Johan Åqvist

Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

Oanca, Gabriel; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 2582-2591, 2024

DOI for Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?
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Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations

Wilkins, Ryan Scott; Lund, Bjarte Aarmo; Isaksen, Geir Villy; Åqvist, Johan et al.

Part of Journal of Chemical Theory and Computation, p. 451-458, 2024

Computational design of the temperature optimum of an enzyme reaction

van der Ent, Florian; Skagseth, Susann; Lund, Bjarte A.; Socan, Jaka et al.

Part of Science Advances, 2023

Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

Koenekoop, Lucien; Åqvist, Johan

Part of Molecular biology and evolution, 2023

Efficient Empirical Valence Bond Simulations with GROMACS

Oanca, Gabriel; van der Ent, Florian; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 6037-6045, 2023

Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"

Åqvist, Johan

Part of ACS Catalysis, p. 10007-10009, 2023

Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

Åqvist, Johan; van der Ent, Florian

Part of Journal of Chemical Theory and Computation, p. 6345-6353, 2022

The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

Koenekoop, Lucien; van der Ent, Florian; Purg, Miha; Åqvist, Johan

Part of Biochemistry, p. 514-522, 2022

DOI for The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

Structure and Mechanism of a Cold-Adapted Bacterial Lipase

van der Ent, Florian; Lund, Bjarte A.; Svalberg, Linn; Purg, Miha et al.

Part of Biochemistry, p. 933-942, 2022

Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

Åqvist, Johan

Part of ACS Catalysis, p. 1452-1460, 2022

Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

Guo, Xiaohu; Söderholm, Annika; Kanchugal Puttaswamy, Sandesh; Isaksen, Geir V et al.

Part of eLIFE, 2021

Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

Reddy Vanga, Sudarsana; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

Part of Frontiers in Molecular Biosciences, 2021

Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer a Sub-zero Temperatures

Machado, Teresa F. G.; Purg, Miha; Åqvist, Johan; da Silva, Rafael G.

Part of Biochemistry, p. 2186-2194, 2021

DOI for Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer a Sub-zero Temperatures

3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

Majellaro, María; Jespers, Willem; Crespo, Abel; Núñez, María J. et al.

Part of Journal of Medicinal Chemistry, p. 458-480, 2021

DOI for 3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A_2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

Jespers, Willem; Heitman, Laura H.; IJzerman, Adriaan P.; Sotelo, Eddy et al.

Part of PloS Computational Biology, 2021

Hidden conformational states and strange temperature optima in enzyme catalysis

Åqvist, Johan; Sočan, Jaka; Purg, Miha

Part of Biochemistry, p. 3844-3855, 2020

Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

Socan, Jaka; Purg, Miha; Åqvist, Johan

Part of Nature Communications, 2020

Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry

Machado, Teresa F. G.; Purg, Miha; McMahon, Stephen A.; Read, Benjamin J. et al.

Part of ACS Catalysis, p. 15019-15032, 2020

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A(2A) Adenosine Receptor Antagonists

Jespers, Willem; Verdon, Gregory; Azuaje, Jhonny; Majellaro, Maria et al.

Part of Angewandte Chemie International Edition, p. 16536-16543, 2020

DOI for X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A(2A) Adenosine Receptor Antagonists

Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists

Vasile, Silvana; Hallberg, Anders; Sallander, Jessica; Hallberg, Mathias et al.

Part of Biomolecules, 2020

Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

Barlow, Nicholas; Reddy Vanga, Sudarsana; Sävmarker, Jonas; Sandström, Anja et al.

Part of RSC Medicinal chemistry, p. 234-244, 2020

DOI for Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors

Engen, Karin; Reddy Vanga, Sudarsana; Lundbäck, Thomas; Agalo, Faith et al.

Part of ChemistryOpen, p. 325-337, 2020

Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair

Kumar, Amit; Åqvist, Johan; Satpati, Priyadarshi

Part of ACS Omega, p. 15539-15548, 2019

Towards Rational Computational Engineering of Psychrophilic Enzymes

Socan, Jaka; Isaksen, Geir Villy; Brandsdal, Björn Olav; Åqvist, Johan

Part of Scientific Reports, 2019

Free energy calculations of RNA interactions

Lind, Christoffer; Esguerra, Mauricio; Jespers, Willem; Satpati, Priyadarshi et al.

