Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics. - Soumendranath Bhakat; Pär Söderhjelm (J. Comput. Aided Mol. Des., 2017)

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling. - Soumendranath Bhakat; Emil Åberg; Pär Söderhjelm (J. Comput. Aided Mol. Des., 2018)

Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. - Soumendranath Bhakat; Pär Söderhjelm (J. Chem. Inf. Model., 2022)