نتائج البحث

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

• Authors : Kulkarni, Mandar; Söderhjelm, Pär

Subjects: Naturvetenskap; Biologi; Biofysiks

• Source: Journal of Chemical Theory and Computation. 19(19):6605-6618

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

• Authors : Bhakat, Soumendranath; Söderhjelm, Pär

Subjects: Medicin och hälsovetenskap; Medicinsk bioteknologi; Medical and Health Sciences

• Source: Journal of Chemical Information and Modeling. 62(4):914-926

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Flexibility and Function of Distal Substrate-Binding Tryptophans in the Blue Mussel β-Mannanase MeMan5A and Their Role in Hydrolysis and Transglycosylation

• Authors : Birgersson, Simon; Morrill, Johan; Stenström, Olof

Subjects: enzymatic synthesis; flexibility; novel glycosides

• Source: Catalysts. 13(9)

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

• Authors : Misini Ignjatović, Majda; Mikulskis, Paulius; Söderhjelm, Pär

Subjects: factor Xa; ferritin; ligand-binding affinities

• Source: Journal of Computational Chemistry eSSENCE: The e-Science Collaboration. 39(7):361-372

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

• Authors : Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

Subjects: D3R; Docking; MD simulation

• Source: Journal of Computer-Aided Molecular Design. 32(1):59-73

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

• Authors : Bhakat, Soumendranath; Söderhjelm, Pär

Subjects: Binding free energy; Host–guest complex; MD simulation

• Source: Journal of Computer-Aided Molecular Design. :119-132

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

• Authors : Olsson, Martin A.; Söderhjelm, Pär; Ryde, Ulf

Subjects: host-guest systems; ligand binding; non-Boltzmann Bennett acceptance ratio method

• Source: Journal of Computational Chemistry. 37(17):1589-1600

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Flexibility and Function of Distal Substrate-Binding Tryptophans in the Blue Mussel β-Mannanase Me Man5A and Their Role in Hydrolysis and Transglycosylation.

• Authors : Birgersson, Simon; Morrill, Johan; Stenström, Olof

Subjects: MYTILUS edulis; MOLECULAR spectroscopy; PLANT cell walls

• Source: Catalysts (2073-4344); Sep2023, Vol. 13 Issue 9, p1281, 20p

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Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods

• Authors : Ryde, Ulf; Söderhjelm, Pär

Subjects: Naturvetenskap; Kemi; Natural Sciences

• Source: Chemical Reviews. 116(9):5520-5566

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

• Authors : Genheden, Samuel; Ryde, Ulf; Söderhjelm, Pär

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Computational Chemistry. 36(28):2114-2124

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The geometry of protein hydration

• Authors : Persson, Filip; Söderhjelm, Pär; Halle, Bertil

Subjects: Naturvetenskap; Kemi; Fysikalisk kemi

• Source: Journal of Chemical Physics. 148(21)

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How proteins modify water dynamics

• Authors : Persson, Filip; Söderhjelm, Pär; Halle, Bertil

Subjects: Naturvetenskap; Kemi; Fysikalisk kemi

• Source: Journal of Chemical Physics. 148(21)

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The spatial range of protein hydration

• Authors : Persson, Filip; Söderhjelm, Pär; Halle, Bertil

Subjects: Naturvetenskap; Kemi; Fysikalisk kemi

• Source: Journal of Chemical Physics. 148(21)

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

• Authors : Mikulskis, Paulius; Cioloboc, Daniela; Andrejić, Milica

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Computer-Aided Molecular Design. 28(4):375-400

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Effect of geometry optimisations on QM-cluster and QM/MM studies of reaction energies in proteins

• Authors : Sumner, Sophie; Söderhjelm, Pär; Ryde, Ulf

Subjects: Quantum mechanical cluster calculations; QM/MM; geometry optimisation

• Source: Journal of Chemical Theory and Computation. 9(9):4205-4214

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

• Authors : Godschalk, Frithjof; Genheden, Samuel; Söderhjelm, Pär

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Physical Chemistry Chemical Physics. 15(20):7731-7739

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Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations

• Authors : Hu, LiHong; Söderhjelm, Pär; Ryde, Ulf

Subjects: Quantum mechanical cluster calculations; QM/MM calculations; continuum solvation

• Source: Journal of Chemical Theory and Computation. 9:640-649

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Quantum mechanics in structure-based ligand design

• Authors : Söderhjelm, Pär; Genheden, Samuel; Ryde, Ulf ...

Subjects: Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; Läkemedelskemi

• Source: Protein-ligand interactions. 53:121-143

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Transferability of conformational dependent charges from protein simulations

• Authors : Genheden, Samuel; Söderhjelm, Pär; Ryde, Ulf

Subjects: conformation dependence; generalized Born solvation; GBSA

• Source: International Journal of Quantum Chemistry. 112(7):1768-1785

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Conformational Dependence of Isotropic Polarizabilities

• Authors : Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Theory and Computation. 7(5):1404-1414

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Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration

• Authors : Genheden, Samuel; Mikulskis, Paulius; Hu, LiHong

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of the American Chemical Society. 133(33):13081-13092

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Ligand affinities estimated by quantum chemical calculations

• Authors : Söderhjelm, Pär; Kongsted, Jacob; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Theory and Computation. 6(5):1726-1737

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Estimates of ligand-binding affinities supported by quantum mechanical methods.