Part of Methods, p. 85-95, 2019

DOI for Free energy calculations of RNA interactions

QligFEP: an automated workflow for small molecule free energy calculations in Q

Jespers, Willem; Esguerra, Mauricio; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

Part of Journal of Cheminformatics, 2019

QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

Jespers, Willem; Isaksen, Geir V; Andberg, Tor A H; Vasile, Silvana et al.

Part of Journal of Chemical Theory and Computation, p. 5461-5473, 2019

DOI for QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

A Series of Analogues to the AT₂R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode

Isaksson, Rebecka; Lindman, Jens; Wannberg, Johan; Sallander, Jessica et al.

Part of ChemistryOpen, p. 114-125, 2019

Inhibition of translation termination by small molecules targeting ribosomal release factors

Ge, Xueliang; Oliveira, Ana; Hjort, Karin; Bergfors, Terese et al.

Part of Scientific Reports, 2019

Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y-₂ Receptor

Xu, Bo; Vasile, Silvana; Østergaard, Søren; Paulsson, Johan F. et al.

Part of Molecular Pharmacology, p. 323-334, 2018

Catalytic Adaptation of Psychrophilic Elastase

Socan, Jaka; Kazemi, Masoud; Isaksen, Geir Villy; Brandsdal, Bjorn Olav et al.

Part of Biochemistry, p. 2984-2993, 2018

DOI for Catalytic Adaptation of Psychrophilic Elastase

Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides

Reddy Vanga, Sudarsana; Sävmarker, Jonas; Ng, Leelee; Larhed, Mats et al.

Part of ACS Omega, p. 4509-4521, 2018

Mechanistic alternatives for peptide bond formation on the ribosome

Kazemi, Masoud; Socan, Jaka; Himo, Fahmi; Åqvist, Johan

Part of Nucleic Acids Research, p. 5345-5354, 2018

Molecular mechanisms in the selectivity of nonsteroidal anti-inflammatory drugs

Shamsudin, Yasmin; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

Part of Biochemistry, p. 1236-1248, 2018

DOI for Molecular mechanisms in the selectivity of nonsteroidal anti-inflammatory drugs

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

Bauer, Paul; Barrozo, Alexandre; Purg, Miha; Amrein, Beat Anton et al.

Part of SoftwareX, p. 388-395, 2018

Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Ge, Xueliang; Mandava, Chandra Sekhar; Lind, Christoffer; Åqvist, Johan et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 4649-4654, 2018

DOI for Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors

Jespers, Willem; Oliveira, Ana; Prieto-Diaz, Ruben; Majellaro, Maria et al.

Part of Molecules, 2017

Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations

Shamsudin, Yasmin; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

Part of Biochemistry, p. 1911-1920, 2017

DOI for Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations

Origin of the omnipotence of eukaryotic release factor 1

Lind, Christoffer; Oliveira, Ana; Åqvist, Johan

Part of Nature Communications, 2017

Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Björn Olav

Part of Biochemistry, p. 306-312, 2017

DOI for Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

Cold Adaptation of Triosephosphate Isomerase

Åqvist, Johan

Part of Biochemistry, p. 4169-4176, 2017

DOI for Cold Adaptation of Triosephosphate Isomerase

The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site

Nohr, Anne Cathrine; Jespers, Willem; Shehata, Mohamed A.; Floryan, Leonard et al.

Part of Scientific Reports, 2017

Effect of Nitrogen Atom Substitution in A(3) Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

Azuaje, Jhonny; Jespers, Willem; Yaziji, Vicente; Mallo, Ana et al.

Part of Journal of Medicinal Chemistry, p. 7502-7511, 2017

DOI for Effect of Nitrogen Atom Substitution in A(3) Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

A close-up view of codon selection in eukaryotic initiation

Lind, Christoffer; Esguerra, Mauricio; Åqvist, Johan

Part of RNA Biology, p. 815-819, 2017

DOI for A close-up view of codon selection in eukaryotic initiation

Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis

Aqvist, Johan; Kamerlin, Shina C. L.

Part of ACS Catalysis, p. 1737-1743, 2016

Principles of start codon recognition in eukaryotic translation initiation

Lind, Christoffer; Åqvist, Johan

Part of Nucleic Acids Research, p. 8425-8432, 2016

DOI for Principles of start codon recognition in eukaryotic translation initiation

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Björn Olav

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 7822-7827, 2016

DOI for Enzyme surface rigidity tunes the temperature dependence of catalytic rates

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase

Isaksen, Geir Villy; Hopmann, Kathrin Helen; Åqvist, Johan; Brandsdal, Björn Olav

Part of Biochemistry, p. 2153-2162, 2016

DOI for Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase

Binding to and Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Macrocyclic Disulfides Enhances Spine Density

Diwakarla, Shanti; Nylander, Erik; Grönbladh, Alfhild; Reddy Vanga, Sudarsana et al.

