Johan Åqvist

Computer Simulations of the Temperature Dependence of Enzyme Reactions

Åqvist, Johan; Brandsdal, Bjørn O.

Ingår i Journal of Chemical Theory and Computation, s. 1017-1028, 2025

• DOI för Computer Simulations of the Temperature Dependence of Enzyme Reactions
• Ladda ner fulltext (pdf) av Computer Simulations of the Temperature Dependence of Enzyme Reactions

Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

Oanca, Gabriel; Åqvist, Johan

Ingår i Journal of Chemical Theory and Computation, s. 2582-2591, 2024

• DOI för Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?
• Ladda ner fulltext (pdf) av Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

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.

Ingår i Journal of Chemical Theory and Computation, s. 451-458, 2024

• DOI för Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations
• Ladda ner fulltext (pdf) av Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations

Computational design of the temperature optimum of an enzyme reaction

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

Ingår i Science Advances, 2023

• DOI för Computational design of the temperature optimum of an enzyme reaction
• Ladda ner fulltext (pdf) av Computational design of the temperature optimum of an enzyme reaction

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

Koenekoop, Lucien; Åqvist, Johan

Ingår i Molecular biology and evolution, 2023

• DOI för Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction
• Ladda ner fulltext (pdf) av Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

Oanca, Gabriel; Åqvist, Johan

Ingår i Journal of Chemical Theory and Computation, s. 2582-2591, 2024

• DOI för Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?
• Ladda ner fulltext (pdf) av Why Do Empirical Valence Bond Simulations Yield Accurate Arrhenius Plots?

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.

Ingår i Journal of Chemical Theory and Computation, s. 451-458, 2024

• DOI för Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations
• Ladda ner fulltext (pdf) av Accurate Computation of Thermodynamic Activation Parameters in the Chorismate Mutase Reaction from Empirical Valence Bond Simulations

Computational design of the temperature optimum of an enzyme reaction

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

Ingår i Science Advances, 2023

• DOI för Computational design of the temperature optimum of an enzyme reaction
• Ladda ner fulltext (pdf) av Computational design of the temperature optimum of an enzyme reaction

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

Koenekoop, Lucien; Åqvist, Johan

Ingår i Molecular biology and evolution, 2023

• DOI för Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction
• Ladda ner fulltext (pdf) av Principles of Cold Adaptation of Fish Lactate Dehydrogenases Revealed by Computer Simulations of the Catalytic Reaction

Efficient Empirical Valence Bond Simulations with GROMACS

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

Ingår i Journal of Chemical Theory and Computation, s. 6037-6045, 2023

• DOI för Efficient Empirical Valence Bond Simulations with GROMACS
• Ladda ner fulltext (pdf) av Efficient Empirical Valence Bond Simulations with GROMACS

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

Åqvist, Johan

Ingår i ACS Catalysis, s. 10007-10009, 2023

• DOI för Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"
• Ladda ner fulltext (pdf) av Reply to Comment on: "Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme"

Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

Åqvist, Johan; van der Ent, Florian

Ingår i Journal of Chemical Theory and Computation, s. 6345-6353, 2022

• DOI för Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding
• Ladda ner fulltext (pdf) av Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

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

Ingår i Biochemistry, s. 514-522, 2022

• DOI för 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.

Ingår i Biochemistry, s. 933-942, 2022

• DOI för Structure and Mechanism of a Cold-Adapted Bacterial Lipase
• Ladda ner fulltext (pdf) av Structure and Mechanism of a Cold-Adapted Bacterial Lipase

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

Åqvist, Johan

Ingår i ACS Catalysis, s. 1452-1460, 2022

• DOI för Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme
• Ladda ner fulltext (pdf) av Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

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.

Ingår i eLIFE, 2021

• DOI för Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family
• Ladda ner fulltext (pdf) av Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

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

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

Ingår i Frontiers in Molecular Biosciences, 2021

• DOI för Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors
• Ladda ner fulltext (pdf) av Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

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.

Ingår i Biochemistry, s. 2186-2194, 2021

• DOI för 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.

Ingår i Journal of Medicinal Chemistry, s. 458-480, 2021

• DOI för 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.

