CaRinDB is an interactive database designed to streamline cancer mutation research by integrating data from The Cancer Genome Atlas (TCGA) and advanced structural analysis tools, along with advanced effect predictions and molecular features such as Residue Interaction Networks (RINs) derived from Protein Data Bank experimental structures and AlphaFoldDB computational models. Covering 33 distinct cancer types, CaRinDB offers a broad spectrum of insights into cancer mutation dynamics.
This platform allows users to extract, visualize, and interactively explore diverse mutations through an intuitive interface, and allows for evaluation of their structural impact.
CaRinDB provides a curated dataset featuring residue connectivity metrics, allele frequencies, references to biological databases, and functional predictions from 22 distinct tools, making it a valuable resource for AI/ML-based research. CaRinDB is well suited for training AI and machine learning models, enabling breakthroughs in understanding the molecular basis of cancer and its clinical implications, such as precision medicine and therapeutic target discovery.
Unlike existing tools, CaRinDB facilitates integration of polymorphism data with protein structural data and residue interaction networks, offering precision in mutation analysis.
CaRinDB integrated to AlphaFold Protein Structure Database:
Complete CaRinDB Variants with SNPs per Samples.
Summary description of selected tissues.
Plots of selected tissues: .
Complete CaRinDB Variants integrated to AlphaFold Protein Structure Database.
Summary description of selected tissues.
Plots of selected tissues: .
Run our guided tour on Home how to use our platform.
The construction of the databases available in CaRinDB involved numerous public data repositories: National Cancer Institute - GDC Data Portal , missense mutations were annotated in ANNOVAR , SnpEFF , NCBI - National Center for Biotechnology Information , ClinVar , Uniprot , and PDB - Protein Data Bank . Residue interaction network data was obtained through the RING program. 3D protein structure predictions were also obtained from Alphafold . Predictions to verify the pathogenicity of mutations were also obtained from AlphaMissense .
CaRinDB: An integrated database of common cancer mutations and residue interaction network parameters. Daniela Coelho Batista Guedes Pereira 1,2 , João Vitor Ferreira Cavalcante 1 , Raul Maia Falcão 1 , Jorge Estefano Santana de Souza 1 , Rodrigo Juliani Siqueira Dalmolin 1 , Gustavo Antônio de Souza 1 , Thaís Gaudencio do Rêgo 1,2 , Patrick Terrematte 1,2 , and João Paulo Matos Santos Lima 1,3 , To be published.
The CaRinDB team is available to assist users who want to import their data on demand. If you have some question, feedback, or request, contact the
Corresponding author:
João Paulo Matos Santos Lima (jpmslima [at] imd.ufrn.br)
Data contained within the CaRinDB Database is provided for non-commercial research.