| The PRIDE database and related tools and resources in 2019: improving support for quantification data Y Perez-Riverol, A Csordas, J Bai, M Bernal-Llinares, S Hewapathirana, ... Nucleic acids research 47 (D1), D442-D450, 2019 | 6584 | 2019 |
| The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences Y Perez-Riverol, J Bai, C Bandla, D García-Seisdedos, S Hewapathirana, ... Nucleic acids research 50 (D1), D543-D552, 2022 | 4485 | 2022 |
| The ProteomeXchange consortium in 2020: enabling ‘big data’approaches in proteomics EW Deutsch, N Bandeira, V Sharma, Y Perez-Riverol, JJ Carver, ... Nucleic acids research 48 (D1), D1145-D1152, 2020 | 737 | 2020 |
| The ProteomeXchange consortium at 10 years: 2023 update EW Deutsch, N Bandeira, Y Perez-Riverol, V Sharma, JJ Carver, ... Nucleic acids research 51 (D1), D1539-D1548, 2023 | 397 | 2023 |
| MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels K Berka, O Hanák, D Sehnal, P Banáš, V Navratilova, D Jaiswal, ... Nucleic acids research 40 (W1), W222-W227, 2012 | 156 | 2012 |
| Expression Atlas update: gene and protein expression in multiple species P Moreno, S Fexova, N George, JR Manning, Z Miao, S Mohammed, ... Nucleic acids research 50 (D1), D129-D140, 2022 | 149 | 2022 |
| A proteomics sample metadata representation for multiomics integration and big data analysis C Dai, A Füllgrabe, J Pfeuffer, EM Solovyeva, J Deng, P Moreno, ... Nature Communications 12 (1), 5854, 2021 | 77 | 2021 |
| An integrated landscape of protein expression in human cancer AF Jarnuczak, H Najgebauer, M Barzine, DJ Kundu, F Ghavidel, ... Scientific data 8 (1), 115, 2021 | 57 | 2021 |
| ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank D Sehnal, R Svobodová Vařeková, L Pravda, CM Ionescu, S Geidl, ... Nucleic acids research 43 (D1), D369-D375, 2015 | 38 | 2015 |
| MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes RS Vařeková, D Jaiswal, D Sehnal, CM Ionescu, S Geidl, L Pravda, ... Nucleic acids research 42 (W1), W227-W233, 2014 | 20 | 2014 |
| The PRIDE database at 20 years: 2025 update Y Perez-Riverol, C Bandla, DJ Kundu, S Kamatchinathan, J Bai, ... Nucleic Acids Research 53 (D1), D543-D553, 2025 | 18 | 2025 |
| Integrated view and comparative analysis of baseline protein expression in mouse and rat tissues S Wang, D García-Seisdedos, A Prakash, DJ Kundu, A Collins, N George, ... PLoS computational biology 18 (6), e1010174, 2022 | 17 | 2022 |
| Integrated view of baseline protein expression in human tissues A Prakash, D García-Seisdedos, S Wang, DJ Kundu, A Collins, N George, ... Journal of Proteome Research 22 (3), 729-742, 2022 | 16 | 2022 |
| Open‐source large language models in action: A bioinformatics chatbot for PRIDE database J Bai, S Kamatchinathan, DJ Kundu, C Bandla, JA Vizcaino, ... Proteomics, 2400005, 2024 | 7 | 2024 |
| Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome KA Ramsbottom, A Prakash, Y Perez-Riverol, OM Camacho, Z Sun, ... Journal of Proteome Research, 2024 | 6 | 2024 |
| Searching for tunnels of proteins–comparison of approaches and available software tools D Jaiswal, RS Vařeková, CM Ionescu, D Sehnal, J Koča Journal of Cheminformatics 4, 1-1, 2012 | 5 | 2012 |
| Ligand structures in the Protein Data Bank–can we trust them? D Sehnal, R Svobodová, CM Ionescu, S Geidl, L Pravda, D Jaiswal, ... | 1 | 2014 |
| Advancing Scientific Communication in Proteomics BC Searle, B Chazarin, BC Collins, DJ Kundu, S Huang, Q Lin, Y Liu, ... Journal of Proteome Research 24 (2), 381-382, 2025 | | 2025 |
| MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes R Svobodová, D Jaiswal, D Sehnal, CM Ionescu, S Geidl, L Pravda, ... | | 2014 |
| ValidatorDB: database of validation results for ligands and non-standard residues from the Protein Data Bank R Svobodová, D Jaiswal, D Sehnal, CM Ionescu, S Geidl, L Pravda, ... | | 2014 |
