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Pär Söderhjelm - Publications

Affiliations: 
Department of Biophysics Lund University, Lund, Skåne län, Sweden 
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43 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Kulkarni M, Söderhjelm P. Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics. Journal of Chemical Theory and Computation. 19: 6605-6618. PMID 37698852 DOI: 10.1021/acs.jctc.3c00460  0.667
2022 Bhakat S, Söderhjelm P. Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems. Journal of Chemical Information and Modeling. 62: 914-926. PMID 35138093 DOI: 10.1021/acs.jcim.1c00840  0.663
2018 Persson F, Söderhjelm P, Halle B. The geometry of protein hydration. The Journal of Chemical Physics. 148: 215101. PMID 29884063 DOI: 10.1063/1.5026744  0.326
2018 Persson F, Söderhjelm P, Halle B. The spatial range of protein hydration. The Journal of Chemical Physics. 148: 215104. PMID 29884061 DOI: 10.1063/1.5031005  0.39
2018 Persson F, Söderhjelm P, Halle B. How proteins modify water dynamics. The Journal of Chemical Physics. 148: 215103. PMID 29884055 DOI: 10.1063/1.5026861  0.353
2017 Misini Ignjatović M, Mikulskis P, Söderhjelm P, Ryde U. Can MM/GBSA calculations be sped up by system truncation? Journal of Computational Chemistry. PMID 29178493 DOI: 10.1002/Jcc.25120  0.688
2017 Bhakat S, Åberg E, Söderhjelm P. Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling. Journal of Computer-Aided Molecular Design. PMID 29052792 DOI: 10.1007/S10822-017-0074-X  0.728
2017 Bhakat S, Söderhjelm P. Resolving the problem of trapped water in binding cavities: prediction of host-guest binding free energies in the SAMPL5 challenge by funnel metadynamics. Journal of Computer-Aided Molecular Design. 31: 119-132. PMID 27573983 DOI: 10.1007/S10822-016-9948-6  0.731
2016 Olsson MA, Söderhjelm P, Ryde U. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level. Journal of Computational Chemistry. PMID 27117350 DOI: 10.1002/Jcc.24375  0.687
2016 Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chemical Reviews. PMID 27077817 DOI: 10.1021/Acs.Chemrev.5B00630  0.688
2016 Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chemical Biology & Drug Design. 88: 159-77. PMID 26872937 DOI: 10.1111/Cbdd.12745  0.701
2015 Genheden S, Ryde U, Söderhjelm P. Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model. Journal of Computational Chemistry. 36: 2114-24. PMID 26280564 DOI: 10.1002/Jcc.24048  0.68
2014 Andreji? M, Ryde U, Mata RA, Söderhjelm P. Coupled-cluster interaction energies for 200-atom host-guest systems. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 15: 3270-81. PMID 25262989 DOI: 10.1002/Cphc.201402379  0.641
2014 Mikulskis P, Cioloboc D, Andreji? M, Khare S, Brorsson J, Genheden S, Mata RA, Söderhjelm P, Ryde U. Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies. Journal of Computer-Aided Molecular Design. 28: 375-400. PMID 24700414 DOI: 10.1007/S10822-014-9739-X  0.678
2014 Manzoni F, Söderhjelm P. Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field. Journal of Computer-Aided Molecular Design. 28: 235-44. PMID 24577872 DOI: 10.1007/S10822-014-9733-3  0.443
2014 Hsiao YW, Söderhjelm P. Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics. Journal of Computer-Aided Molecular Design. 28: 443-54. PMID 24535628 DOI: 10.1007/S10822-014-9724-4  0.471
2013 Sumner S, Söderhjelm P, Ryde U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. Journal of Chemical Theory and Computation. 9: 4205-14. PMID 26592409 DOI: 10.1021/Ct400339C  0.589
2013 Hu L, Söderhjelm P, Ryde U. Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations. Journal of Chemical Theory and Computation. 9: 640-9. PMID 26589061 DOI: 10.1021/Ct3005003  0.666
2013 Godschalk F, Genheden S, Söderhjelm P, Ryde U. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations. Physical Chemistry Chemical Physics : Pccp. 15: 7731-9. PMID 23595060 DOI: 10.1039/C3Cp00116D  0.674
2012 Söderhjelm P, Tribello GA, Parrinello M. Locating binding poses in protein-ligand systems using reconnaissance metadynamics Proceedings of the National Academy of Sciences of the United States of America. 109: 5170-5175. PMID 22440749 DOI: 10.1073/Pnas.1201940109  0.575
2012 Söderhjelm P. Polarization effects in protein–ligand calculations extend farther than the actual induction energy Theoretical Chemistry Accounts. 131: 1159. DOI: 10.1007/S00214-012-1159-1  0.481
2012 Genheden S, Söderhjelm P, Ryde U. Transferability of conformational dependent charges from protein simulations International Journal of Quantum Chemistry. 112: 1768-1785. DOI: 10.1002/Qua.22967  0.596