Part of Molecular Pharmacology, p. 413-424, 2016

DOI for Binding to and Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Macrocyclic Disulfides Enhances Spine Density

Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis

Kazemi, Masoud; Himo, Fahmi; Åqvist, Johan

Part of ACS Catalysis, p. 8432-8439, 2016

Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures

Diwakarla, Shanti; Nylander, Erik; Grönbladh, Alfhild; Vanga, Sudarsana Reddy et al.

Part of ACS Chemical Neuroscience, p. 1383-1392, 2016

DOI for Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures

The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

Duarte, Fernanda; Barrozo, Alexandre; Åqvist, Johan; Williams, Nicholas H. et al.

Part of Journal of the American Chemical Society, p. 10664-10673, 2016

Structural determinants of subtype selectivity and functional activity of angiotensin II receptors

Sallander, Jessica; Wallinder, Charlotta; Hallberg, Anders; Åqvist, Johan et al.

Part of Bioorganic & Medicinal Chemistry Letters, p. 1355-1359, 2016

DOI for Structural determinants of subtype selectivity and functional activity of angiotensin II receptors

Enzyme catalysis by entropy without Circe effect

Kazemi, Masoud; Himo, Fahmi; Åqvist, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 2406-2411, 2016

DOI for Enzyme catalysis by entropy without Circe effect

Computing the temperature dependence of chemical reactions inside and outside of living things

Åqvist, Johan

Part of European Biophysics Journal, 2015

The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

Åqvist, Johan; Kamerlin, Lynn Shina Caroline

Part of Biochemistry, p. 546-556, 2015

Special Issue Recent Developments of Molecular Dynamics preface

Nilsson, Lennart; Åqvist, Johan

Part of Biochimica et Biophysica Acta - General Subjects, p. 859-860, 2015

DOI for Special Issue Recent Developments of Molecular Dynamics preface

Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1

Shamsudin, Yasmin; Kazemi, Masoud; Gutierrez-de-Teran, Hugo; Åqvist, Johan

Part of Biochemistry, p. 7283-7291, 2015

DOI for Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1

Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems

Isaksen, Geir Villy; Andberg, Tor Arne Heim; Åqvist, Johan; Brandsdal, Bjorn Olav

Part of Journal of Molecular Graphics and Modelling, p. 15-23, 2015

DOI for Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

Kazemi, Masoud; Åqvist, Johan

Part of Nature Communications, 2015

Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome

Aqvist, Johan; Kamerlin, Shina C. Lynn

Part of Scientific Reports, 2015

Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch

Sund, Johan; Lind, Christoffer; Åqvist, Johan

Part of Journal of Physical Chemistry B, p. 773-782, 2015

DOI for Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch

Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis.

Duarte, Fernanda; Åqvist, Johan; Williams, Nicholas H; Kamerlin, Shina C Lynn

Part of Journal of the American Chemical Society, p. 1081-93, 2015

Free energy calculations of A(2A) adenosine receptor mutation effects on agonist binding

Keränen, Henrik; Åqvist, Johan; Gutierrez-de-Teran, Hugo

Part of Chemical Communications, p. 3522-3525, 2015

DOI for Free energy calculations of A(2A) adenosine receptor mutation effects on agonist binding

Characterizing an engineered release factor capable of reading all three stop codons

Korkmaz, Gürkan; Lind, Christoffer; Åqvist, Johan; Sanyal, Suparna

Part of The FASEB Journal, 2014

Why base tautomerization does not cause errors in mRNA decoding on the ribosome

Satpati, Priyadarshi; Åqvist, Johan

Part of Nucleic Acids Research, p. 12876-12884, 2014

Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors

Boukharta, Lars; Gutierréz de Terán, Hugo; Åqvist, Johan

Part of PloS Computational Biology, 2014

Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels

Horn, Richard; Roux, Benoit; Åqvist, Johan

Part of Biophysical Journal, p. 1859-1863, 2014

DOI for Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels

Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX-1 Inhibitors

Shamsudin, Yasmin; Gutiérrez de Terán, Hugo; Boukharta, Lars; Åqvist, Johan

Part of Journal of Chemical Information and Modeling, p. 1488-1499, 2014

DOI for Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX-1 Inhibitors

Structural and Energetic Effects of A_2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

Keränen, Henrik; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

Part of PLOS ONE, 2014

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

Duarte, Fernanda; Bauer, Paul; Barrozo, Alexandre; Amrein, Beat Anton et al.

