Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models. - Pär Söderhjelm; J. W. Krogh; Gunnar Karlström; Ulf Ryde; Roland Lindh (J. Comput. Chem., 2007)

How accurate are continuum solvation models for drug-like molecules? - Jacob Kongsted; Pär Söderhjelm; Ulf Ryde (J. Comput. Aided Mol. Des., 2009)

Conformational dependence of charges in protein simulations. - Pär Söderhjelm; Ulf Ryde (J. Comput. Chem., 2009)

Students' performance on programming-related tasks in an informatics contest in Finland, Sweden and Lithuania. - Valentina Dagiene; Linda Mannila; Timo Poranen; Lennart Rolandsson; Pär Söderhjelm (ITiCSE, 2014)

Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics. - Ya-Wen Hsiao; Pär Söderhjelm (J. Comput. Aided Mol. Des., 2014)

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field. - Francesco Manzoni; Pär Söderhjelm (J. Comput. Aided Mol. Des., 2014)

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. - Paulius Mikulskis; Daniela Cioloboc; Milica Andrejic; Sakshi Khare; Joakim Brorsson; Samuel Genheden; Ricardo A. Mata; Pär Söderhjelm; Ulf Ryde (J. Comput. Aided Mol. Des., 2014)

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. - Samuel Genheden; Ulf Ryde; Pär Söderhjelm (J. Comput. Chem., 2015)

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. - Martin A. Olsson; Pär Söderhjelm; Ulf Ryde (J. Comput. Chem., 2016)

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)

Can MM/GBSA calculations be sped up by system truncation? - Majda Misini Ignjatovic; Paulius Mikulskis; Pär Söderhjelm; Ulf Ryde (J. Comput. Chem., 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)