.Molecular biology of the cell · 2014Article
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Authors and funding
3 authors at 1 institution in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The MCPep server (http://bental.tau.ac.il/MCPep/) is designed for non-experts wishing to perform Monte Carlo (MC) simulations of helical peptides in association with lipid membranes. MCPep is a web implementation of a previously developed MC simulation model. The model has been tested on a variety of peptides and protein fragments. The simulations successfully reproduced available empirical data and provided new molecular insights, such as the preferred locations of peptides in the membrane and the contribution of individual amino acids to membrane association. MCPep simulates the peptide in the aqueous phase and membrane environments, both described implicitly. In the former, the peptide is subjected solely to internal conformational changes, and in the latter, each MC cycle includes additional external rigid body rotational and translational motions to allow the peptide to change its location in the membrane. The server can explore the interaction of helical peptides of any amino-acid composition with membranes of various lipid compositions. Given the peptide's sequence or structure and the natural width and surface charge of the membrane, MCPep reports the main determinants of peptide-membrane interactions, e.g. average location and orientation in the membrane, free energy of membrane association and the peptide's helical content. Snapshots of example simulations are also provided.
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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.