Part of Journal of Physical Chemistry B, p. 4351-4362, 2014

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Bjorn Olav

Part of PloS Computational Biology, 2014

Energetic Tuning by tRNA Modifications Ensures Correct Decoding of Isoleucine and Methionine on the Ribosome

Satpati, Priyadarshi; Bauer, Paul; Åqvist, Johan

Part of Chemistry - A European Journal, p. 10271-10275, 2014

DOI for Energetic Tuning by tRNA Modifications Ensures Correct Decoding of Isoleucine and Methionine on the Ribosome

Structure-Based Energetics of mRNA Decoding on the Ribosome

Satpati, Priyadarshi; Sund, Johan; Åqvist, Johan

Part of Biochemistry, p. 1714-1722, 2014

DOI for Structure-Based Energetics of mRNA Decoding on the Ribosome

Energetics of activation of GTP hydrolysis on the ribosome

Wallin, Göran; Kamerlin, Lynn; Åqvist, Johan

Part of Nature Communications, p. 1733, 2013

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

Lind, Christoffer; Sund, Johan; Åqvist, Johan

Part of Nature Communications, 2013

DOI for Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY

Xu, Bo; Fällmar, Helena; Boukharta, Lars; Pruner, Jasna et al.

Part of Biochemistry, p. 7987-7998, 2013

DOI for Mutagenesis and Computational Modeling of Human G‑Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY

Evaluation of Adamantane Derivatives as Inhibitors of Dengue Virus mRNA Cap Methyltransferase by Docking and Molecular Dynamics Simulations

Luzhkov, Victor; Decroly, Etienne; Canard, Bruno; Selisko, Barbara et al.

Part of MOLECULAR INFORMATICS, p. 155-164, 2013

DOI for Evaluation of Adamantane Derivatives as Inhibitors of Dengue Virus mRNA Cap Methyltransferase by Docking and Molecular Dynamics Simulations

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

Mishra, Sushil Kumar; Sund, Johan; Åqvist, Johan; Koca, Jaroslav

Part of Journal of Computational Chemistry, p. 2340-2350, 2012

DOI for Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models

A Role for the 2 ' OH of Peptidyl-tRNA Substrate in Peptide Release on the Ribosome Revealed through RF-Mediated Rescue

Shaw, Jeffrey J.; Trobro, Stefan; He, Shan L.; Åqvist, Johan et al.

Part of Chemistry and Biology, p. 983-993, 2012

DOI for A Role for the 2 ' OH of Peptidyl-tRNA Substrate in Peptide Release on the Ribosome Revealed through RF-Mediated Rescue

Folding-Reaction Coupling in a Self-Cleaving Protein

Wallin, Göran; Härd, Torleif; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 3871-3879, 2012

DOI for Folding-Reaction Coupling in a Self-Cleaving Protein

High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C

Willander, Hanna; Askarieh, Glareh; Landreh, Michael; Westermark, Per et al.

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 2325-2329, 2012

DOI for High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C

Bridging the gap between ribosome structure and biochemistry by mechanistic computations

Aqvist, Johan; Lind, Christoffer; Sund, Johan; Wallin, Goran

Part of Current opinion in structural biology, p. 815-823, 2012

DOI for Bridging the gap between ribosome structure and biochemistry by mechanistic computations

Computational Prediction of Structure-Activity Relationships for the Binding of Aminocyclitols to beta-Glucocerebrosidase

Diaz, Lucia; Bujons, Jordi; Delgado, Antonio; Gutierrez-de-Teran, Hugo et al.

Part of Journal of Chemical Information and Modeling, p. 601-611, 2011

DOI for Computational Prediction of Structure-Activity Relationships for the Binding of Aminocyclitols to beta-Glucocerebrosidase

Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers

Boukharta, Lars; Keränen, Henrik; Stary-Weinzinger, Anna; Wallin, Göran et al.

