Publications

The ACS published documents (*) are the unedited author's versions of the Submitted Works that were subsequently accepted for publication in the relative Journals, copyright © American Chemical Society after peer review. To access the final edited and published work see the author-directed links.

2018

2017

Jespers, W., Oliveira, A., Prieto-Díaz, R., Majellaro, M., Åqvist, J., Sotelo, E., Gutiérrez-de-Terán, H. (2017) Molecules DOI: 10.3390/molecules22111945 "Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors". [Open-Access Manuscript]

Lind, C., Oliveira, A., Åqvist, J. (2017) Nature Communications DOI: 10.1038/s41467-017-01757-0 "Origin of the omnipotence of eukaryotic release factor 1". [Open-Access Manuscript]

Hamnevik, E., Reddy Enugala, T., Maurer, D., Ntuku, S., Oliveira, A., Dobritzsch, D., Widersten, M. (2017) The FEBS Journal DOI: 10.1111/febs.14279 "Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer".

Azuaje, J., Jespers, W., Yaziji, V., Mallo, A., Majellaro, M., Caamaño, O., Loza, M.I., Cadavid, M.I., Brea, J., Åqvist, J., Sotelo, E., Gutiérrez-de-Terán, H. (2017) J. Med Chem. DOI: 10.1021/acs.jmedchem.7b00860 "Effect of Nitrogen Atom Substitution in A3 Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists". [Accepted Manuscript]

Åqvist, J. (2017) Biochemistry DOI: 10.1021/acs.biochem.7b00523 "Cold Adaptation of Triosephosphate Isomerase".

Åqvist, J., Isaksen, G.V., Brandsdal, B.O. (2017) Nature Reviews Chemistry DOI: 10.1038/s41570-017-0051 "Computation of enzyme cold adaptation".

Nøhr, A.C., Jespers, W., Shehata, M.A., Floryan, L., Isberg, V., Bayer Andersen, K., Åqvist, J., Gutiérrez-de-Terán, H., Bräuner-Osborne, H., Gloriam, D.E. (2017) Scientific Reports DOI: 10.1038/s41598-017-01049-z "The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site". [Open-Access Manuscript]

Carbajales, C., Azuaje, J., Oliveira, A., Loza, M.I., Brea, J., Cadavid, M.I., Masaguer, C.F., García-Mera, X., Gutiérrez-de-Terán, H., Sotelo, E. (2017) Journal of Medicinal Chemistry DOI: 10.1021/acs.jmedchem.7b00138 "Enantiospecific Recognition at the A2B Adenosine Receptor by Alkyl 2-Cyanoimino-4-substituted-6-methyl-1,2,3,4-tetrahydropyrimidine-5-carboxylates". [Accepted Manuscript]*

Khan, Y.S.,  Gutiérrez-de-Terán, H., Åqvist, J. (2017) Biochemistry DOI: 10.1021/acs.biochem.6b01006 "Probing the Time Dependency of Cyclooxygenase‑1 Inhibitors by Computer Simulations".

Lind, C., Esguerra, M., Åqvist, J. (2017) RNA Biology DOI: 10.1080/15476286.2017.1308998 "A close-up view of codon selection in eukariotic initiation"

Åqvist, J., Kazemi, M., Isaksen, G.V., Brandsdal, B.O. (2017) Acc. Chem. Res. DOI:10.1021/acs.accounts.6b00321 "Entropy and Enzyme Catalysis". [Open-Access Manuscript]

2016

Isaksen, G.V., Åqvist, J., Brandsdal, B.O. (2016) Biochemistry DOI:10.1021/acs/biochem/6b00967 "Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations".    

Kazemi, M., Himo, F., Åqvist, J. (2016) ACS Catal. DOI: 10.1021/acscatal.6b02842 "Peptide Release on the Ribosome Involves Substrate-Assisted Base Catalysis". [Open-Access Manuscript]

Lind, C., Åqvist, J. (2016) Nucl. Acids Res. DOI:10.1093/nar/gkw534 "Principles of start codon recognition in eukaryotic translation initiation". [Open-Access Manuscript]

