HotMAPS @ Karchin lab

HotMAPS (Hotspot Missense mutation Areas in Protein Structures)

detects somatic mutation hotspot regions in 3D protein structures from a cohort of cancer samples.

Missense mutations in cancer can often be difficult to interpret their effect, but missense mutations occurring at hotspots tend to implicate a driving role in cancer. Hotspot regions are identified at an individual residue basis, and can be of varying sizes (e.g., 1, 5, or other number of residues). Protein structures often have multiple protein chains, which may arise from the same gene and thus be mutated at the same residue position. Identical chains are accounted for in the model to prevent errors induced by assuming chains are independent. For example, an annotated mutation in a gene forming a homodimer will always contain the same mutation in both chains. PDB biological assemblies are used when available to best reveal biologically meaningful 3D hotspots.

HotMAPS is free for non-commercial use. For more details please refer to our Software License. Commercial users should contact the Johns Hopkins Technology Transfer office.

Current stable release is HotMAPS.1.0.0, last updated on 06/7/2016.

Source Code Releases

You can view the current source code on github.

HotMAPS-1.0.0.tar.gz    06/7/2016    Initial relase.


Please consult the project wiki page for installation and usage details.

Example workflow

An example of running HotMAPS is described on project wiki. Please follow the wiki page for a step-by-step walk-through.


HotMAPS is intended to run on linux operating systems. It needs both python and java. Please see the installation instructions.

Primary citation

If you use our software for a publication, please cite the following:
Tokheim C, Bhattacharya R, Niknafs N, Gygax DM, Kim R, Ryan M, Masica DL, Karchin R (2016) Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure. Cancer Research. Apr. 28.pii: canres.3190.2015. [Epub ahead of print]

Software primary contact/developer

Collin Tokheim:  ctokheim at jhu dot edu