Pär Söderhjelm

发表

Estimates of ligand-binding affinities supported by quantum mechanical methods

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Interdisciplinary Sciences: Computational Life Sciences.

Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects.

Francesco Aquilante, Pär Söderhjelm, Ulf Ryde, 2009, The journal of physical chemistry. B.

Ligand Affinities Estimated by Quantum Chemical Calculations.

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2010, Journal of chemical theory and computation.

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations.

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2009, The journal of physical chemistry. A.

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

U. Ryde, Pär Söderhjelm, A. Weis, 2006, Journal of Medicinal Chemistry.

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

U. Ryde, Pär Söderhjelm, 2016, Chemical reviews.

Quantum Mechanics in Structure‐Based Ligand Design

S. Genheden, U. Ryde, Pär Söderhjelm, 2012 .

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2011, Journal of the American Chemical Society.

Flap Dynamics in Aspartic Proteases: A Computational Perspective

S. Bhakat, Pär Söderhjelm, Mukul Mahanti, 2016, Chemical biology & drug design.

The geometry of protein hydration.

B. Halle, Pär Söderhjelm, Filip Persson, 2018, The Journal of chemical physics.

Flap Dynamics in Pepsin-Like Aspartic Proteases: A Computational Perspective Using Plasmepsin-II and BACE-1 as Model Systems

S. Bhakat, Pär Söderhjelm, 2020, bioRxiv.

Conformational Dependence of Isotropic Polarizabilities.

U. Ryde, J. Kongsted, Pär Söderhjelm, 2011, Journal of chemical theory and computation.

Computational modelling of local fluctuations causing transient solvent exposure of protein amides

S. Bhakat, Pär Söderhjelm, 2022, bioRxiv.

How proteins modify water dynamics.

B. Halle, Pär Söderhjelm, Filip Persson, 2018, The Journal of chemical physics.

Polarization effects in protein–ligand calculations extend farther than the actual induction energy

Pär Söderhjelm, 2012, Theoretical Chemistry Accounts.

Combined computational and crystallographic study of the oxidised states of [NiFe] hydrogenase

U. Ryde, Pär Söderhjelm, 2006 .

Free-Energy Landscape and Rate Estimation of the Aromatic Ring Flips in Basic Pancreatic Trypsin Inhibitors Using Metadynamics

Pär Söderhjelm, M. Kulkarni, 2021, bioRxiv.

How accurate are continuum solvation models for drug-like molecules?

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde, 2009, J. Comput. Aided Mol. Des..

On the Convergence of QM/MM Energies.

Pär Söderhjelm, Ulf Ryde, LiHong Hu, 2011, Journal of chemical theory and computation.

On the performance of quantum chemical methods to predict solvatochromic effects: the case of acrolein in aqueous solution.

K. Mikkelsen, J. Kongsted, K. Aidas, 2008, The Journal of chemical physics.

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations.

Pär Söderhjelm, Ulf Ryde, LiHong Hu, 2013, Journal of chemical theory and computation.

Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

Pär Söderhjelm, Ulf Ryde, Martin A. Olsson, 2016, J. Comput. Chem..

The spatial range of protein hydration.

B. Halle, Pär Söderhjelm, Filip Persson, 2018, The Journal of chemical physics.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities.

Pär Söderhjelm, Massimo Olivucci, Ulf Ryde, 2009, Journal of chemical theory and computation.

The ozone ring closure as a test for multi-state multi-configurational second order perturbation theory (MS-CASPT2)

B. Roos, Pär Söderhjelm, Luís Pegado, 2008 .

Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations.

Pär Söderhjelm, Ulf Ryde, Jimmy Heimdal, 2008, Journal of chemical theory and computation.

Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics

Pär Söderhjelm, Soumendranath Bhakat, S. Bhakat, 2016, Journal of Computer-Aided Molecular Design.

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2013, Physical chemistry chemical physics : PCCP.