Bharate, S.B., Singh, B., Kachier, S., Oliveira, A., Kumar, V., Bharate, S.S., Vishwakarma, R.A., Klotz, K., Gutiérrez-de-Terán, H. (2016) J. Med. Chem. DOI:10.1021/acs.jmedchem.6b00552 "Discovery of 7-(Prolinol-N-yl)-2-phenylamino-thiazolo[5,4-d]pyrimidines as Novel Non-Nucleoside Partial Agonists for the A_2A Adenosine Receptor: Prediction from Molecular Modeling" [Accepted Manuscript]*

Esguerra, M., Siretskiy, A., Bello, X., Sallander, J., Gutiérrez-de-Terán, H. (2016) Nucl. Acids Res. DOI: 10.1093/nar/gkw403 "GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors".[Open-Access Manuscript]

Kazemi, M., Himo, F., Åqvist, J. (2016) PNAS 113 (9), 2406-2411 "Enzyme catalysis by entropy without Circe effect"

Diwarkala, S., Nylander, E., Gronbladh, A., Vanga, S.R., Shamsudin Khan, Y., Gutiérrez-de-Terán, H., Ng, L., Pham, V., Savmarker, J., Lundback, T., Jenmalm-Jensen, A., Andersson, H., Engen, K., Rosenstrom, U., Larhed, M.,  Åqvist, J., Chai, S.Y., Hallberg, M. (2016) Molecular Pharmacology  DOI: 10.1124/mol.115.102533 "Binding to and inhibition of insulin-regulated aminopeptidase (IRAP) by macrocyclic disulfides enhances spine density". [Open-Access Manuscript]

Sallander, J., Wallinder, C., Hallberg, A., Åqvist, J., Gutiérrez-de-Terán, H. (2016) Bioorganic & Medicinal Chemistry Letters 26 (4), 1355-1359 "Structural determinants of subtype selectivity and functional activity of angiotensin II receptors". [Published Manuscript]

Åqvist, J., Kamerlin, S.C.L. (2016) ACS Catal. 6 (3), 1737-1743 "Conserved Motifs in Different Classes of GTPases Dictate their Specific Modes of Catalysis". [Open-Access Manuscript]

2015

Kazemi M, Åqvist J. (2015) Nature Commun. 6:7293 "Chemical reaction mechanisms in solution from brute force computational Arrhenius plots". [Open-Access Manuscript].

Keränen H, Åqvist J, Gutiérrez-de-Terán H. (2015) Chem. Commun. 51, 3522-3525. "Free energy calculations of A2A adenosine receptor mutation effects on agonist binding". [Open-Access Manuscript].

Åqvist J, Kamerlin SCL. (2015) Biochemistry. 54, 546-556. The conformation of a catalytic loop is the central to GTPase activity on the ribosome.

Shamsudin Khan, Y., Kazemi, M., Gutiérrez-de-Terán, H., Åqvist J. (2015) Biochemistry 54 (49), 7283-7291. "Origin of the Enigmatic Stepwise Tight-Binding Inhibition of Cyclooxygenase-1". [Open-Access Manuscript]

Åqvist, J., Kamerlin, S.C.L. (2015) Sci. Rep. 5, 15817. "Exceptionally large entropy contributions enable the high rates of GTP hydrolysis on the ribosome". [Open-Access Manuscript]

2014

Keränen H, Gutiérrez-de-Terán H, Åqvist J. (2014) PLoS One. 9, 1-12. "Structural and Energetic Effects of A_2A Adenosine Receptor Mutations on Agonist and Antagonist Binding". [Open-Access Manuscript]

Satpati P, Bauer P, Åqvist J. (2014) Chemistry. 20, 10271-10275. "Energetic Tuning by tRNA Modifications Ensures Correct Decoding of Isoleucine and Methionine on the Ribosome".

Sund J, Lind C, Åqvist J., (2014) J Phys Chem B.  "Binding Site Preorganization and Ligand Discrimination in the Purine Riboswitch".

Shamsudin Khan Y, Gutiérrez-de-Terán H, Boukharta L, Åqvist J. (2014). J Chem Inf Model. 54, 1488-1499. "Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX‐1 Inhibitors" [ Open-Access Manuscript]

Boukharta L, Gutiérrez-de-Terán H, Åqvist J. (2014) PLoS Comput Biol. 10, 1-11. "Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors". [Open-Access Manuscript]

Satpati P, Sund J, Åqvist J. (2014) Biochemistry. 53, 1714-1722. "Structure-Based Energetics of mRNA Decoding on the Ribosome".

