Cossio P - Search Results

1

Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.

Mazzaferro N, Sasmal S, Cossio P, Hocky GM. Mazzaferro N, et al. Among authors: cossio p. J Chem Theory Comput. 2024 Jul 23;20(14):5901-5912. doi: 10.1021/acs.jctc.4c00425. Epub 2024 Jul 2. J Chem Theory Comput. 2024. PMID: 38954555 Free PMC article.

2

Catching actin proteins in action.

Cossio P, Hocky GM. Cossio P, et al. Nature. 2022 Nov;611(7935):241-243. doi: 10.1038/d41586-022-03343-x. Nature. 2022. PMID: 36289412 No abstract available.

3

Active Learning of Boltzmann Samplers and Potential Energies with Quantum Mechanical Accuracy.

Molina-Taborda A, Cossio P, Lopez-Acevedo O, Gabrié M. Molina-Taborda A, et al. Among authors: cossio p. J Chem Theory Comput. 2024 Oct 22;20(20):8833-8843. doi: 10.1021/acs.jctc.4c00506. Epub 2024 Oct 6. J Chem Theory Comput. 2024. PMID: 39370622

4

Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations.

Palacio-Rodriguez K, Vroylandt H, Stelzl LS, Pietrucci F, Hummer G, Cossio P. Palacio-Rodriguez K, et al. Among authors: cossio p. J Phys Chem Lett. 2022 Aug 18;13(32):7490-7496. doi: 10.1021/acs.jpclett.2c01807. Epub 2022 Aug 8. J Phys Chem Lett. 2022. PMID: 35939819

5

Ensemble Reweighting Using Cryo-EM Particle Images.

Tang WS, Silva-Sánchez D, Giraldo-Barreto J, Carpenter B, Hanson SM, Barnett AH, Thiede EH, Cossio P. Tang WS, et al. Among authors: cossio p. J Phys Chem B. 2023 Jun 22;127(24):5410-5421. doi: 10.1021/acs.jpcb.3c01087. Epub 2023 Jun 9. J Phys Chem B. 2023. PMID: 37293763

6

Multiple-Allele MHC Class II Epitope Engineering by a Molecular Dynamics-Based Evolution Protocol.

Ochoa R, Lunardelli VAS, Rosa DS, Laio A, Cossio P. Ochoa R, et al. Among authors: cossio p. Front Immunol. 2022 Apr 27;13:862851. doi: 10.3389/fimmu.2022.862851. eCollection 2022. Front Immunol. 2022. PMID: 35572587 Free PMC article.

7

Protocol for iterative optimization of modified peptides bound to protein targets.

Ochoa R, Cossio P, Fox T. Ochoa R, et al. Among authors: cossio p. J Comput Aided Mol Des. 2022 Nov;36(11):825-835. doi: 10.1007/s10822-022-00482-1. Epub 2022 Oct 19. J Comput Aided Mol Des. 2022. PMID: 36258137 Free PMC article.

8

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments.

Giraldo-Barreto J, Ortiz S, Thiede EH, Palacio-Rodriguez K, Carpenter B, Barnett AH, Cossio P. Giraldo-Barreto J, et al. Among authors: cossio p. Sci Rep. 2021 Jul 1;11(1):13657. doi: 10.1038/s41598-021-92621-1. Sci Rep. 2021. PMID: 34211017 Free PMC article.

9

Application of ensemble pharmacophore-based virtual screening to the discovery of novel antimitotic tubulin inhibitors.

Gallego-Yerga L, Ochoa R, Lans I, Peña-Varas C, Alegría-Arcos M, Cossio P, Ramírez D, Peláez R. Gallego-Yerga L, et al. Among authors: cossio p. Comput Struct Biotechnol J. 2021 Aug 3;19:4360-4372. doi: 10.1016/j.csbj.2021.07.039. eCollection 2021. Comput Struct Biotechnol J. 2021. PMID: 34429853 Free PMC article.

10

Exponential consensus ranking improves the outcome in docking and receptor ensemble docking.

Palacio-Rodríguez K, Lans I, Cavasotto CN, Cossio P. Palacio-Rodríguez K, et al. Among authors: cossio p. Sci Rep. 2019 Mar 26;9(1):5142. doi: 10.1038/s41598-019-41594-3. Sci Rep. 2019. PMID: 30914702 Free PMC article.

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