| CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories A Jurcik, D Bednar, J Byska, SM Marques, K Furmanova, L Daniel, ... Bioinformatics 34 (20), 3586-3588, 2018 | 302 | 2018 |
| Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport J Stourac, O Vavra, P Kokkonen, J Filipovic, G Pinto, J Brezovsky, ... Nucleic acids research 47 (W1), W414-W422, 2019 | 198 | 2019 |
| Engineering enzyme access tunnels P Kokkonen, D Bednar, G Pinto, Z Prokop, J Damborsky Biotechnology advances 37 (6), 107386, 2019 | 164 | 2019 |
| Transcription and translation inhibitors in cancer treatment N Laham-Karam, GP Pinto, A Poso, P Kokkonen Frontiers in Chemistry 8, 276, 2020 | 76 | 2020 |
| Studying SIRT6 regulation using H3K56 based substrate and small molecules P Kokkonen, M Rahnasto-Rilla, P Mellini, E Jarho, M Lahtela-Kakkonen, ... European Journal of Pharmaceutical Sciences 63, 71-76, 2014 | 61 | 2014 |
| Substrate inhibition by the blockage of product release and its control by tunnel engineering P Kokkonen, A Beier, S Mazurenko, J Damborsky, D Bednar, Z Prokop RSC chemical biology 2 (2), 645-655, 2021 | 59 | 2021 |
| Peptides and pseudopeptides as SIRT6 deacetylation inhibitors P Kokkonen, M Rahnasto-Rilla, PH Kiviranta, T Huhtiniemi, T Laitinen, ... ACS Medicinal Chemistry Letters 3 (12), 969-974, 2012 | 41 | 2012 |
| Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling D Hess, V Dockalova, P Kokkonen, D Bednar, J Damborsky, A DeMello, ... Chem 7 (4), 1066-1079, 2021 | 31 | 2021 |
| Molecular gating of an engineered enzyme captured in real time P Kokkonen, J Sykora, Z Prokop, A Ghose, D Bednar, M Amaro, ... Journal of the American Chemical Society 140 (51), 17999-18008, 2018 | 31 | 2018 |
| Virtual screening approach of sirtuin inhibitors results in two new scaffolds P Kokkonen, T Kokkola, T Suuronen, A Poso, E Jarho, ... European Journal of Pharmaceutical Sciences 76, 27-32, 2015 | 23 | 2015 |
| The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step P Kokkonen, M Slanska, V Dockalova, GP Pinto, EM Sánchez-Carnerero, ... Computational and Structural Biotechnology Journal 18, 805-813, 2020 | 20 | 2020 |
| Structure of POPC lipid bilayers in OPLS3e force field M Kurki, A Poso, P Bartos, MS Miettinen Journal of Chemical Information and Modeling 62 (24), 6462-6474, 2022 | 17 | 2022 |
| Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site P Kokkonen, D Bednar, V Dockalova, Z Prokop, J Damborsky Journal of Biological Chemistry 293 (29), 11505-11512, 2018 | 14 | 2018 |
| Structure-function relationships and engineering of haloalkane dehalogenases P Kokkonen, T Koudelakova, R Chaloupkova, L Daniel, Z Prokop, ... Aerobic utilization of hydrocarbons, oils and lipids. Cham: Springer …, 2017 | 13 | 2017 |
| Quantitative insights for the design of substrate-based SIRT1 inhibitors P Kokkonen, P Mellini, O Nyrhilä, M Rahnasto-Rilla, T Suuronen, ... European Journal of Pharmaceutical Sciences 59, 12-19, 2014 | 10 | 2014 |
| Direct pathway cloning and expression of the radiosumin biosynthetic gene cluster X Ouyang, PM D'Agostino, M Wahlsten, E Delbaje, J Jokela, P Permi, ... Organic & Biomolecular Chemistry 21 (23), 4893-4908, 2023 | 7 | 2023 |
| Follistatin-like 1 and its paralogs in heart development and cardiovascular disease M Horak, DL Fairweather, P Kokkonen, D Bednar, J Bienertova-Vasku Heart failure reviews 27 (6), 2251-2265, 2022 | 7 | 2022 |
| RNA-protein complexes and force field polarizability H Baltrukevich, P Bartos Frontiers in Chemistry 11, 2023 | 1 | 2023 |
| Studying sirtuin inhibitors with in silico and in vitro approaches P Kokkonen Itä-Suomen yliopisto, 2015 | | 2015 |
