List of works - Johan Åqvist

3,4-Dihydropyrimidin-2(1<i>H</i>)-ones as Antagonists of the Human A<sub>2B</sub> Adenosine Receptor: Optimization, Structure-Activity Relationship Studies, and Enantiospecific Recognition

scientific article published on 29 December 2020

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

scientific article published on August 24, 2012

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

scientific article published on 24 January 2019

A close-up view of codon selection in eukaryotic initiation.

scientific article published on 24 March 2017

A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis

scientific article published in September 2007

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

scientific article published on 01 April 2005

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

scientific article published on 01 July 2009

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

scientific article

Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer

scientific article published on 01 June 2006

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

scientific article

Author Correction: Inhibition of translation termination by small molecules targeting ribosomal release factors

scientific article published on 13 March 2020

Binding affinity prediction with different force fields: examination of the linear interaction energy method

scientific article published in July 2004

Binding mode of the peptide YY carboxyterminus to the human Y2 receptor

scientific article published on 24 January 2018

Binding site preorganization and ligand discrimination in the purine riboswitch

scientific article published on 18 July 2014

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

scientific article published on 14 January 2016

Bridging the gap between ribosome structure and biochemistry by mechanistic computations.

scientific article

C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions

scientific article

Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

scientific article published in 2022

Calculations of solute and solvent entropies from molecular dynamics simulations

scientific article published on 08 September 2006

Catalysis and linear free energy relationships in aspartic proteases

scientific article published in June 2006

Catalytic Adaptation of Psychrophilic Elastase

scientific article published on 10 May 2018

Characterization of Ligand Binding to GPCRs Through Computational Methods

scientific article published in January 2018

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

scientific article published on 01 February 2009

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

scientific article published on June 2015

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

scientific article published in January 2013

Cold Adaptation of Triosephosphate Isomerase.

scientific article published on 21 July 2017

Cold adaptation of enzyme reaction rates.

scientific article

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

scientific article published on 12 April 2008

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

scientific article published on 01 July 2011

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

scientific article

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

scientific article published on 23 April 2018

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

scientific article published on 08 March 2011

Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor.

scientific article

Computational and NMR study of quaternary ammonium ion conformations in solution

Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine.

scientific article

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

scientific article (publication date: April 2014)

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

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

scientific article published in November 2004

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

scientific article published in September 2006

Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions

scientific article published in August 2002

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

scientific article

Computer Simulations of Structure–Activity Relationships for hERG Channel Blockers ⬇️

scientific article published on June 16, 2011

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

scientific article published on 26 May 2020

Computer-aided design of GPCR ligands

scientific article published on January 2015

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

Continuum solvation models in the linear interaction energy method

scientific article published on 01 June 2006

Corrigendum to “Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2′O)-methyltransferase” [Bioorg. Med. Chem. 15 (2007) 7795–7802]

scholarly article published in Bioorganic & Medicinal Chemistry

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations

scientific article published on 24 November 2021

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

scientific article published in May 2004

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

scientific article (publication date: 21 April 2009)

Editorial preface

scientific article published on 20 January 2015

Effect of Nitrogen Atom Substitution in A3 Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

scientific article published on 9 August 2017

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

scientific article published in February 2007

Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome

scientific article published on 17 July 2014

Energetics of activation of GTP hydrolysis on the ribosome

scientific article published in January 2013

Energetics of codon-anticodon recognition on the small ribosomal subunit

scientific article published on 01 January 2007

Entropy and Enzyme Catalysis

scientific article

Enzyme catalysis by entropy without Circe effect

scientific article

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

scientific article

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

scientific article

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

scientific article published on 23 April 2020

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

scientific article

Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods

scientific article published on May 2005

Folding-Reaction Coupling in a Self-Cleaving Protein

scientific article published on 3 May 2012

Force field independent metal parameters using a nonbonded dummy model

scientific article

Free energy calculations and ligand binding

scientific article published on January 2003

Free energy calculations of A2A adenosine receptor mutation effects on agonist binding

scientific article published on 01 February 2015

Free energy calculations of RNA interactions

scientific article published on 19 February 2019

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

scientific article published on 01 August 2006

Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis

scientific article published on 25 September 2020

Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies

scientific article published on 01 November 2007

Inhibition of translation termination by small molecules targeting ribosomal release factors

scientific article published on 28 October 2019

Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum

scientific article published in September 2006

Ligand binding affinities from MD simulations.

scientific article

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

scientific article published on 28 September 2007

Linear Interaction Energy: Method and Applications in Drug Design

scientific article published on 01 January 2012

Mechanism of peptide bond synthesis on the ribosome

scientific article

Mechanism of the translation termination reaction on the ribosome

scientific article published in December 2009

Mechanistic alternatives for peptide bond formation on the ribosome.

scientific article published in June 2018

Modeling the mechanisms of biological GTP hydrolysis

scientific article published on 27 February 2015

Molecular Mechanisms in the Selectivity of Nonsteroidal Anti-Inflammatory Drugs.

scientific article published on 18 January 2018

Molecular dynamics study of heparin based coatings

scientific article published on 23 August 2008

Mutagenesis and computational modeling of human G-protein-coupled receptor Y2 for neuropeptide Y and peptide YY.

scientific article published on 31 October 2013

Mutagenesis and homology modeling of the Tn21 integron integrase IntI1.

