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Fatima Pardo-Avila
Fatima Pardo-Avila
Verified email at stanford.edu
Title
Cited by
Cited by
Year
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 Labăo-Almeida, LR Ali, ...
Nature 565 (7738), 186-191, 2019
4092019
Comprehensive computational design of ordered peptide macrocycles
P Hosseinzadeh, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, ...
Science 358 (6369), 1461-1466, 2017
1622017
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
1622014
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
912016
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
732018
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
632016
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
632013
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
412021
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
232018
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
192015
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
172018
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
102019
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
102019
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
92016
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
62013
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
42021
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, ...
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