Part of Biochemistry, p. 6146-6156, 2011

DOI for Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers

Comment on "The mechanism for activation of GTP hydrolysis on the ribosome"

Liljas, Anders; Ehrenberg, Måns; Åqvist, Johan

Part of Science, p. 37, 2011

DOI for Comment on "The mechanism for activation of GTP hydrolysis on the ribosome"

Principles of stop-codon reading on the ribosome

Sund, Johan; Andér, Martin; Åqvist, Johan

Part of Nature, p. 947-U12, 2010

DOI for Principles of stop-codon reading on the ribosome

The transition state for peptide bond formation reveals the ribosome as a water trap

Wallin, Göran; Åqvist, Johan

Part of Proceedings of the National Academy of Sciences of the United States of America, p. 1888-1893, 2010

DOI for The transition state for peptide bond formation reveals the ribosome as a water trap

Phe369(7.38) at human 5-HT7 receptors confers interspecies selectivity to antagonists and partial agonists

Varin, Thibault; Gutierrez-de-Teran, Hugo; Castro, Marian; Brea, Jose et al.

Part of British Journal of Pharmacology, p. 1069-1081, 2010

DOI for Phe369(7.38) at human 5-HT7 receptors confers interspecies selectivity to antagonists and partial agonists

Toward a Consensus Model of the hERG Potassium Channel

Stary, Anna; Wacker, Soeren J.; Boukharta, Lars; Zachariae, Ulrich et al.

Part of ChemMedChem, p. 455-467, 2010

DOI for Toward a Consensus Model of the hERG Potassium Channel

Mutagenesis and homology modelling of the Tn21 integron integrase IntI1

Johansson, Carolina; Boukharta, Lars; Eriksson, Jens; Åqvist, Johan et al.

Part of Biochemistry, p. 1743-1753, 2009

DOI for Mutagenesis and homology modelling of the Tn21 integron integrase IntI1

Mechanism of the Translation Termination Reaction on the Ribosome

Trobro, Stefan; Åqvist, Johan

Part of Biochemistry, p. 11296-11303, 2009

DOI for Mechanism of the Translation Termination Reaction on the Ribosome

Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

Wallin, Göran; Nervall, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 380-395, 2009

DOI for Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Journal of Physical Chemistry B, p. 10255-10260, 2009

DOI for Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

α-Substituted Norstatines as the Transistion-State Mimic in Inhibitors of Multiple Digestive Vacuole Malaria Aspartic Proteases

Orrling, Kristina M.; Marzahn, Melissa; Gutiérrez-de-Terán, Hugo; Åqvist, Johan et al.

Part of Bioorganic & Medicinal Chemistry, p. 5933-5949, 2009

DOI for α-Substituted Norstatines as the Transistion-State Mimic in Inhibitors of Multiple Digestive Vacuole Malaria Aspartic Proteases

Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors?

Andér, Martin; Åqvist, Johan

Part of Biochemistry, p. 3483-3489, 2009

DOI for Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors?

Protein Autoproteolysis: Conformational Strain Linked to the Rate of Peptide Cleavage by the pH Dependence of the N -> O Acyl Shift Reaction

Johansson, Denny G. A.; Wallin, Göran; Sandberg, Anders; Macao, Bertil et al.

Part of Journal of the American Chemical Society, p. 9475-9477, 2009

DOI for Protein Autoproteolysis: Conformational Strain Linked to the Rate of Peptide Cleavage by the pH Dependence of the N -> O Acyl Shift Reaction

Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state - Docking and computer simulations of a homology model

Andér, Martin; Luzhkov, Victor B.; Åqvist, Johan

Part of Biophysical Journal, p. 820-831, 2008

DOI for Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state - Docking and computer simulations of a homology model

Predicting Binding Modes from Free Energy Calculations

Nervall, Martin; Hanspers, Peter; Carlsson, Jens; Boukharta, Lars et al.

Part of Journal of Medicinal Chemistry, p. 2657-2667, 2008

DOI for Predicting Binding Modes from Free Energy Calculations

Cold adaptation of enzyme reaction rates

Bjelic, Sinisa; Brandsdal, Bjørn O; Åqvist, Johan

Part of Biochemistry, p. 10049-10057, 2008

DOI for Cold adaptation of enzyme reaction rates

Role of ribosomal protein L27 in peptidyl transfer

Trobro, Stefan; Åqvist, Johan

Part of Biochemistry, p. 4898-4906, 2008

DOI for Role of ribosomal protein L27 in peptidyl transfer

Molecular dynamics study of heparin based coatings

Almlöf, Martin; Kristensen, Emma M. E.; Siegbahn, Hans; Åqvist, Johan

Part of Biomaterials, p. 4463-4469, 2008

DOI for Molecular dynamics study of heparin based coatings

Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase

Carlsson, Jens; Boukharta, Lars; Åqvist, Johan

Part of Journal of Medicinal Chemistry, p. 2648-56, 2008

DOI for Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase

Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate

Thomaeus, Ann; Carlsson, Jens; Åqvist, Johan; Widersten, Mikael

Part of Biochemistry, p. 2466-2479, 2007

DOI for Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate

Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

Warshel, Arieh; Sharma, Pankaz K.; Chu, Zhen T.; Åqvist, Johan

Part of Biochemistry, p. 1466-1476, 2007

DOI for Electrostatic contributions to binding of transition state analogues can be very different from the corresponding contributions to catalysis: phenolates binding to the oxyanion hole of ketosteroid isomerase

Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis

Henriksson, Lena M.; Unge, Torsten; Carlsson, Jens; Åqvist, Johan et al.

Part of Journal of Biological Chemistry, p. 19905-19916, 2007

DOI for Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis

A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis

Trobro, Stefan; Åqvist, Johan

Part of Molecular Cell, p. 758-766, 2007

DOI for A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis

Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2'O)-methyltransferase

Luzhkov, Victor B.; Selisko, Barbara; Nordqvist, Anneli; Peyrane, Frédéric et al.

Part of Bioorganic & Medicinal Chemistry, p. 7795-7802, 2007

DOI for Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2'O)-methyltransferase

Improving the accuracy of the linear interaction energy method for solvation free energies

Almlöf, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 2162-2175, 2007

DOI for Improving the accuracy of the linear interaction energy method for solvation free energies

Computational inhibitor design against malaria plasmepsins

Bjelic, Sinisa; Nervall, Martin; Gutiérrez-de-Terán, Hugo; Ersmark, Karolina et al.

Part of Cellular and Molecular Life Sciences (CMLS), p. 2285-2305, 2007

DOI for Computational inhibitor design against malaria plasmepsins

Energetics of codon-anticodon recognition on the small ribosomal subunit

Almlöf, Martin; Andér, Martin; Åqvist, Johan

Part of Biochemistry, p. 200-209, 2007

DOI for Energetics of codon-anticodon recognition on the small ribosomal subunit

Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV

Ersmark, Karolina; Nervall, Martin; Gutiérrez-de-Terán, Hugo; Hamelink, Elizabeth et al.

Part of Biorganic & Medicinal Chemistry, p. 2197-2208, 2006

DOI for Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV

Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor

Gutiérrez-de-Terán, Hugo; Nervall, Martin; Dunn, Ben M.; Clemente, Jose C. et al.

Part of FEBS Letters, p. 5910-5916, 2006

DOI for Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor

Calculations of solute and solvent entropies from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Physical Chemistry, Chemical Physics - PCCP, p. 5385-5395, 2006

DOI for Calculations of solute and solvent entropies from molecular dynamics simulations

Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB

Luzhkov, Victor B.; Almlöf, Martin; Nervall, Martin; Åqvist, Johan

Part of Biochemistry, p. 10807-10814, 2006

DOI for Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB

Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer.

Trobro, Stefan; Aqvist, Johan

Part of Biochemistry, p. 7049-56, 2006

Continuum solvation models in the linear interaction energy method.

Part of J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, p. 12034-41, 2006

Probing the effect of point mutations at protein-protein interfaces with free energy calculations.

Almlöf, Martin; Aqvist, Johan; Smalås, Arne O; Brandsdal, Björn O

Part of Biophys J, p. 433-42, 2006

Catalysis and linear free energy relationships in aspartic proteases.

Bjelic, Sinisa; Aqvist, Johan

Part of Biochemistry, p. 7709-23, 2006

Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin.

Brandsdal, Björn O; Smalås, Arne O; Åqvist, Johan

Part of Proteins, p. 740-8, 2006

Resolving the energy paradox of chaperone/usher-mediated fibre assembly

Zavialov, Anton V; Tischenko, Vladimir M; Fooks, Laura J; Brandsdal, Björn O et al.

Part of Biochemical Journal, p. 685-694, 2005

Absolute and relative entropies from computer simulation with applications to ligand binding.

Carlsson, Jens; Aqvist, Johan

Part of J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, p. 6448-56, 2005

Mechanism of peptide bond synthesis on the ribosome.

Trobro, Stefan; Aqvist, Johan

Part of Proc Natl Acad Sci U S A, p. 12395-400, 2005

Ions and blockers in potassium channels: insights from free energy simulations.

