Welcome to HotSpot3D

Analyse Mutations in Protein 3D Structures

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Analysing Your Own Mutation Data for Clusters

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Coloum Number Name State Description
1 Hugo_Symbol Standard Hugo_symbols refer to the naming of human genes from the HUGO Gene Nomenclature Committee.
2 Chromosome Standard Chromosome field is a numeric value, for example, 18 indicates that the mutation appears on chromosome 18.
3 Start_Position Standard The starting position.
4 End_Position Standard The end position.
5 Varient_classfication Standard No need to screen for mutation types provided. Any varriant classfications can for HOTSPOT3D, not just missense mutation.
6 Reference_Allele Standard Reference allele refers to the base that is found in the reference genome.
7 Reference_Allele1 Standard
8 Reference_Allele2 Standard
9 Tumor_Sample_Barcode Standard
10 Transcript_name Non-standard A transcript ID column, referring to Ensembl coding transcript ID's (ENST).
11 amino_acid_change Non-standard A protein peptide change column (HGVS p. single letter abbreviations, ie p.T790M)


HotSpot3D, to identify spatial hotspots (clusters) and to interpret the potential function of variants within them.
We applied HotSpot3D to >4,400 TCGA tumors across 33 cancer types, and obtained the following results:



Druggable Mutations


Rare Mutations


Medium Reccurence Mutations


Hotspot3D is a high-precision software for identifying high-frequency mutation hotspots in pan-cancer somatic cells.


Hotspot3D is a high-precision software for identifying high-frequency mutation hotspots in pan-cancer cells. HotSpot3D Web is dedicated to providing researchers with an easier way: you can quickly get software results using the HotSpot3D kernel with a single click of the prepared mutant data file.

Visualization and Re-visualization

Hotspot3D Web provides you with result data files and 3D visualization of the mutation hotspots. In addition, re-visualization is supported. Anytime, you can view mutation hotspots on protein 3D structure by uploading the results file.


We applied Hotspot3D to TCGA to >4,400 TCGA tumors across 19 cancer types including BLCA, BRCA, CESC and so on. We directly provide results and visualization of clustering data on mutations here .

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