This study uses free energy of perturbation calculations to assess how the R346K mutation in the Mu SARS-CoV-2 variant affects binding to class 2 monoclonal antibodies.

27 citations

virusstatistical model

𝕏 PostBluesky

Molecular BiologyJournal of Chemical Information and ModelingPeer-reviewedNov 22, 2021

The N501Y and K417N mutations in the spike protein of SARS-CoV-2 alter the interactions with both hACE2 and human derived antibody: A Free energy of perturbation study

F. Fratev

This study uses free energy perturbation to analyze how N501Y and K417N mutations in SARS-CoV-2 spike protein affect interactions with hACE2 and an antibody, showing increased binding to ACE2 and decreased binding to the antibody.

97 citationstop 2%

humanprotein structure

𝕏 PostBluesky

BiophysicsbioRxivPreprintJan 4, 2019

Discovery of New Classes of Glycine transporter 2 (GlyT2) Inhibitors and Study of GlyT2 Selectivity by Combination of Novel Structural Based Virtual Screening Approach and Free Energy Perturbation (FEP+) Calculations

Filip Fratev, Manuel Miranda-Arango, Elvia Padilla, Suman Sirimulla

The paper discovers new GlyT2 inhibitors with high selectivity over GlyT1 using virtual screening and FEP+ calculations, and suggests potential for treating chronic pain and pancreatic cancer.

DOI 10.1101/510487

humanprotein structure

𝕏 PostBluesky

BioinformaticsACS OmegaPeer-reviewedApr 20, 2018

Prediction of Accurate Binding Modes using Combination of classical and accelerated Molecular dynamics and Free Energy Perturbation Calculations: An Application to Toxicity Studies

F. Fratev, Thomas B. Steinbrecher, Svava Ósk Jónsdóttir

The paper predicts accurate binding modes of PFCAs in PPARγ using combined docking, MD simulations, and FEP+ to improve toxicity studies.

32 citations

protein structuremixed model

𝕏 PostBluesky