Luzhkov, V B; Aqvist, J

Part of Biochim Biophys Acta, p. 109-20, 2005

Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding

Carlsson, Jens; Åqvist, Johan

Part of J. Phys. Chem. B, p. 6448, 2005

Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii

Graffner-Nordberg, Malin; Kolmodin, Karin; Åqvist, Johan; Queener, Sherry F et al.

Part of European Journal of Pharmaceutical Sciences, p. 43-54, 2004

DOI for Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii

Comparative analysis of putative agonist-binding modes in the human A1 adenosine

Gutiérrez-de-Terán, Hugo; Pastor, Manuel; Centeno, Nuria B; Aqvist, Johan et al.

Part of Chembiochem, p. 841-9, 2004

Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm

Åqvist, J; Wennerström, P; Nervall, M; Bjelic, S et al.

Part of Chem. Phys. Lett., p. 288, 2004

Binding affinity prediction with different force fields: examination of the

Almlöf, Martin; Brandsdal, Bjørn O; Aqvist, Johan

Part of J Comput Chem, p. 1242-54, 2004

Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site.

Bjelic, Sinisa; Aqvist, Johan

Part of Biochemistry, p. 14521-8, 2004

Free Energy Calculations and Ligand Binding

Brandsdal, B.; Åqvist, J

Part of Adv. Prot. Chem., p. 123, 2003

Computational Modeling of the Open-State Kv1.5 Ion Channel Block by Bupivacaine

Luzhkov, V; Nilsson, J; Århem, P; Åqvist, J

Part of Biochim. Biophys. Acta, p. 35, 2003

Correction: The Catalytic Power of Ketosteroid Isomerase Investigated by Computer Simulation

Feierberg, I.; Åqvist, J

Part of Biochemistry, p. 2258, 2003

Computational modeling of enzymatic keto-enol isomerization reactions

Feierberg, Isabella; Åqvist, Johan

Part of Theoretical Chemistry accounts, p. 71-84, 2002

DOI for Computational modeling of enzymatic keto-enol isomerization reactions

The catalytic power of ketosteroid isomerase investigated by computer simulation

Feierberg, Isabella; Åqvist, Johan

Part of Biochemistry, p. 15728-15735, 2002

DOI for The catalytic power of ketosteroid isomerase investigated by computer simulation

Computational Study of the Influence of Solvent on 16O/18O Equilibrium Isotope Effects in Phosphate Deprotonation Reactions

Kolmodin, K.; Åqvist, J

Part of J. Am. Chem. Soc., p. 10130, 2002

Design, Synthesis, Computational Prediction and Biological Evaluation of Ester Soft Drugs as Inhibitors of Dihydrofolate Reductase from Pneumocystis Carinii

Graffner-Nordberg, Malin; Åqvist, J; Queener, SF; Hallberg, A et al.

Part of Journal of Medicinal Chemistry, p. 2391-2402, 2001

DOI for Design, Synthesis, Computational Prediction and Biological Evaluation of Ester Soft Drugs as Inhibitors of Dihydrofolate Reductase from Pneumocystis Carinii

Sensitivity of an Empirical Affinity Scoring Function to Changes in Receptor-Ligand Complex Conformations

Marelius, J.; Ljungberg, Kajsa; Åqvist, J

Part of European Journal of Pharmaceutical Sciences, p. 87-95, 2001

DOI for Sensitivity of an Empirical Affinity Scoring Function to Changes in Receptor-Ligand Complex Conformations

Computational Modelling of Inhibitor Binding to Human Thrombin

Ljungberg, Kajsa B; Marelius, J; Musil, D; Svensson, P et al.

Part of Eur. J. Pharm. Sci., p. 441-446, 2001

DOI for Computational Modelling of Inhibitor Binding to Human Thrombin

Mechanisms of Tetraethylammonium Ion Block in the KcsA Potassium Channel

Luzhkov, V; Åqvist, J

Part of FEBS Lett., p. 191, 2001

Electrostatic Effects Play a Central Role in Cold Adaptation of Trypsin

Brandsdal, B.O.; Åqvist, J

Part of FEBS Lett., p. 171, 2001

The Catalytic Mechanism of Protein Tyrosine Phosphatases Revisited

Kolmodin, K.; Åqvist, J

Part of FEBS Lett., p. 208, 2001

K+/Na+ Selectivity of the KcsA Potassium Channel from Microscopic Free Energy Perturbation Calculations

Luzhkov, V; Åqvist, J

Part of Biochim. Biophys. Acta, p. 194, 2001

Computational Analysis of Binding of P1-Variants to Trypsin

Brandsdal, B.O.; Åqvist, J; Smalås, A.O.

