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1

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

Ryde, Ulf, Söderhjelm, Pär

Journal:

Chemical Reviews

Year:

2016

Language:

english

File:

PDF, 3.34 MB

english, 2016

2

Flap Dynamics in Aspartic Proteases: A Computational Perspective

Mahanti, Mukul, Bhakat, Soumendranath, Nilsson, Ulf J., Söderhjelm, Pär

Journal:

Chemical Biology & Drug Design

Year:

2016

Language:

english

File:

PDF, 3.54 MB

english, 2016

3

How proteins modify water dynamics

Persson, Filip, Söderhjelm, Pär, Halle, Bertil

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 2.19 MB

english, 2018

4

Conformational dependence of charges in protein simulations

Pär Söderhjelm, Ulf Ryde

Journal:

Journal of Computational Chemistry

Year:

2009

Language:

english

File:

PDF, 456 KB

english, 2009

5

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

Luca De Vico, Luis Pegado, Jimmy Heimdal, Pär Söderhjelm, Björn O. Roos

Journal:

Chemical Physics Letters

Year:

2008

Language:

english

File:

PDF, 236 KB

english, 2008

6

On the coupling of intermolecular polarization and repulsion through pseudo-potentials

Pär Söderhjelm, Anders Öhrn

Journal:

Chemical Physics Letters

Year:

2009

Language:

english

File:

PDF, 204 KB

english, 2009

7

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

Pär Söderhjelm, Ulf Ryde

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

2006

Language:

english

File:

PDF, 610 KB

english, 2006

8

Transferability of conformational dependent charges from protein simulations

Samuel Genheden, Pär Söderhjelm, Ulf Ryde

Journal:

International Journal of Quantum Chemistry

Year:

2012

Language:

english

File:

PDF, 1.91 MB

english, 2012

9

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

Jacob Kongsted, Pär Söderhjelm, Ulf Ryde

Journal:

Journal of Computer-Aided Molecular Design

Year:

2009

Language:

english

File:

PDF, 333 KB

english, 2009

10

Estimates of ligand-binding affinities supported by quantum mechanical methods

Pär Söderhjelm, Jacob Kongsted, Samuel Genheden, Ulf Ryde

Journal:

Interdisciplinary Sciences: Computational Life Sciences

Year:

2010

Language:

english

File:

PDF, 587 KB

english, 2010

11

Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field

Weis, Aaron, Katebzadeh, Kambiz, Söderhjelm, Pär, Nilsson, Ingemar, Ryde, Ulf

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 125 KB

english, 2006

12

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

Pär Söderhjelm

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2012

Language:

english

File:

PDF, 538 KB

english, 2012

13

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

Hu, LiHong, Söderhjelm, Pär, Ryde, Ulf

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.39 MB

english, 2013

14

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

Manzoni, Francesco, Söderhjelm, Pär

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 623 KB

english, 2014

15

Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics

Hsiao, Ya-Wen, Söderhjelm, Pär

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 1.75 MB

english, 2014

16

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

Mikulskis, Paulius, Cioloboc, Daniela, Andrejić, Milica, Khare, Sakshi, Brorsson, Joakim, Genheden, Samuel, Mata, Ricardo A., Söderhjelm, Pär, Ryde, Ulf

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 3.75 MB

english, 2014

17

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

Kaukonen, Markus, Söderhjelm, Pär, Heimdal, Jimmy, Ryde, Ulf

Journal:

Journal of Chemical Theory and Computation

Year:

2008

Language:

english

File:

PDF, 1.35 MB

english, 2008

18

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

Sumner, Sophie, Söderhjelm, Pär, Ryde, Ulf

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 2.13 MB

english, 2013

19

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

Godschalk, Frithjof, Genheden, Samuel, Söderhjelm, Pär, Ryde, Ulf

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.52 MB

english, 2013

20

Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems

Andrejić, Milica, Ryde, Ulf, Mata, Ricardo A., Söderhjelm, Pär

Journal:

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

21

[ACM Press the 2014 conference - Uppsala, Sweden (2014.06.21-2014.06.25)] Proceedings of the 2014 conference on Innovation & technology in computer science education - ITiCSE '14 - Students' performance on programming-related tasks in an informatics contest in Finland, Sweden and Lithuania

Dagiene, Valentina, Mannila, Linda, Poranen, Timo, Rolandsson, Lennart, Söderhjelm, Pär

Year:

2014

Language:

english

File:

PDF, 1.06 MB

english, 2014

22

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

Genheden, Samuel, Ryde, Ulf, Söderhjelm, Pär

Journal:

Journal of Computational Chemistry

Year:

2015

Language:

english

File:

PDF, 627 KB

english, 2015

23

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

Olsson, Martin A., Söderhjelm, Pär, Ryde, Ulf

Journal:

Journal of Computational Chemistry

Year:

2016

Language:

english

File:

PDF, 575 KB

english, 2016

24

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

Bhakat, Soumendranath, Söderhjelm, Pär

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 1.57 MB

english, 2017

25

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

Bhakat, Soumendranath, Åberg, Emil, Söderhjelm, Pär

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 1.05 MB

english, 2017

26

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

Misini Ignjatović, Majda, Mikulskis, Paulius, Söderhjelm, Pär, Ryde, Ulf

Journal:

Journal of Computational Chemistry

Year:

2018

Language:

english

File:

PDF, 1.51 MB

english, 2018

27

The geometry of protein hydration

Persson, Filip, Söderhjelm, Pär, Halle, Bertil

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 9.07 MB

english, 2018

28

The spatial range of protein hydration

Persson, Filip, Söderhjelm, Pär, Halle, Bertil

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 796 KB

english, 2018

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