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Abstract
The Curated Protein Aggregation Database (CPAD) is a manually curated and open-access database dedicated to providing comprehensive information related to mechanistic, kinetic and structural aspects of protein and peptide aggregation. The database has been updated to CPAD 2.0 by significantly expanding datasets and improving the user-interface. Key features of CPAD 2.0 are (i) 83,098 data points on aggregation kinetics experiments, (ii) 565 structures related to aggregation, which are classified into proteins, fibrils, and protein-ligand complexes, (iii) 2031 aggregating/non-aggregating peptides with pre-calculated aggregation properties, and (iv) 912 aggregation-prone regions in amyloidogenic proteins. This database will help the scientific community (a) by facilitating research leading to improved understanding of protein aggregation, (b) by helping develop, validate and benchmark mechanistic and kinetic models of protein aggregation, and (c) by assisting experimentalists with design of their investigations and dissemination of data generated by their studies. CPAD 2.0 can be accessed at https://web.iitm.ac.in/bioinfo2/cpad2/index.html.
Acknowledgement
We thank Bioinformatics Infrastructure facility, Department of Biotechnology and Indian Institute of Technology Madras for computational facilities and Ministry of human resource and development (MHRD) for HTRA scholarship to PR.
Disclosure statement
Sandeep Kumar is an employee of Boehringer Ingelheim Pharmaceutical Inc. USA
Links to other databases
CPAD 2.0 protein entries are linked to the UniProt (https://www.uniprot.org/) and PDB (http://www.rcsb.org) database and the references entries are linked to the PubMed (http://www.ncbi.nlm.nih.gov/pubmed/) literature database. We have also provided links to other aggregation related databases and prediction servers in the CPAD 2.0.
Database availability and management
The database can be freely accessed at https://web.iitm.ac.in/bioinfo2/cpad2/index.html. We actively maintain the database and update regularly. All the suggestions and comments are welcome and should be addressed to [email protected]. Researchers can use the upload portal in the databases to submit newly published results. All uploaded material will go through manual inspection before getting published in the CPAD 2.0.