2013

Christoffer Lind, Johan Sund & Johan Åqvist, (2013). Nature Commun. 4, 2940. "Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons".[Open-Access Manuscript]

Bo Xu, Helena Fällmar, Lars Boukharta, Jasna Pruner, Ingrid Lundell, Nina Mohell, Hugo Gutiérrez-de-Terán, Johan Åqvist and Dan Larhammar. (2013). Biochemistry, 52, 7987-7998."Mutagenesis and Computational Modeling of Human G-Protein-Coupled Receptor Y2 for Neuropeptide Y and Peptide YY". [Open-Access Manuscript]

Wallin, G., Kamerlin, S.C.L. & Åqvist, J. (2013) . Nature Commun. 4, 1733. “Energetics of Activation of GTP hydrolysis on the Ribosome”.[Open-Access Manuscript]

Luzhkov V., Decroly, E., Canard B, Selisko, B. & Åqvist, J. (2013). Mol. Inf. 32, 155. Evaluation of Adamantane Derivatives as Inhibitors of Dengue Virus mRNA Cap Methyltransferase by Docking and Molecular Dynamics Simulations.[Open-Access Manuscript] 

2012

Shaw, J., Trobro, S., He, S., Åqvist, J., Green, R. (2012). A Role for the 2 ' OH of Peptidyl-tRNA Substrate in Peptide Release on the Ribosome Revealed through RF-Mediated Rescue. Chemistry and Biology, 19(8): 983-993.

Wallin, G., Härd, T., Åqvist, J. (2012). Folding-Reaction Coupling in a Self-Cleaving Protein. Journal of Chemical Theory and Computation, 8(10): 3871-3879. [Open-Access Manuscript]

Mishra, S., Sund, J., Åqvist, J., Koca, J. (2012). Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. Journal of Computational Chemistry, 33(29): 2340-2350.

Aqvist, J., Lind, C., Sund, J., Wallin, G. (2012). Bridging the gap between ribosome structure and biochemistry by mechanistic computations. Current opinion in structural biology, 22(6): 815-823. [Open-Access Manuscript]

Willander, H., Askarieh, G., Landreh, M., Westermark, P., Nordling, K. et al. (2012). High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C. Proceedings of the National Academy of Sciences of the United States of America, 109(7): 2325-2329.

Gutiérrez-de-Terán, H. & Åqvist, J. (2012). In A Course on Biomolecular Simulations (J. Villa-Freixa, Ed.), Huygens Editorial, Barcelona, in press. “Estimation of ligand-binding affinities with the Linear Interaction Energy and related methods”. In press.

Gutiérrez-de-Terán, H. & Åqvist, J. (2012). Methods Mol. Biol., 819, 305. ”LIE: Method and Applications in Drug Design”. [Open-Access Manuscript]

2011

Boukharta, L, Keränen, H, Stary-Weinzinger, A, Wallin, G, de Groot, BL, Aqvist, J.; Computer simulations of structure-activity relationships for HERG channel blockers, Biochemistry, 50, 6146, (2011)[Open-Access Manuscript]

Liljas, A., Ehrenberg, M. & Åqvist, J. (2011). Science, 333, 37a. ” The GTP hydrolysis mechanism for translational GTPases”.

Johansson, M., Ieong, K.-W., Trobro, S., Strazewski, P., Åqvist, J., Pavlov, M.Y., & Ehrenberg, M. (2011). Proc. Natl. Acad. Sci. U.S.A. 108, 79.”pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA”.

Johansson, M., Ieong, K.-W., Åqvist, J., Pavlov, M.Y., & Ehrenberg, M. (2011).  In Ribosomes: Structure, Function and Dynamics (M.V. Rodnina, W. Wintermeyer & R. Green, Eds.), pp. 225-235, Springer.  “Rate and accuracy of messenger RNA translation on the ribosome”.