Students' performance on programming-related tasks in an informatics contest in Finland, Sweden and Lithuania

Timo Poranen, Valentina Dagiene, Linda Mannila, 2014, ITiCSE '14.

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins.

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2013, Journal of chemical theory and computation.

Accuracy of typical approximations in classical models of intermolecular polarization.

Pär Söderhjelm, Ulf Ryde, Gunnar Karlström, 2008, The Journal of chemical physics.

Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models

Roland Lindh, Pär Söderhjelm, Ulf Ryde, 2007, J. Comput. Chem..

Comparison of overlap-based models for approximating the exchange-repulsion energy.

U. Ryde, G. Karlström, Pär Söderhjelm, 2006, The Journal of chemical physics.

Prediction of binding poses to FXR using multi-targeted docking combined with molecular dynamics and enhanced sampling

Pär Söderhjelm, Soumendranath Bhakat, Emil Åberg, 2017, Journal of Computer-Aided Molecular Design.

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2015, J. Comput. Chem..

Coupled-cluster interaction energies for 200-atom host-guest systems.

Pär Söderhjelm, Ulf Ryde, Ricardo A Mata, 2014, Chemphyschem : a European journal of chemical physics and physical chemistry.

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host–guest binding energies

Ricardo A. Mata, Samuel Genheden, Pär Söderhjelm, 2014, Journal of Computer-Aided Molecular Design.

Transferability of conformational dependent charges from protein simulations

Samuel Genheden, Pär Söderhjelm, Ulf Ryde, 2012 .

Conformational dependence of charges in protein simulations

Pär Söderhjelm, Ulf Ryde, U. Ryde, 2009, J. Comput. Chem..

Nonpolar Solvation Free Energies of Protein-Ligand Complexes.

Jacob Kongsted, Samuel Genheden, Pär Söderhjelm, 2010, Journal of chemical theory and computation.

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.

Lihong Hu, S. Genheden, U. Ryde, 2011, Journal of the American Chemical Society.

Can MM/GBSA calculations be sped up by system truncation?

Pär Söderhjelm, Paulius Mikulskis, Ulf Ryde, 2018, J. Comput. Chem..

Ligand Affinities Estimated by Quantum Chemical Calculations.

U. Ryde, J. Kongsted, Pär Söderhjelm, 2010, Journal of chemical theory and computation.

Conformational dependence of charges in protein simulations

U. Ryde, Pär Söderhjelm, 2009, J. Comput. Chem..

On the Convergence of QM/MM Energies.

Lihong Hu, U. Ryde, Pär Söderhjelm, 2011, Journal of chemical theory and computation.

QM/MM-PBSA method to estimate free energies for reactions in proteins.

U. Ryde, Pär Söderhjelm, J. Heimdal, 2008, The journal of physical chemistry. B.

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

S. Genheden, U. Ryde, Pär Söderhjelm, 2015, J. Comput. Chem..

Prediction of hydration free energies for the SAMPL4 data set with the AMOEBA polarizable force field

Pär Söderhjelm, Francesco Manzoni, Pär Söderhjelm, 2014, Journal of Computer-Aided Molecular Design.

The spatial range of protein hydration.

B. Halle, Pär Söderhjelm, Filip Persson, 2018, The Journal of chemical physics.

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities.

U. Ryde, M. Olivucci, Pär Söderhjelm, 2009, Journal of chemical theory and computation.

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

Michele Parrinello, Gareth A Tribello, Pär Söderhjelm, 2012, Proceedings of the National Academy of Sciences.

Baltic Olympiads in Informatics: Challenges for Training Together

Timo Poranen, Antti Laaksonen, Marcin Kubica, 2009 .

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations.

S. Genheden, U. Ryde, Pär Söderhjelm, 2013, Physical chemistry chemical physics : PCCP.

Conformational Dependence of Isotropic Polarizabilities.

U. Ryde, J. Kongsted, Pär Söderhjelm, 2011, Journal of chemical theory and computation.