Efficient optimization of van der Waals parameters from bulk properties. - Steven K. Burger; G. Andrés Cisneros (J. Comput. Chem., 2013)

LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. - Eric G. Kratz; Alice R. Walker; Louis Lagardère; Filippo Lipparini; Jean-Philip Piquemal; G. Andrés Cisneros (J. Comput. Chem., 2016)

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding. - Alice R. Walker; Pavel Silvestrov; Tina A. Müller; Robert H. Podolsky; Gregory Dyson; Robert P. Hausinger; Gerardo Andrés Cisneros (PLoS Comput. Biol., 2017)

Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase. - Sehr Naseem-Khan; Madison B. Berger; Emmett M. Leddin; Yazdan Maghsoud; G. Andrés Cisneros (J. Chem. Inf. Model., 2022)

Computational Investigation of a Series of Small Molecules as Potential Compounds for Lysyl Hydroxylase-2 (LH2) Inhibition. - Yazdan Maghsoud; Erik Antonio Vázquez-Montelongo; Xudong Yang; Chengwen Liu; Zhifeng Jing; Juhoon Lee; Matthew Harger; Ally K. Smith; Miguel Espinoza; Hou-Fu Guo; Jonathan M. Kurie; Kevin N. Dalby; et al. (J. Chem. Inf. Model., 2023)

Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study. - Yazdan Maghsoud; Chao Dong; G. Andrés Cisneros (J. Chem. Inf. Model., 2023)

AmberTools. - David A. Case; Hasan Metin Aktulga; Kellon Belfon; David S. Cerutti; G. Andrés Cisneros; Vinícius Wilian D. Cruzeiro; Negin Forouzesh; Timothy J. Giese; Andreas W. Götz; Holger Gohlke; Saeed Izadi; Koushik Kasavajhala; et al. (J. Chem. Inf. Model., 2023)

Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. - Yazdan Maghsoud; Vindi M. Jayasinghe-Arachchige; Pratibha Kumari 003; G. Andrés Cisneros; Jin Liu 005 (J. Chem. Inf. Model., 2023)

Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. - Yazdan Maghsoud; Arkanil Roy; Emmett M. Leddin; G. Andrés Cisneros (J. Chem. Inf. Model., 2024)