Díaz, L., Bujons, J., Delgado, A., Gutiérrez-de-Terán, H. & Åqvist, J. (2011). J. Chem. Inf. Model. 51, 601. “Computational Prediction of Structure-Activity Relationships for the Binding of Aminocyclitols to β-Glucocerebrosidase”. [Open-Access Manuscript]
 

2010

Wallin G and Åqvist J; The transition state for peptide bond formation reveals the ribosome as a water trap, Proc Natl Acad Sci U S A, 107, 1888, (2010)[Open-Access Manuscript]

Sund, J., Andér, M., and Åqvist, J. Principles of stop-codon reading on the ribosome, Nature, 465, 947, (2010)[Open-Access Manuscript]

Åkerberg, H., Fällmar, H., Sjödin, P., Boukharta, L., Gutiérrez-de-Terán, H., Lundell, I., Mohell, N., Larhammar, D. Mutagenesis of human neuropeptide Y/peptide YY receptor Y2 reveals additional differences to Y1 in interactions with highly conserved ligand positions, Regul. Peptides, 163, 120, (2010)

Stary, A., Wacker, S. J., Boukharta, L., Zachariae, U., Karimi-Nejad, Y., Åqvist, J., Vriend, G., de Groot, B. L. Toward a Consensus Model of the hERG Potassium Channel,  Chem.Med.Chem., 5, 455, (2010) [Open-Access Manuscript]

2009

Trobro, S. & Åqvist, J. (2009). Biochemistry, 48, 11296. “Mechanism of the Translation Termination Reaction on the Ribosome”.

Carlsson, J. & Åqvist, J. (2009). J. Phys. Chem. B 113, 10255. “Absolute Hydration Entropies of Alkali Metal Ions from Molecular Dynamics Simulations”.

Andér, M, Åqvist, J Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors? Biochemistry48, 3483, (2009)

Johansson DGA, Wallin G, Sandberg A, Macao B, Åqvist J and Härd T; Protein Autoproteolysis: Conformational Strain Linked to the Rate of Peptide Cleavage by the pH Dependence of the N -> O Acyl Shift Reaction J. Am. Chem. Soc.131, 9475, (2009)

Wallin G, Nervall M, Carlsson J and Åqvist J; Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method J. Chem. Theory Comput.5, 380, (2009)

Orrling, K.M., Marzahn, M.R., Guiterrez de Teran, H., Åqvist, J., Dunn, B.M. & Larhed M. (2009). Bioorg. Med. Chem. 17, 5933. “α-Substituted Norstatines as the Transition-State Mimic in Inhibitors of Multiple  Digestive Vacuole Malaria Aspartic Proteases”.

Rodrigo, J., Varin, T., Gutiérrez-de-Teran, H., Castro M., Brea J., Fabis, F., Dauphin, F., Åqvist, J.,  Perez, P., Burgueño, J., Vela, J.M. & Loza, M.I. (2009). Brit. J. Pharmacol. 159, 1069."Phe 369(7.38) at Human 5-HT7 Serotonin Receptors Confers Interspecies Selectivity to Antagonists and Partial Agonists. A Multidisciplinary Study Combining Pharmacological Evaluation, Molecular Modelling and Site-Directed Mutagenesis."

Johansson, C., Boukharta, L., Eriksson, J., Åqvist, J., Sundström, L. Mutagenesis and Homology Modeling of the Tn21 Integron Integrase IntI1, Biochemistry, 48, 1743, (2009)

2008

Almlöf, M., Kristensen, E.M.E., Siegbahn, H. & Åqvist, J. (2008). Biomaterials 29, 4463. “Molecular Dynamics Study of Heparin Based Biocompatible Coatings”.

Bjelic, S., Brandsdal, B.O. & Åqvist, J. (2008). Biochemistry 47, 10049. ”Cold-Adaptation of Enzyme Reaction Rates”.

Trobro, S. & Åqvist, J. (2008). Biochemistry 47, 4898. “Role of Ribosomal Protein L27 in Peptidyl Transfer”.

Luzhkov, V.B., Selisko, B., Nordqvist, A., Peyrane, F., Decroly, E., Karlén, A., Canard, B. & Åqvist, J. (2008). Bioorg. Med. Chem. 165, 3462. ”Corrigendum to: Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2’O)-methyltransferase”.

Coutard, B. et al. (2008). Antivir. Res. 78, 37. “The VIZIER project: Preparedness against pathogenic RNA viruses”.

Andér, M., Luzhkov, V.B., Åqvist, J. Ligand binding to the voltage gated Kv1.5 potassium channel in the open state - docking and computer simulations of a homology model. Biophys. J. 94, 820, (2008)

Nervall, M., Hanspers, P., Carlsson, J., Boukharta, L., Åqvist, J. Predicting binding modes from free energy calculations. J. Med. Chem. 51, 2657, (2008)

Carlsson, J., Boukharta, L., Aqvist, J. 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. J. Med. Chem. 51, 2648, (2008)

2007

Almlöf, M., Carlsson , J. & Åqvist, J. (2007). J. Chem. Theor. Comput. 3, 2162. “Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies”.

