Daniel-Adriano Silva
Daniel-Adriano Silva
Monod Bio, Inc
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Macromolecular modeling and design in Rosetta: recent methods and frameworks
JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ...
Nature methods 17 (7), 665-680, 2020
Massively parallel de novo protein design for targeted therapeutics
A Chevalier, DA Silva, GJ Rocklin, DR Hicks, R Vergara, P Murapa, ...
Nature 550 (7674), 74-79, 2017
Monitoring and Inhibition of Insulin Fibrillation by a Small Organic Fluorogen with Aggregation-Induced Emission Characteristics
Y Hong, L Meng, S Chen, CWT Leung, L Da, M Faisal, DA Silva Manzano, ...
Journal of the American Chemical Society, 2012
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 LabŃo-Almeida, LR Ali, ...
Nature 565 (7738), 186-191, 2019
A role for both conformational selection and induced fit in ligand binding by the LAO protein
DA Silva, GR Bowman, A Sosa-Peinado, X Huang
PLoS computational biology 7 (5), e1002054, 2011
De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
TW Linsky, R Vergara, N Codina, JW Nelson, MJ Walker, W Su, ...
Science 370 (6521), 1208-1214, 2020
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
Comprehensive computational design of ordered peptide macrocycles
P Hosseinzadeh, G Bhardwaj, VK Mulligan, MD Shortridge, TW Craven, ...
Science 358 (6369), 1461-1466, 2017
Principles for designing proteins with cavities formed by curved β sheets
E Marcos, B Basanta, TM Chidyausiku, Y Tang, G Oberdorfer, G Liu, ...
Science 355 (6321), 201-206, 2017
De novo protein design by citizen scientists
B Koepnick, J Flatten, T Husain, A Ford, DA Silva, MJ Bick, A Bauer, G Liu, ...
Nature 570 (7761), 390-394, 2019
Computationally designed high specificity inhibitors delineate the roles of BCL2 family proteins in cancer
S Berger, E Procko, D Margineantu, EF Lee, BW Shen, A Zelter, DA Silva, ...
elife 5, e20352, 2016
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
Initiation complex structure and promoter proofreading
X Liu, DA Bushnell, DA Silva, X Huang, RD Kornberg
Science 333 (6042), 633-637, 2011
Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
W Zhuang, RZ Cui, DA Silva, X Huang
The Journal of Physical Chemistry B, 2011
Quantitatively characterizing the ligand binding mechanisms of choline binding protein using Markov state model analysis
S Gu, DA Silva, L Meng, A Yue, X Huang
PLoS computational biology 10 (8), e1003767, 2014
Hierarchical Nystr÷m methods for constructing Markov state models for conformational dynamics
Y Yao, RZ Cui, GR Bowman, DA Silva, J Sun, X Huang
The Journal of chemical physics 138 (17), 05B602_1, 2013
Force field development for cofactors in the photosystem II
L Zhang, DA Silva, YJ Yan, X Huang
Journal of computational chemistry 33 (25), 1969-1980, 2012
De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
B Dang, H Wu, VK Mulligan, M Mravic, Y Wu, T Lemmin, A Ford, DA Silva, ...
Proceedings of the National Academy of Sciences 114 (41), 10852-10857, 2017
Dynamic protein conformations preferentially drive energy transfer along the active chain of the photosystem II reaction centre
L Zhang, DA Silva, H Zhang, A Yue, YJ Yan, X Huang
Nature Communications 5 (1), 4170, 2014
Essentials of de novo protein design: Methods and applications
E Marcos, DA Silva
Wiley Interdisciplinary Reviews: Computational Molecular Science, e1374, 2018
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