| De novo design of potent and selective mimics of IL-2 and IL-15 DA Silva, S Yu, UY Ulge, JB Spangler, KM Jude, C Labão-Almeida, LR Ali, ... Nature 565 (7738), 186-191, 2019 | 491 | 2019 |
| Comprehensive computational design of ordered peptide macrocycles P Hosseinzadeh, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, ... Science 358 (6369), 1461-1466, 2017 | 201 | 2017 |
| Millisecond dynamics of RNA polymerase II translocation at atomic resolution DA Silva, DR Weiss, F Pardo Avila, LT Da, M Levitt, D Wang, X Huang Proceedings of the National Academy of Sciences 111 (21), 7665-7670, 2014 | 166 | 2014 |
| Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue LT Da, F Pardo-Avila, L Xu, DA Silva, L Zhang, X Gao, D Wang, X Huang Nature communications 7 (1), 11244, 2016 | 97 | 2016 |
| The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding R Kudva, P Tian, F Pardo-Avila, M Carroni, RB Best, HD Bernstein, ... Elife 7, e36326, 2018 | 82 | 2018 |
| Elucidation of the dynamics of transcription elongation by RNA polymerase II using kinetic network models L Zhang, F Pardo-Avila, IC Unarta, PPH Cheung, G Wang, D Wang, ... Accounts of chemical research 49 (4), 687-694, 2016 | 66 | 2016 |
| A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase LT Da, F Pardo Avila, D Wang, X Huang PLoS computational biology 9 (4), e1003020, 2013 | 65 | 2013 |
| Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites P Hosseinzadeh, PR Watson, TW Craven, X Li, S Rettie, F Pardo-Avila, ... Nature Communications 12 (1), 3384, 2021 | 63 | 2021 |
| Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature ME O’Sullivan, F Poitevin, RG Sierra, C Gati, EH Dao, Y Rao, F Aksit, ... Nucleic acids research 46 (18), 9793-9804, 2018 | 28 | 2018 |
| Structural model of RNA polymerase II elongation complex with complete transcription bubble reveals NTP entry routes L Zhang, DA Silva, F Pardo-Avila, D Wang, X Huang PLoS computational biology 11 (7), e1004354, 2015 | 23 | 2015 |
| Structure of the 30S ribosomal decoding complex at ambient temperature EH Dao, F Poitevin, RG Sierra, C Gati, Y Rao, HI Ciftci, F Akşit, A McGurk, ... Rna 24 (12), 1667-1676, 2018 | 20 | 2018 |
| 8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II KA Konovalov, F Pardo-Avila, CKM Tse, J Oh, D Wang, X Huang Journal of Biological Chemistry 294 (13), 4924-4933, 2019 | 15 | 2019 |
| Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function M Schulte‐Sasse, F Pardo‐Ávila, NO Pulido‐Mayoral, A Vázquez‐Lobo, ... The FEBS Journal 286 (5), 882-900, 2019 | 10 | 2019 |
| Constructing kinetic network models to elucidate mechanisms of functional conformational changes of enzymes and their recognition with ligands L Zhang, H Jiang, FK Sheong, F Pardo-Avila, PPH Cheung, X Huang Methods in Enzymology 578, 343-371, 2016 | 8 | 2016 |
| Theoretical investigations on elucidating fundamental mechanisms of catalysis and dynamics involved in transcription by RNA polymerase F Pardo-Avila, LT Da, Y Wang, X Huang Journal of Theoretical and Computational Chemistry 12 (08), 1341005, 2013 | 6 | 2013 |
| Probing interplays between human XBP1u translational arrest peptide and 80S ribosome F Di Palma, S Decherchi, F Pardo-Avila, S Succi, M Levitt, G von Heijne, ... Journal of chemical theory and computation 18 (3), 1905-1914, 2021 | 5 | 2021 |
| PDBCleanV2: A Python Library for Generating Consistent Structure Datasets F Pardo-Avila, L Weiner, P Cabral, NC Corsepius, F Poitevin, M Levitt bioRxiv, 2025.02. 14.638326, 2025 | | 2025 |
| Single-residue effects on the behavior of a nascent polypeptide chain inside the ribosome exit tunnel F Pardo-Avila, R Kudva, M Levitt, G Von Heijne bioRxiv, 2024 | | 2024 |
| Dynamics of the transcription elongation process of RNA polymerase elucidated at atomic resolution by molecular dynamics and Markov state models FA Pardo Avila | | 2015 |
| Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature EO Mary, F Poitevin, RG Sierra, C Gati, E Han, YR Dao, F Aksit, H Ciftci, ... | | |