Warshel, A., Sharma, P.K., Chu, Z.T., Åqvist, J. Electrostatic Contributions to Binding of Transition State Analogues can be Different from the Corresponding Contributions to Catalysis: Phenolates Binding to the Oxyanion Hole of Ketosteroid Isomerase. Biochemistry46, 1466, (2007)

Guiterrez-de-Teran, H., Nervall, M., Dunn, B.M., Clemente, J.C. & Åqvist, J. (2006). FEBS Lett. 580, 5910. “Computational Analysis of Plasmepsin IV Bound to an Allophenylnorstatine Inhibitor”.

Almlöf, M., Andér, M., Åqvist, J. Energetics of Codon-Anticodon Recognition on the Small Ribosomal Subunit. Biochemistry46, 200, (2007)

Thomaeus, A., Carlsson, J., Åqvist, J., Widersten, M. Active Site of Epoxide Hydrolases Revisited: a Non-Canonical Residue in Potato StEH1 Promotes Both Formation and Breakdown of the Alkylenzyme Intermediate. Biochemistry46, 2466, (2007)

Bjelic, S., Nervall, M., Guiterrez-de-Teran, H., Ersmark, K., Hallberg, A. & Åqvist, J. (2007). Cell. Mol. Life Sci. 64, 2285. “Computational Inhibitor Design against Malaria Plasmepsins”.

Luzhkov, V.B., Selisko, B., Nordqvist, A., Peyrane, F., Decroly, E., Karlén, A., Canard, B. & Åqvist, J. (2007). Bioorg. Med. Chem. 15, 7795. ”Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2’O)-methyltransferase”.

Henriksson, L.M., Unge, T., Carlsson, J., Åqvist, J., Mowbray, S.L., Jones, T.A. Structures of Mycobacterium tuberculosis 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Provide New Insights into Catalysis. J. Biol. Chem.282, 19905, (2007)

Trobro, S., Åqvist, J. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis Mol. Cell27, 758, (2007)

2006

Brandsdal, B.O., Smalås, A.O., Åqvist, J. Free Energy Calculations Show that Acidic P1 Variants Undergo Large pKa Shifts Upon Binding to Trypsin. Proteins64, 740, (2006)

Luzhkov, V., Almlöf, M., Nervall, M., Åqvist, J. Computational Study of Binding Affinity and Selectivity of the Bacterial Ammonium Transporter AmtB. Biochemistry45, 10807, (2006)

Almlöf, M., Åqvist, J., Smalås, A.O., Brandsdal, B.O. Probing the Effect of Point Mutations at Protein-Protein Interfaces with Free Energy Calculations. Biophys. J.90, 433, (2006)

Carlsson, J., Andér, M., Nervall, M., Åqvist, J. Continuum Solvation Models in the Linear Interaction Energy Method. J. Phys. Chem. B110, 12034, (2006)

Carlsson, J., Åqvist, J. Calculations of Solute and Solvent Entropies from Molecular Dynamics Simulations. Phys. Chem. Chem. Phys.8, 5385, (2006)

Trobro, S., Åqvist, J. Analysis of Predictions for the Catalytic Mechanism of Ribosomal Peptidyl transfer. Biochemistry45, 7049, (2006)

Ersmark, K., Nervall, M., Guiterrez de Teran, H., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Gogoll, A., Samuelsson, B., Åqvist, J., Hallberg, A. Macrocyclic Inhibitors of the Malarial Aspartic Proteases Plasmepsin Plm II and IV. Bioorg, Med. Chem.14, 2197, (2006)

Guiterrez de Teran, H., Nervall, M., Ersmark, K., Liu, P., Janka, L.K., Dunn, B., Hallberg, A., Åqvist, J. Inhibitor Binding to the Plasmepsin IV Aspartic Protease from Plasmodium falciparum. Biochemistry45, 10529, (2006)

Guiterrez-de-Teran, H., Nervall, M., Dunn, B.M., Clemente, J.C., Åqvist, J. Computational Analysis of Plasmepsin IV Bound to an Allophenylnorstatine Inhibitor. FEBS Lett.580, 5910, (2006)

Bjelic, S., Åqvist, J. Catalysis and Linear Free Energy Relationships in Aspartic Proteases. Biochemistry45, 7709, (2006)