Ingår i PloS Computational Biology, 2021

• DOI för Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations
• Ladda ner fulltext (pdf) av Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

Hidden conformational states and strange temperature optima in enzyme catalysis

Åqvist, Johan; Sočan, Jaka; Purg, Miha

Ingår i Biochemistry, s. 3844-3855, 2020

• DOI för Hidden conformational states and strange temperature optima in enzyme catalysis
• Ladda ner fulltext (pdf) av Hidden conformational states and strange temperature optima in enzyme catalysis

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

Socan, Jaka; Purg, Miha; Åqvist, Johan

Ingår i Nature Communications, 2020

• DOI för Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme
• Ladda ner fulltext (pdf) av Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

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.

Ingår i ACS Catalysis, s. 15019-15032, 2020

• DOI för Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry
• Ladda ner fulltext (pdf) av Dissecting the Mechanism of (R)-3-Hydroxybutyrate Dehydrogenase by Kinetic Isotope Effects, Protein Crystallography, and Computational Chemistry

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.

Ingår i Angewandte Chemie International Edition, s. 16536-16543, 2020

• DOI för 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.

Ingår i Biomolecules, 2020

• DOI för Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists
• Ladda ner fulltext (pdf) av Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists

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

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

Ingår i RSC Medicinal chemistry, s. 234-244, 2020

• DOI för 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.

Ingår i ChemistryOpen, s. 325-337, 2020

• DOI för Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors
• Ladda ner fulltext (pdf) av Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors

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

Kumar, Amit; Åqvist, Johan; Satpati, Priyadarshi

Ingår i ACS Omega, s. 15539-15548, 2019

• DOI för Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair
• Ladda ner fulltext (pdf) av Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair

Towards Rational Computational Engineering of Psychrophilic Enzymes

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

Ingår i Scientific Reports, 2019

• DOI för Towards Rational Computational Engineering of Psychrophilic Enzymes
• Ladda ner fulltext (pdf) av Towards Rational Computational Engineering of Psychrophilic Enzymes

Free energy calculations of RNA interactions

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

Ingår i Methods, s. 85-95, 2019

• DOI för 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

Ingår i Journal of Cheminformatics, 2019

• DOI för QligFEP: an automated workflow for small molecule free energy calculations in Q
• Ladda ner fulltext (pdf) av QligFEP: an automated workflow for small molecule free energy calculations in Q

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.

Ingår i Journal of Chemical Theory and Computation, s. 5461-5473, 2019

• DOI för 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.

Ingår i ChemistryOpen, s. 114-125, 2019

• DOI för A Series of Analogues to the AT₂R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode
• Ladda ner fulltext (pdf) av A Series of Analogues to the AT₂R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode

Inhibition of translation termination by small molecules targeting ribosomal release factors

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

Ingår i Scientific Reports, 2019

• DOI för Inhibition of translation termination by small molecules targeting ribosomal release factors
• Ladda ner fulltext (pdf) av Inhibition of translation termination by small molecules targeting ribosomal release factors

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.

Ingår i Molecular Pharmacology, s. 323-334, 2018

• DOI för Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y-₂ Receptor
• Ladda ner fulltext (pdf) av Elucidation of the Binding Mode of the Carboxyterminal Region of Peptide YY to the Human Y-₂ Receptor

Catalytic Adaptation of Psychrophilic Elastase

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

Ingår i Biochemistry, s. 2984-2993, 2018

• DOI för 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.

Ingår i ACS Omega, s. 4509-4521, 2018

• DOI för Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides
• Ladda ner fulltext (pdf) av Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides

Mechanistic alternatives for peptide bond formation on the ribosome

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

Ingår i Nucleic Acids Research, s. 5345-5354, 2018

• DOI för Mechanistic alternatives for peptide bond formation on the ribosome
• Ladda ner fulltext (pdf) av Mechanistic alternatives for peptide bond formation on the ribosome

Molecular mechanisms in the selectivity of nonsteroidal anti-inflammatory drugs

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

Ingår i Biochemistry, s. 1236-1248, 2018

• DOI för 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.

Ingår i SoftwareX, s. 388-395, 2018

• DOI för Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations
• Ladda ner fulltext (pdf) av Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 4649-4654, 2018

• DOI för 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.

Ingår i Molecules, 2017

• DOI för Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors
• Ladda ner fulltext (pdf) av Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors

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

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

Ingår i Biochemistry, s. 1911-1920, 2017

• DOI för 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

Ingår i Nature Communications, 2017

• DOI för Origin of the omnipotence of eukaryotic release factor 1
• Ladda ner fulltext (pdf) av Origin of the omnipotence of eukaryotic release factor 1

Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

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

Ingår i Biochemistry, s. 306-312, 2017

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

Cold Adaptation of Triosephosphate Isomerase

Åqvist, Johan

Ingår i Biochemistry, s. 4169-4176, 2017

• DOI för 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.