Part of Protein Sci., p. 1584, 2001

Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction

Feierberg, Isabella; Luzhkov, Victor; Åqvist, Johan

Part of Journal of Biological Chemistry, p. 22657-22662, 2000

DOI for Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction

The Deacylation Step of Acetylcholine Esterase: Computer Simulation Studies

Vagedes, P; Åqvist, J; Rabenstein, B; Marelius, J et al.

Part of J. Am. Chem. Soc., p. 12254, 2000

Computer Simulation of Primary Kinetic Isotope Effects in the Proposed Rate Limiting Step of the Glyoxalase I Reaction

Feierberg, I; Åqvist, J; Luzhkov, V

Part of J. Biol. Chem., p. 22657, 2000

A Computational Study of Ion Binding and Protonation States in the KcsA Potassium Channel

Luzhkov, V; Åqvist, J

Part of Biochim. Biophys. Acta, p. 360, 2000

Prediction of a Ligand Induced Conformational Change in the Catalytic Core of Cdc25A

Kolmodin, K.; Åqvist, J

Part of FEBS Lett., p. 8, 2000

Energetics of the proposed rate-determining step of the glyoxalase I reaction

Feierberg, Isabella; Cameron, Alexander D; Åqvist, Johan

Part of FEBS Letters, p. 90-94, 1999

DOI for Energetics of the proposed rate-determining step of the glyoxalase I reaction

Molecular Dynamics Simulations of Substrate Dephosphorylation by Low Molecular Weight Protein Tyrosine Phosphatase

Kolmodin, K.; Åqvist, J

Part of ACS Symp. Ser., p. 370, 1999

Computational Modelling of the Rate-Limiting Step in Low Molecular Weight Protein Tyrosine Phosphatase

Kolmodin, K.; Åqvist, J

Part of FEBS Lett., p. 301, 1999

Free Energy Perturbation Calculations of Binding and Transition State Energies: Hydrolysis of Phenyl Esters by b-Cyclodextrin

Luzhkov, V.; Åqvist, J

Part of Chem. Phys. Lett., p. 267, 1999

Computational Modelling of Catalysis and Binding in Low Molecular Weight Protein Tyrosine Phosphatase

Kolmodin, K.; Åqvist, J

Part of Int. J. Quantum Chem., p. 147, 1999

Computation of Affinity and Selectivity: Binding of 2,4-Diaminopteridine and 2,4-Diaminoquinazoline Inhibitors to Dihydrofolate Reductases

Marelius, J.; Graffner-Nordberg, Malin; Hansson, T; Hallberg, A et al.

Part of J. Comput.-Aided Mol. Design, p. 119-131, 1998

DOI for Computation of Affinity and Selectivity: Binding of 2,4-Diaminopteridine and 2,4-Diaminoquinazoline Inhibitors to Dihydrofolate Reductases

Calculation of Ligand Binding Free Energies from Molecular Dynamics Simulations

Marelius, J.; Åqvist, J

Part of Int. J. Quantum Chem., p. 77, 1998

Computer Simulation of Phenyl Ester Cleavage by b-Cyclodextrin in Solution

Luzhkov, V; Åqvist, J

Part of J. Am. Chem. Soc., p. 6131, 1998

Ligand Binding Affinity Prediction by Linear Interaction Energy Methods

Hansson, T.; Åqvist, J

Part of J. Comput.-Aided Mol. Design, p. 27, 1998

On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution

Florian, J.; Åqvist, J; Warshel, A

Part of J. Am. Chem. Soc., p. 11524, 1998

Q: An MD Program for Free Energy Calculations and Empirical Valence Bond Simulations in Biomolecular Systems

Marelius, J.; Åqvist, J

Part of J. Mol. Graph. Model, p. 213, 1998

Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase

Hansson, T.; Åqvist, J

Part of J. Mol. Biol., p. 118, 1997

Sugar Recognition by a Glucose/Galactose Receptor: Evaluation of Binding Energetics from Molecular Dynamics Simulations

Åqvist, Johan; Mowbray, Sherry L.

Part of Journal of Biological Chemistry, p. 9978-9981, 1995

DOI for Sugar Recognition by a Glucose/Galactose Receptor: Evaluation of Binding Energetics from Molecular Dynamics Simulations

Estimation of Binding Free Energies for HIV Proteinase Inhibitors by Molecular Dynamics Simulations

Hansson, T.; Åqvist, J

Part of Protein Eng., p. 1137, 1995

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