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SURFMAP: Two-Dimensional Mapping of Protein Surface Features Such as Electrostatics and Hydrophobicity
SURFMAP is a free, standalone command-line software for mapping protein surface features in two dimensions. Developed by Hugo Schweke, Marie-Helene Mucchielli, Nicolas Chevrollier, Simon Gosset and Anne Lopes, it projects properties of a 3D protein surface onto a flat map so they can be read at a glance. The software is written in Python and R, bundles the MSMS surface program, and is released under the MIT license.
A protein surface is a curved 3D object, and comparing properties such as charge or hydrophobicity across the whole surface, or across several proteins, is hard to do by rotating a structure on screen. A 2D map places every surface region in a fixed position, which makes patches easy to see and to compare.
Property | Detail |
|---|---|
Purpose | 2D projection of protein surface features |
Input | A PDB file, or a SURFMAP-format matrix text file |
Features | Electrostatics, Kyte-Doolittle and Wimley-White hydrophobicity, stickiness, circular variance (surface relief), B-factor and binding sites |
Output | A PDF map (PNG optional) and a smoothed matrix text file |
Default projection | Flamsteed (Mollweide and Lambert also available) |
License | MIT |
Why 2D Protein Surface Maps Help Analyze Interfaces and Binding Sites
Surface properties govern how proteins recognize partners, ligands and membranes. Reducing the surface to a map lets you compare electrostatic patches, hydrophobic regions and surface relief side by side. Any per-atom descriptor stored in the temperature factor column of a PDB file can also be mapped, which extends the tool beyond the built-in features.
How SURFMAP Generates Surface Maps
Workflow
Compute the surface: the bundled MSMS program builds the molecular surface, with 3.0 angstroms added to atomic radii by default.
Assign the feature: the chosen property, such as Kyte-Doolittle hydrophobicity or electrostatics, is attached to the surface.
Project to 2D: the surface is projected with Flamsteed by default, or Mollweide or Lambert.
Grid and smooth: values are placed on a grid (cell size 5.0 by default) and smoothed, producing the final map and a matrix file.
Supported Surface Features
Hydrophobicity: Kyte-Doolittle and Wimley-White scales.
Electrostatics: computed with the CHARMM force field by default; the optional APBS program is needed for this feature.
Stickiness and surface relief: stickiness and circular variance, the latter describing surface relief.
Custom descriptors: B-factor values or discrete binding site labels stored in the PDB file.
What is Tamarind Bio?
Tamarind Bio is a no-code bioinformatics platform built to give life scientists and researchers access to powerful computational tools. Many cutting-edge machine learning models are hard to deploy and use. Tamarind provides an intuitive, web-based environment that removes the complexity of high-performance computing, software dependencies and command-line interfaces.
The platform is designed for biologists, chemists and other researchers who may not have a background in programming or cloud infrastructure but want to run models on their own data. Key features include:
A user-friendly graphical interface for setting up and launching experiments
A robust API for integration into existing research pipelines
An automated system for managing and scaling computational resources
Tamarind treats information and data security as a top priority, as detailed in its Trust Center and Terms of Service.
Accelerating Discovery with SURFMAP on Tamarind Bio
Surface property analysis: view electrostatic and hydrophobic patches of a protein in one flat map.
Interface and binding site visualization: map discrete binding site labels stored in the B-factor column.
Comparative analysis: generate maps for several proteins with the same settings and compare them.
How to Use SURFMAP on Tamarind Bio
Log in: go to tamarind.bio and open the SURFMAP tool.
Provide the structure: upload a protein structure as a PDB file.
Choose the feature: select what to map, such as Kyte-Doolittle or Wimley-White hydrophobicity, stickiness, circular variance, electrostatics, B-factor or binding sites, if exposed.
Set parameters: if exposed, choose the projection (Flamsteed, Mollweide or Lambert) and the grid cell size.
Run: submit the job and wait for the map to be generated.
Download outputs: collect the map image and the smoothed matrix text file.
Interpret: look for patches of high or low values and compare them across proteins or conformations.
Use downstream: use the maps to guide interface analysis, mutagenesis or design decisions.
Things to Keep in Mind
Binding site mapping needs discrete B-factor values such as 0, 1 and 2, and the no-smoothing option should be used only with discrete values.
Electrostatics maps rely on the optional APBS program.
The grid cell size must be a multiple of 180.
The repository does not provide scripts for averaging matrices.
Source: Schweke H, Mucchielli MH, Chevrollier N, Gosset S, Lopes A. SURFMAP: a software for mapping in two dimensions protein surface features. J. Chem. Inf. Model. (2022), DOI 10.1021/acs.jcim.1c01269. Code: github.com/i2bc/SURFMAP.