Ingår i Scientific Reports, 2017

• DOI för The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site
• Ladda ner fulltext (pdf) av The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site

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.

Ingår i Journal of Medicinal Chemistry, s. 7502-7511, 2017

• DOI för 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

Ingår i RNA Biology, s. 815-819, 2017

• DOI för 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.

Ingår i ACS Catalysis, s. 1737-1743, 2016

• DOI för Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis
• Ladda ner fulltext (pdf) av Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis

Principles of start codon recognition in eukaryotic translation initiation

Lind, Christoffer; Åqvist, Johan

Ingår i Nucleic Acids Research, s. 8425-8432, 2016

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 7822-7827, 2016

• DOI för 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

Ingår i Biochemistry, s. 2153-2162, 2016

• DOI för 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.

Ingår i Molecular Pharmacology, s. 413-424, 2016

• DOI för 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

Ingår i ACS Catalysis, s. 8432-8439, 2016

• DOI för Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis
• Ladda ner fulltext (pdf) av Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis

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.

Ingår i ACS Chemical Neuroscience, s. 1383-1392, 2016

• DOI för 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.

Ingår i Journal of the American Chemical Society, s. 10664-10673, 2016

• DOI för The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis
• Ladda ner fulltext (pdf) av The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

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

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

Ingår i Bioorganic & Medicinal Chemistry Letters, s. 1355-1359, 2016

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 2406-2411, 2016

• DOI för Enzyme catalysis by entropy without Circe effect

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

Åqvist, Johan

Ingår i European Biophysics Journal, 2015

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

Åqvist, Johan; Kamerlin, Lynn Shina Caroline

Ingår i Biochemistry, s. 546-556, 2015

• DOI för The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome
• Ladda ner fulltext (pdf) av The Conformation of a Catalytic Loop Is Central to GTPase Activity on the Ribosome

Special Issue Recent Developments of Molecular Dynamics preface

Nilsson, Lennart; Åqvist, Johan

Ingår i Biochimica et Biophysica Acta - General Subjects, s. 859-860, 2015

• DOI för 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

Ingår i Biochemistry, s. 7283-7291, 2015

• DOI för 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

Ingår i Journal of Molecular Graphics and Modelling, s. 15-23, 2015

• DOI för 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

Ingår i Nature Communications, 2015

• DOI för Chemical reaction mechanisms in solution from brute force computational Arrhenius plots
• Ladda ner fulltext (pdf) av Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

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

Aqvist, Johan; Kamerlin, Shina C. Lynn

Ingår i Scientific Reports, 2015

• DOI för Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome
• Ladda ner fulltext (pdf) av Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome

Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch

Sund, Johan; Lind, Christoffer; Åqvist, Johan

Ingår i Journal of Physical Chemistry B, s. 773-782, 2015

• DOI för 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

Ingår i Journal of the American Chemical Society, s. 1081-93, 2015

• DOI för Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis.
• Ladda ner fulltext (pdf) av Resolving apparent conflicts between theoretical and experimental models of phosphate monoester hydrolysis.

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

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

Ingår i Chemical Communications, s. 3522-3525, 2015

• DOI för 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

Ingår i The FASEB Journal, 2014

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

Satpati, Priyadarshi; Åqvist, Johan

Ingår i Nucleic Acids Research, s. 12876-12884, 2014

• DOI för Why base tautomerization does not cause errors in mRNA decoding on the ribosome
• Ladda ner fulltext (pdf) av Why base tautomerization does not cause errors in mRNA decoding on the ribosome

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

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

Ingår i PloS Computational Biology, 2014

• DOI för Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors
• Ladda ner fulltext (pdf) av Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors

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

Horn, Richard; Roux, Benoit; Åqvist, Johan

Ingår i Biophysical Journal, s. 1859-1863, 2014

• DOI för 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

Ingår i Journal of Chemical Information and Modeling, s. 1488-1499, 2014

• DOI för 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

Ingår i PLOS ONE, 2014

• DOI för Structural and Energetic Effects of A_2A Adenosine Receptor Mutations on Agonist and Antagonist Binding
• Ladda ner fulltext (pdf) av Structural and Energetic Effects of A_2A Adenosine Receptor Mutations on Agonist and Antagonist Binding

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

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

Ingår i Journal of Physical Chemistry B, s. 4351-4362, 2014

• DOI för Force Field Independent Metal Parameters Using a Nonbonded Dummy Model
• Ladda ner fulltext (pdf) av Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

