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SURFMAP: A Software for Mapping in Two Dimensions Protein Surface Features
Open accessPublished version of a preprint
Abstract
Molecular cartography using two-dimensional (2D) representation of protein surfaces has been shown to be very promising for protein surface analysis. Here, we present SURFMAP, a free standalone and easy-to-use software that enables the fast and automated 2D projection of either predefined features of protein surface (i.e., electrostatic potential, hydrophobicity, stickiness, and surface relief) or any descriptor encoded in the temperature factor column of a PDB file. SURFMAP proposes three different "equal-area" projections that have the advantage of preserving the area measures. It provides the user with (i) 2D maps that enable the easy and visual analysis of protein surface features of interest and (ii) maps in a text file format allowing the fast and straightforward quantitative comparison of 2D maps of homologous proteins.
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Sorted by citations
Protein representations: Encoding biological information for machine learning in biocatalysis
Harding-Larsen, D., Funk, J., Madsen, N. G., Gharabli, H., Acevedo-Rocha, C. G., Mazurenko, S., & Welner, D. H. (2024) · Biotechnology Advances · doi:10.1016/j.biotechadv.2024.108459 · Cited by 38
Metadata
- Authors
- Schweke, H., Mucchielli, M.-H., Chevrollier, N., Gosset, S., & Lopes, A.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-Yvette 91190, France
- Independent investigator, Nyoiseau 49500, France
- Corresponding author
- Schweke, Hugo
- Lopes, Anne
- Venue
- Journal of Chemical Information and Modeling
- Publisher
- American Chemical Society (ACS)
- Published
- 2022-03-29
- Volume
- 62
- Issue
- 7
- Pages
- 1595-1601
- ISSN
- 1549-9596 (ISSN-L)
- 1549-960X
- OpenAlex
- W4225503951
- Cited by
- 30
- References
- 1
- Citations by year
- 2026: 2 · 2025: 9 · 2024: 8 · 2023: 10 · 2022: 1
- FWCI
- 2.29
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Licence
- Locations
- Journal of Chemical Information and Modeling (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
- Keywords
- electrostatic potential, hydrophobicity, stickiness, surface relief, equal-area projection
- MeSH terms
- Software, Static Electricity
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