Searching for tunnels of proteins - comparison of approaches and available software tools. - Deepti Jaiswal Kundu; Radka Svobodová Vareková; Crina-Maria Ionescu; David Sehnal; Jaroslav Koca (J. Cheminformatics, 2012)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

Consistency of sugar structures and their annotation in the PDB. - Deepti Jaiswal Kundu; David Sehnal; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2014)

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. - Radka Svobodová Vareková; Deepti Jaiswal Kundu; David Sehnal; Crina-Maria Ionescu; Stanislav Geidl; Lukás Pravda; Vladimír Horský; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2014)

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. - David Sehnal; Radka Svobodová Vareková; Lukás Pravda; Crina-Maria Ionescu; Stanislav Geidl; Vladimír Horský; Deepti Jaiswal Kundu; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2015)

The PRIDE database and related tools and resources in 2019: improving support for quantification data. - Yasset Pérez-Riverol; Attila Csordas; Jingwen Bai 003; Manuel Bernal Llinares; Suresh Hewapathirana; Deepti Jaiswal Kundu; Avinash Inuganti; Johannes Griss; Gerhard Mayer; Martin Eisenacher; Enrique Pérez; Julian Uszkoreit; et al. (Nucleic Acids Res., 2019)

The ProteomeXchange consortium in 2020: enabling 'big data' approaches in proteomics. - Eric W. Deutsch; Nuno Bandeira; Vagisha Sharma; Yasset Pérez-Riverol; Jeremy Carver; Deepti Jaiswal Kundu; David García-Seisdedos; Andrew F. Jarnuczak; Suresh Hewapathirana; Benjamin S. Pullman; Julie Wertz; Zhi Sun; et al. (Nucleic Acids Res., 2020)

Expression Atlas update: gene and protein expression in multiple species. - Pablo A. Moreno; Silvie Fexova; Nancy George; Jonathan R. Manning; Zhichao Miao; Suhaib Mohammed; Alfonso Muñoz-Pomer Fuentes; Anja Füllgrabe; Yalan Bi; Natassja Bush; Haider Iqbal; Upendra Kumbham; et al. (Nucleic Acids Res., 2022)

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. - Yasset Pérez-Riverol; Jingwen Bai 003; Chakradhar Bandla; David García-Seisdedos; Suresh Hewapathirana; Selvakumar Kamatchinathan; Deepti Jaiswal Kundu; Ananth Prakash; Anika Frericks-Zipper; Martin Eisenacher; Mathias Walzer; Shengbo Wang; et al. (Nucleic Acids Res., 2022)

Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues. - Shengbo Wang; David García-Seisdedos; Ananth Prakash; Deepti Jaiswal Kundu; Andrew Collins 003; Nancy George; Silvie Fexova; Pablo A. Moreno; Irene Papatheodorou; Andrew R. Jones; Juan Antonio Vizcaíno (PLoS Comput. Biol., 2022)

The ProteomeXchange consortium at 10 years: 2023 update. - Eric W. Deutsch; Nuno Bandeira; Yasset Pérez-Riverol; Vagisha Sharma; Jeremy Carver; Luis Mendoza; Deepti Jaiswal Kundu; Shengbo Wang; Chakradhar Bandla; Selvakumar Kamatchinathan; Suresh Hewapathirana; Benjamin S. Pullman; et al. (Nucleic Acids Res., 2023)