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

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

Ingår i PloS Computational Biology, 2014

• DOI för Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin
• Ladda ner fulltext (pdf) av Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin

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

Satpati, Priyadarshi; Bauer, Paul; Åqvist, Johan

Ingår i Chemistry - A European Journal, s. 10271-10275, 2014

• DOI för 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

Ingår i Biochemistry, s. 1714-1722, 2014

• DOI för Structure-Based Energetics of mRNA Decoding on the Ribosome

Energetics of activation of GTP hydrolysis on the ribosome

Wallin, Göran; Kamerlin, Lynn; Åqvist, Johan

Ingår i Nature Communications, s. 1733, 2013

• DOI för Energetics of activation of GTP hydrolysis on the ribosome
• Ladda ner fulltext (pdf) av Energetics of activation of GTP hydrolysis on the ribosome

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

Lind, Christoffer; Sund, Johan; Åqvist, Johan

Ingår i Nature Communications, 2013

• DOI för 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.

Ingår i Biochemistry, s. 7987-7998, 2013

• DOI för 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.

Ingår i MOLECULAR INFORMATICS, s. 155-164, 2013

• DOI för 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

Ingår i Journal of Computational Chemistry, s. 2340-2350, 2012

• DOI för 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.

Ingår i Chemistry and Biology, s. 983-993, 2012

• DOI för 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

Ingår i Journal of Chemical Theory and Computation, s. 3871-3879, 2012

• DOI för 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.

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 2325-2329, 2012

• DOI för 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

Ingår i Current opinion in structural biology, s. 815-823, 2012

• DOI för 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.

Ingår i Journal of Chemical Information and Modeling, s. 601-611, 2011

• DOI för 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.

Ingår i Biochemistry, s. 6146-6156, 2011

• DOI för 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

Ingår i Science, s. 37, 2011

• DOI för 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

Ingår i Nature, s. 947-U12, 2010

• DOI för 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

Ingår i Proceedings of the National Academy of Sciences of the United States of America, s. 1888-1893, 2010

• DOI för 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.

Ingår i British Journal of Pharmacology, s. 1069-1081, 2010

• DOI för 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.

Ingår i ChemMedChem, s. 455-467, 2010

• DOI för 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.

Ingår i Biochemistry, s. 1743-1753, 2009

• DOI för Mutagenesis and homology modelling of the Tn21 integron integrase IntI1

Mechanism of the Translation Termination Reaction on the Ribosome

Trobro, Stefan; Åqvist, Johan

Ingår i Biochemistry, s. 11296-11303, 2009

• DOI för 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

Ingår i Journal of Chemical Theory and Computation, s. 380-395, 2009

• DOI för 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

Ingår i Journal of Physical Chemistry B, s. 10255-10260, 2009

• DOI för 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.

Ingår i Bioorganic & Medicinal Chemistry, s. 5933-5949, 2009

• DOI för 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

Ingår i Biochemistry, s. 3483-3489, 2009

• DOI för 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.

Ingår i Journal of the American Chemical Society, s. 9475-9477, 2009

• DOI för 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

Ingår i Biophysical Journal, s. 820-831, 2008

• DOI för 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.

Ingår i Journal of Medicinal Chemistry, s. 2657-2667, 2008

• DOI för Predicting Binding Modes from Free Energy Calculations

Cold adaptation of enzyme reaction rates

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

Ingår i Biochemistry, s. 10049-10057, 2008

• DOI för Cold adaptation of enzyme reaction rates

Role of ribosomal protein L27 in peptidyl transfer

Trobro, Stefan; Åqvist, Johan

Ingår i Biochemistry, s. 4898-4906, 2008

• DOI för 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

Ingår i Biomaterials, s. 4463-4469, 2008

• DOI för 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

Ingår i Journal of Medicinal Chemistry, s. 2648-56, 2008

• DOI för 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

Ingår i Biochemistry, s. 2466-2479, 2007

• DOI för 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

Ingår i Biochemistry, s. 1466-1476, 2007

• DOI för 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.

Ingår i Journal of Biological Chemistry, s. 19905-19916, 2007

• DOI för 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

Ingår i Molecular Cell, s. 758-766, 2007

• DOI för 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.

Ingår i Bioorganic & Medicinal Chemistry, s. 7795-7802, 2007

• DOI för 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

Ingår i Journal of Chemical Theory and Computation, s. 2162-2175, 2007

• DOI för 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.