• Authors : Söderhjelm, Pär; Kongsted, Jacob; Genheden, Samuel

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Interdisciplinary sciences, computational life sciences. 2(1):21-37

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Nonpolar Solvation Free Energies of Protein-Ligand Complexes

• Authors : Genheden, Samuel; Kongsted, Jacob; Söderhjelm, Pär

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Theory and Computation. 6(11):3558-3568

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Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

• Authors : Söderhjelm, Pär; Husberg, Charlotte; Strambi, Angela

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Theory and Computation. 5(3):649-658

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

• Authors : Kongsted, Jacob; Söderhjelm, Pär; Ryde, Ulf

Subjects: Free energy of hydration; Continuum methods; PCM

• Source: Journal of Computer-Aided Molecular Design. 23(7):395-409

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Conformational dependence of charges in protein simulations

• Authors : Söderhjelm, Pär; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Computational Chemistry. 30(5):750-760

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How Accurate Can a Force Field Become? A Polarizable Multipole Model Combined with Fragment-wise Quantum-Mechanical Calculations

• Authors : Söderhjelm, Pär; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of physical chemistry. A. 113(3):617-627

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Calculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects

• Authors : Söderhjelm, Pär; Aquilante, Francesco; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: The Journal of Physical Chemistry Part B. 113(32):11085-11094

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Proton transfer at metal sites in proteins studied by quantum mechanical free-energy perturbations

• Authors : Kaukonen, Markus; Söderhjelm, Pär; Heimdal, Jimmy

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Theory and Computation. 4(6):985-1001

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

• Authors : Kaukonen, Markus; Söderhjelm, Pär; Heimdal, Jimmy

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: The Journal of Physical Chemistry Part B. 112(39):12537-12548

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

• Authors : Söderhjelm, Pär; Krogh, Jesper Wisborg; Karlström, Gunnar

Subjects: multipole moments; polarizabilities; MOLCAS

• Source: Journal of Computational Chemistry. 28(6):1083-1090

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

• Authors : Söderhjelm, Pär; Ryde, Ulf

Subjects: QM/MM methods; [NiFe] hydrogenase; crystallographic refinement

• Source: Journal of molecular structure. Theochem. 770(1-3):199-219

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

• Authors : Weis, Aaron; Katebzadeh, Kambiz; Söderhjelm, Pär

Subjects: Medicin och hälsovetenskap; Medicinska och farmaceutiska grundvetenskaper; Läkemedelskemi

• Source: Journal of Medicinal Chemistry. 49(22):6596-6606

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

• Authors : Bhakat, Soumendranath; Åberg, Emil; Söderhjelm, Pär

Subjects: Article

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Locating binding poses in protein-ligand systems using reconnaissance metadynamics

• Authors : Söderhjelm, Pär; Tribello, Gareth A.; Parrinello, Michele

• Source: Proceedings of the National Academy of Sciences of the United States of America, 2012 Apr 01. 109(14), 5170-5175.

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

• Authors : Bhakat, Soumendranath; Söderhjelm, Pär

Subjects: Article

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Locating binding poses in protein-ligand systems using reconnaissance metadynamics

• Authors : Soederhjelm, Paer; Tribello, Gareth A.; Parrinello, Michele

Subjects: /dk/atira/pure/subjectarea/asjc/1000; General

• Source: Soederhjelm , P , Tribello , G A & Parrinello , M 2012 , ' Locating binding poses in protein-ligand systems using reconnaissance metadynamics ' , Proceedings of the

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A first-principles approach to protein–ligand interaction

• Authors : Söderhjelm, Pär

Subjects: solvation; exchange repulsion; polarizable force fields

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Accuracy of typical approximations in classical models of intermolecular polarization

• Authors : Söderhjelm, Pär; Öhrn, Anders; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Physics. 128(1)

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On the Convergence of QM/MM Energies

• Authors : Hu, LiHong; Soederhjelm, Paer; Ryde, Ulf

Subjects: Theoretical Chemistry

• Source: Journal of Chemical Theory and Computation; 7(3), pp 761-777 (2011) ; ISSN: 1549-9618

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

• Authors : Söderhjelm, Pär; Karlström, Gunnar; Ryde, Ulf

Subjects: Naturvetenskap; Kemi; Teoretisk kemi

• Source: Journal of Chemical Physics. 124(24)

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Flap Dynamics in Aspartic Proteases : A Computational Perspective

• Authors : Mahanti, Mukul; Bhakat, Soumendranath; Nilsson, Ulf J.

Subjects: aspartic protease; beta amino secretase; flap

• Source: Chemical Biology and Drug Design. 88(2):159-177

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Prediction of SAMPL4 host-guest binding affinities using funnel metadynamics.

• Authors : Hsiao, Ya-Wen¹ ; Söderhjelm, Pär²

Subjects: *HOST-guest chemistry; *CHEMICAL affinity; *MACROMOLECULES

• Source: Journal of Computer-Aided Molecular Design. Apr2014, Vol. 28 Issue 4, p443-454. 12p.

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

• Authors : Manzoni, Francesco¹ ; Söderhjelm, Pär¹

Subjects: *HYDRATION; *FREE energy (Thermodynamics); *PERTURBATION theory

• Source: Journal of Computer-Aided Molecular Design. Mar2014, Vol. 28 Issue 3, p235-244. 10p.

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

• Authors : Söderhjelm, Pär¹

• Source: Theoretical Chemistry Accounts: Theory, Computation, & Modeling. Mar2012, Vol. 131 Issue 3, p1-12. 12p. 2 Diagrams, 3 Charts, 6 Graphs.

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