scientific article

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

scientific article published on 12 November 2015

Origin of the omnipotence of eukaryotic release factor 1.

scientific article published on 10 November 2017

Permeation redux: thermodynamics and kinetics of ion movement through potassium channels

scientific article published on May 2014

Phe369(7.38) at human 5-HT(7) receptors confers interspecies selectivity to antagonists and partial agonists.

scientific article published on 18 November 2009

Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity

scientific article

Predicting binding modes from free energy calculations

scientific article published on 12 April 2008

Principles of start codon recognition in eukaryotic translation initiation

scientific article

Principles of stop-codon reading on the ribosome

scientific article published in Nature

Principles of tRNAAla Selection by Alanyl-tRNA Synthetase Based on the Critical G3·U70 Base Pair

scientific article published on 11 September 2019

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

scientific article

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

scientific article published on 4 November 2005

Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction.

scientific article

Protein surface softness is the origin of enzyme cold-adaptation of trypsin

scientific article

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

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

scientific article

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

scientific article published on 02 April 2019

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

scientific article published on 04 September 2019

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

scientific article

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

scientific article published on August 2005

Role of ribosomal protein L27 in peptidyl transfer

scientific article published on 8 April 2008

Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches

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

scientific article published on 25 April 2018

Structural and energetic effects of A2A adenosine receptor mutations on agonist and antagonist binding

scientific article

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

scientific article published on 29 October 2015

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

scientific article published on 10 November 2017

Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions

scientific article

Structure-based energetics of mRNA decoding on the ribosome

scientific article published on 05 March 2014

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

scientific article

Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations

scientific article published in September 2005

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

scientific article published on 02 March 2020

The Competing Mechanisms of Phosphate Monoester Dianion Hydrolysis

scientific article

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

scientific article

The catalytic power of ketosteroid isomerase investigated by computer simulation

scientific article

The conformation of a catalytic loop is central to GTPase activity on the ribosome

scientific article published on 30 December 2014

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

scientific article

Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations.

scientific article published on 15 December 2016

Toward a consensus model of the HERG potassium channel

scientific article published in March 2010

Toward an optimal docking and free energy calculation scheme in ligand design with application to COX-1 inhibitors

scientific article

Towards Rational Computational Engineering of Psychrophilic Enzymes

scientific article published on 16 December 2019

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

scientific article

X-Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

scientific article published on 16 June 2020

alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases

scientific article published on 3 July 2009

pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA.

scientific article

List of works by Johan Åqvist

3,4-Dihydropyrimidin-2(1<i>H</i>)-ones as Antagonists of the Human A<sub>2B</sub> Adenosine Receptor: Optimization, Structure-Activity Relationship Studies, and Enantiospecific Recognition

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

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

A close-up view of codon selection in eukaryotic initiation.

A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis

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

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

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

Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer

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

Author Correction: Inhibition of translation termination by small molecules targeting ribosomal release factors

Binding affinity prediction with different force fields: examination of the linear interaction energy method

Binding mode of the peptide YY carboxyterminus to the human Y2 receptor

Binding site preorganization and ligand discrimination in the purine riboswitch

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

Bridging the gap between ribosome structure and biochemistry by mechanistic computations.

C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions

Calculation of Heat Capacity Changes in Enzyme Catalysis and Ligand Binding

Calculations of solute and solvent entropies from molecular dynamics simulations

Catalysis and linear free energy relationships in aspartic proteases

Catalytic Adaptation of Psychrophilic Elastase

Characterization of Ligand Binding to GPCRs Through Computational Methods

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

Chemical reaction mechanisms in solution from brute force computational Arrhenius plots

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

Cold Adaptation of Triosephosphate Isomerase.

Cold adaptation of enzyme reaction rates.

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

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

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

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

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

Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor.

Computational and NMR study of quaternary ammonium ion conformations in solution

Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine.

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

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

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

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

Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions

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

Computer Simulations of Structure–Activity Relationships for hERG Channel Blockers ⬇️

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

Computer-aided design of GPCR ligands

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

Continuum solvation models in the linear interaction energy method

Corrigendum to “Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2′O)-methyltransferase” [Bioorg. Med. Chem. 15 (2007) 7795–7802]

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations

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

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

Editorial preface

Effect of Nitrogen Atom Substitution in A3 Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

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

Energetic tuning by tRNA modifications ensures correct decoding of isoleucine and methionine on the ribosome

Energetics of activation of GTP hydrolysis on the ribosome

Energetics of codon-anticodon recognition on the small ribosomal subunit

Entropy and Enzyme Catalysis

Enzyme catalysis by entropy without Circe effect

Enzyme surface rigidity tunes the temperature dependence of catalytic rates

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

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

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

Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods

Folding-Reaction Coupling in a Self-Cleaving Protein

Force field independent metal parameters using a nonbonded dummy model

Free energy calculations and ligand binding

Free energy calculations of A2A adenosine receptor mutation effects on agonist binding

Free energy calculations of RNA interactions

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

Hidden Conformational States and Strange Temperature Optima in Enzyme Catalysis

Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies

Inhibition of translation termination by small molecules targeting ribosomal release factors

Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum

Ligand binding affinities from MD simulations.

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

Linear Interaction Energy: Method and Applications in Drug Design

Mechanism of peptide bond synthesis on the ribosome

Mechanism of the translation termination reaction on the ribosome

Mechanistic alternatives for peptide bond formation on the ribosome.