Ingår i Cellular and Molecular Life Sciences (CMLS), s. 2285-2305, 2007

• DOI för Computational inhibitor design against malaria plasmepsins

Energetics of codon-anticodon recognition on the small ribosomal subunit

Almlöf, Martin; Andér, Martin; Åqvist, Johan

Ingår i Biochemistry, s. 200-209, 2007

• DOI för 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.

Ingår i Biorganic & Medicinal Chemistry, s. 2197-2208, 2006

• DOI för 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.

Ingår i FEBS Letters, s. 5910-5916, 2006

• DOI för Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor

Calculations of solute and solvent entropies from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 5385-5395, 2006

• DOI för 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

Ingår i Biochemistry, s. 10807-10814, 2006

• DOI för 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

Ingår i Biochemistry, s. 7049-56, 2006

Continuum solvation models in the linear interaction energy method.

Carlsson, Jens; Andér, Martin; Nervall, Martin; Aqvist, Johan

Ingår i J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, s. 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

Ingår i Biophys J, s. 433-42, 2006

Catalysis and linear free energy relationships in aspartic proteases.

Bjelic, Sinisa; Aqvist, Johan

Ingår i Biochemistry, s. 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

Ingår i Proteins, s. 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.

Ingår i Biochemical Journal, s. 685-694, 2005

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

Carlsson, Jens; Aqvist, Johan

Ingår i J Phys Chem B Condens Matter Mater Surf Interfaces Biophys, s. 6448-56, 2005

Mechanism of peptide bond synthesis on the ribosome.

Trobro, Stefan; Aqvist, Johan

Ingår i Proc Natl Acad Sci U S A, s. 12395-400, 2005

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

Luzhkov, V B; Aqvist, J

Ingår i Biochim Biophys Acta, s. 109-20, 2005

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

Carlsson, Jens; Åqvist, Johan

Ingår i J. Phys. Chem. B, s. 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.

Ingår i European Journal of Pharmaceutical Sciences, s. 43-54, 2004

• DOI för 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.

Ingår i Chembiochem, s. 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.

Ingår i Chem. Phys. Lett., s. 288, 2004

Binding affinity prediction with different force fields: examination of the

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

Ingår i J Comput Chem, s. 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

Ingår i Biochemistry, s. 14521-8, 2004

Free Energy Calculations and Ligand Binding

Brandsdal, B.; Åqvist, J

Ingår i Adv. Prot. Chem., s. 123, 2003

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

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

Ingår i Biochim. Biophys. Acta, s. 35, 2003

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

Feierberg, I.; Åqvist, J

Ingår i Biochemistry, s. 2258, 2003

Computational modeling of enzymatic keto-enol isomerization reactions

Feierberg, Isabella; Åqvist, Johan

Ingår i Theoretical Chemistry accounts, s. 71-84, 2002

• DOI för Computational modeling of enzymatic keto-enol isomerization reactions

The catalytic power of ketosteroid isomerase investigated by computer simulation

Feierberg, Isabella; Åqvist, Johan

Ingår i Biochemistry, s. 15728-15735, 2002

• DOI för 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

Ingår i J. Am. Chem. Soc., s. 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.

Ingår i Journal of Medicinal Chemistry, s. 2391-2402, 2001

• DOI för 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

Ingår i European Journal of Pharmaceutical Sciences, s. 87-95, 2001

• DOI för 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.

Ingår i Eur. J. Pharm. Sci., s. 441-446, 2001

• DOI för Computational Modelling of Inhibitor Binding to Human Thrombin

Mechanisms of Tetraethylammonium Ion Block in the KcsA Potassium Channel

Luzhkov, V; Åqvist, J

Ingår i FEBS Lett., s. 191, 2001

Electrostatic Effects Play a Central Role in Cold Adaptation of Trypsin

Brandsdal, B.O.; Åqvist, J

Ingår i FEBS Lett., s. 171, 2001

The Catalytic Mechanism of Protein Tyrosine Phosphatases Revisited

Kolmodin, K.; Åqvist, J

Ingår i FEBS Lett., s. 208, 2001

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

Luzhkov, V; Åqvist, J

Ingår i Biochim. Biophys. Acta, s. 194, 2001

Computational Analysis of Binding of P1-Variants to Trypsin

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

Ingår i Protein Sci., s. 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

Ingår i Journal of Biological Chemistry, s. 22657-22662, 2000

• DOI för 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.