2011 Söderhjelm P, Kongsted J, Ryde U. Conformational Dependence of Isotropic Polarizabilities. Journal of Chemical Theory and Computation. 7: 1404-14. PMID 26610132 DOI: 10.1021/Ct100714E  0.606
2011 Hu L, Söderhjelm P, Ryde U. On the Convergence of QM/MM Energies. Journal of Chemical Theory and Computation. 7: 761-77. PMID 26596307 DOI: 10.1021/Ct100530R  0.577
2011 Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration. Journal of the American Chemical Society. 133: 13081-92. PMID 21728337 DOI: 10.1021/Ja202972M  0.647
2010 Genheden S, Kongsted J, Söderhjelm P, Ryde U. Nonpolar Solvation Free Energies of Protein-Ligand Complexes. Journal of Chemical Theory and Computation. 6: 3558-68. PMID 26617102 DOI: 10.1021/Ct100272S  0.682
2010 Söderhjelm P, Kongsted J, Ryde U. Ligand Affinities Estimated by Quantum Chemical Calculations. Journal of Chemical Theory and Computation. 6: 1726-37. PMID 26615702 DOI: 10.1021/Ct9006986  0.655
2010 Söderhjelm P, Kongsted J, Genheden S, Ryde U. Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdisciplinary Sciences, Computational Life Sciences. 2: 21-37. PMID 20640794 DOI: 10.1007/S12539-010-0083-0  0.708
2009 Söderhjelm P, Husberg C, Strambi A, Olivucci M, Ryde U. Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities. Journal of Chemical Theory and Computation. 5: 649-658. PMID 26610229 DOI: 10.1021/Ct800459T  0.618
2009 Söderhjelm P, Aquilante F, Ryde U. Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects. The Journal of Physical Chemistry. B. 113: 11085-94. PMID 19618955 DOI: 10.1021/Jp810551H  0.653
2009 Kongsted J, Söderhjelm P, Ryde U. How accurate are continuum solvation models for drug-like molecules? Journal of Computer-Aided Molecular Design. 23: 395-409. PMID 19444622 DOI: 10.1007/S10822-009-9271-6  0.606
2009 Söderhjelm P, Ryde U. How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations. The Journal of Physical Chemistry. A. 113: 617-27. PMID 19093829 DOI: 10.1021/Jp8073514  0.656
2009 Söderhjelm P, Ryde U. Conformational dependence of charges in protein simulations. Journal of Computational Chemistry. 30: 750-60. PMID 18773405 DOI: 10.1002/Jcc.21097  0.619
2009 Söderhjelm P, Öhrn A. On the coupling of intermolecular polarization and repulsion through pseudo-potentials Chemical Physics Letters. 468: 94-99. DOI: 10.1016/J.Cplett.2008.11.074  0.424
2008 Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations. Journal of Chemical Theory and Computation. 4: 985-1001. PMID 26621239 DOI: 10.1021/Ct700347H  0.656
2008 Kaukonen M, Söderhjelm P, Heimdal J, Ryde U. QM/MM-PBSA method to estimate free energies for reactions in proteins. The Journal of Physical Chemistry. B. 112: 12537-48. PMID 18781715 DOI: 10.1021/Jp802648K  0.644
2008 Aidas K, Møgelhoj A, Nilsson EJ, Johnson MS, Mikkelsen KV, Christiansen O, Söderhjelm P, Kongsted J. On the performance of quantum chemical methods to predict solvatochromic effects: the case of acrolein in aqueous solution. The Journal of Chemical Physics. 128: 194503. PMID 18500876 DOI: 10.1063/1.2918537  0.403
2008 Söderhjelm P, Ohrn A, Ryde U, Karlström G. Accuracy of typical approximations in classical models of intermolecular polarization. The Journal of Chemical Physics. 128: 014102. PMID 18190180 DOI: 10.1063/1.2814240  0.545
2008 De Vico L, Pegado L, Heimdal J, Söderhjelm P, Roos BO. The ozone ring closure as a test for multi-state multi-configurational second order perturbation theory (MS-CASPT2) Chemical Physics Letters. 461: 136-141. DOI: 10.1016/J.Cplett.2008.06.065  0.47
2007 Söderhjelm P, Krogh JW, Karlström G, Ryde U, Lindh R. Accuracy of distributed multipoles and polarizabilities: comparison between the LoProp and MpProp models. Journal of Computational Chemistry. 28: 1083-90. PMID 17279548 DOI: 10.1002/Jcc.20632  0.605
2006 Weis A, Katebzadeh K, Söderhjelm P, Nilsson I, Ryde U. Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field. Journal of Medicinal Chemistry. 49: 6596-606. PMID 17064078 DOI: 10.1021/Jm0608210  0.658
2006 Söderhjelm P, Karlström G, Ryde U. Comparison of overlap-based models for approximating the exchange-repulsion energy. The Journal of Chemical Physics. 124: 244101. PMID 16821967 DOI: 10.1063/1.2206182  0.582
2006 Söderhjelm P, Ryde U. Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase Journal of Molecular Structure: Theochem. 770: 199-219. DOI: 10.1016/J.Theochem.2006.06.008  0.562
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