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RCDPeaks: memory-efficient density peaks clustering of long molecular dynamics.
Platero-Rochart D, González-Alemán R, Hernández-Rodríguez EW, Leclerc F, Caballero J, Montero-Cabrera L. Platero-Rochart D, et al. Among authors: caballero j. Bioinformatics. 2022 Mar 28;38(7):1863-1869. doi: 10.1093/bioinformatics/btac021. Bioinformatics. 2022. PMID: 35020783
MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics.
González-Alemán R, Platero-Rochart D, Rodríguez-Serradet A, Hernández-Rodríguez EW, Caballero J, Leclerc F, Montero-Cabrera L. González-Alemán R, et al. Among authors: caballero j. Bioinformatics. 2022 Nov 30;38(23):5191-5198. doi: 10.1093/bioinformatics/btac666. Bioinformatics. 2022. PMID: 36205607
Computational study of the binding orientation and affinity of noncovalent inhibitors of the papain-like protease (PLpro) from SARS-CoV-1 considering the protein flexibility by using molecular dynamics and cross-docking.
Castillo-Campos L, Velázquez-Libera JL, Caballero J. Castillo-Campos L, et al. Among authors: caballero j. Front Mol Biosci. 2023 Jun 23;10:1215499. doi: 10.3389/fmolb.2023.1215499. eCollection 2023. Front Mol Biosci. 2023. PMID: 37426421 Free PMC article.
Understanding the Interactions of Ubiquitin-Specific Protease 7 with Its Substrates through Molecular Dynamics Simulations: Insights into the Role of Its C-Terminal Domains in Substrate Recognition.
Velázquez-Libera JL, Caballero J, Alzate-Morales J, Ruiz-Pernía JJ, Tuñón I. Velázquez-Libera JL, et al. Among authors: caballero j. J Chem Inf Model. 2024 May 4. doi: 10.1021/acs.jcim.3c01971. Online ahead of print. J Chem Inf Model. 2024. PMID: 38703206
664 results