Ingår i J. Am. Chem. Soc., s. 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

Ingår i J. Biol. Chem., s. 22657, 2000

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

Luzhkov, V; Åqvist, J

Ingår i Biochim. Biophys. Acta, s. 360, 2000

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

Kolmodin, K.; Åqvist, J

Ingår i FEBS Lett., s. 8, 2000

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

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

Ingår i FEBS Letters, s. 90-94, 1999

• DOI för 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

Ingår i ACS Symp. Ser., s. 370, 1999

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

Kolmodin, K.; Åqvist, J

Ingår i FEBS Lett., s. 301, 1999

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

Luzhkov, V.; Åqvist, J

Ingår i Chem. Phys. Lett., s. 267, 1999

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

Kolmodin, K.; Åqvist, J

Ingår i Int. J. Quantum Chem., s. 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.

Ingår i J. Comput.-Aided Mol. Design, s. 119-131, 1998

• DOI för 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

Ingår i Int. J. Quantum Chem., s. 77, 1998

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

Luzhkov, V; Åqvist, J

Ingår i J. Am. Chem. Soc., s. 6131, 1998

Ligand Binding Affinity Prediction by Linear Interaction Energy Methods

Hansson, T.; Åqvist, J

Ingår i J. Comput.-Aided Mol. Design, s. 27, 1998

On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution

Florian, J.; Åqvist, J; Warshel, A

Ingår i J. Am. Chem. Soc., s. 11524, 1998

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

Marelius, J.; Åqvist, J

Ingår i J. Mol. Graph. Model, s. 213, 1998

Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase

Hansson, T.; Åqvist, J

Ingår i J. Mol. Biol., s. 118, 1997

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

Åqvist, Johan; Mowbray, Sherry L.

Ingår i Journal of Biological Chemistry, s. 9978-9981, 1995

• DOI för 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

Ingår i Protein Eng., s. 1137, 1995

Computer Simulations of the Temperature Dependence of Enzyme Reactions

Åqvist, Johan; Brandsdal, Bjørn O.

Ingår i Journal of Chemical Theory and Computation, s. 1017-1028, 2025

• DOI för Computer Simulations of the Temperature Dependence of Enzyme Reactions
• Ladda ner fulltext (pdf) av Computer Simulations of the Temperature Dependence of Enzyme Reactions

Computation of enzyme cold adaptation

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

Ingår i Nature Reviews Chemistry, 2017

• DOI för Computation of enzyme cold adaptation

Entropy and Enzyme Catalysis

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

Ingår i Accounts of Chemical Research, s. 199-207, 2017

• DOI för Entropy and Enzyme Catalysis
• Ladda ner fulltext (pdf) av Entropy and Enzyme Catalysis

Modeling the mechanisms of biological GTP hydrolysis

Carvalho, Alexandra T. P.; Szeler, Klaudia; Vavitsas, Konstantinos; Åqvist, Johan et al.

Ingår i Archives of Biochemistry and Biophysics, s. 80-90, 2015

• DOI för Modeling the mechanisms of biological GTP hydrolysis
• Ladda ner fulltext (pdf) av Modeling the mechanisms of biological GTP hydrolysis

Free energy calculations for protein-ligand binding prediction

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

Ingår i Protein-Ligand Interactions and Drug Design, s. 203-226, Springer Nature, 2021

• DOI för Free energy calculations for protein-ligand binding prediction

Characterization of Ligand Binding to GPCRs Through Computational Methods

Vasile, Silvana; Esguerra, Mauricio; Jespers, Willem; Oliveira, Ana et al.

Ingår i Computational Methods for GPCR Drug Discovery, s. 23-44, Humana Press, 2018

• DOI för Characterization of Ligand Binding to GPCRs Through Computational Methods

Computational Enzymology: Protein Tyrosine Phosphatase Reactions

Kolmodin, K.; Åqvist, J

Ingår i Theoretical Biochemistry - Processes and Properties of Biological Systems, s. 253, 2001

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A_2A Adenosine Receptor Antagonists

Jespers, Willem; Verdon, Grégory; Azuaje, Jhonny; Jhonny, Maria et al.

Predicting conformational selectivity in a prototypical GPCR

Jespers, Willem; Torres, Katherin; van Veen, Amber; Wang, Xuesong et al.

Structure of a phage-encoded SAMase enzyme provides insights in substrate binding and mechanism

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

Q Manual for Version 4

Marelius, J.; Åqvist, J

2000