Lovmar, M., Nilsson, K., Vimberg, V., Tenson, T., Nervall, M., Ehrenberg, M. The Molecular Mechanism of Peptide-Mediated Erythromycin Resistance. J. Biol. Chem.281, 6742, (2006)

2005

Zavialov, A.V., Tischenko, V.M., Brandsdal, B.O., Åqvist, J., Zavialov, V.P., Knight, S.D. Resolving the Energy Paradox of Chaperone/Usher-Mediated Fibre Assembly. Biochem. J.389, 685, (2005)

Luzhkov, V.B. Mechanisms of antioxidant activity: DFT study of hydrogen abstraction from phenol and toluene by the hydroperoxyl radical. Chem. Phys.314, 211, (2005)

Luzhkov, V.B. Theoretical study of deuterium kinetic isotope effects in peroxidation of phenol and toluene. Chem. Phys.320, 1, (2005)

Trobro, S., Åqvist, J. Mechanism of Peptide Bond Synthesis on the Ribosome. Proc. Natl. Acad. Sci. U.S.A.102, 12395, (2005)

Österberg, F., Åqvist, J. Exploring Blocker Binding to a Homology Model of the Open hERG K+ Channel using Docking and Molecular Dynamics Methods. FEBS Lett.579, 2939, (2005)

Carlsson, J., Åqvist, J. Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding. J. Phys. Chem. B109, 6448, (2005)

Ersmark, K., Nervall, M., Hamelink, E., Janka, L.K., Clemente, J.C., Dunn, B.M., Blackman, M.J., Samuelsson, B., Åqvist, J., Hallberg, A. Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations. J. Med. Chem.48, 6090, (2005)

Luzhkov, V.B., Åqvist, J. Ions and Blockers in Potassium Channels: Insights from Free Energy Simulations. Biochim. Biophys. Acta1747, 109, (2005)

2004

Graffner-Nordberg, M., Kolmodin, K., Ohlsson, S., Andersson, P., Åqvist, J., Queener, S.F., Hallberg, A. Design, Synthesis and Computational Prediction of Ester Soft Drugs as Inhibitors of Dihydrofolate Reductase from Pneumocystis Carinii. Eur. J. Pharm. Sci.22, 43, (2004)

Gutierrez de Teran, H., Pastor, M., Centeno, N.B., Åqvist, J., Sanz, F. Comparative Analysis of Putative Agonist Binding Modes in the Human A1 Adenosine Receptor. ChemBioChem5, 841, (2004)

Marelius, J., Kolmodin, K., Åqvist, J. Q Manual for Version 5. Software manual 80 pp. Uppsala University (2004)

Almlöf, M., Brandsdal B.O., Åqvist, J. Binding Affinity Prediction with Different Force Fields: Evaluation of the Linear Interaction Energy Method. J. Comput. Chem.25, 1242, (2004)

Åqvist, J., Wennerström, P., Nervall, M., Bjelic, S., Brandsdal, B.O. Molecular Dynamics Simulations of Water and Biomolecules with a Monte Carlo Constant Pressure Algorithm. Chem. Phys. Lett.384, 288, (2004)

Bjelic, S., Åqvist, J. Computational Prediction of Structure, Substrate Binding Mode, Mechanism and Rate for a Malaria Protease with a Novel Type of Active Site. Biochemistry43, 14521, (2004)

Ersmark, K., Bjelic, S., Feierberg, I., Hamerlink, E., Hackett, F., Blackman, M.J., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. Potent Inhibitors of the P. falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity. J. Med. Chem.47, 110, (2004)

2003

Feierberg, I., Åqvist, J. Correction: The Catalytic Power of Ketosteroid Isomerase Investigated by Computer Simulation. Biochemistry42, 2258, (2003)

Brandsdal, B., Österberg, F., Almlöf, M., Feierberg, I., Luzhkov, V.B., Åqvist, J. Free Energy Calculations and Ligand Binding. Adv. Prot. Chem.66, 123, (2003)

Ersmark, K., Feierberg, I., Bjelic, S., Hultén J., Samuelsson, B., Åqvist, J., Hallberg, A. C2-Symmetric Inhibitors of Plasmodium falciparum Plasmepsin II: Synthesis and Theoretical Predictions. Bioorg. Med. Chem.11, 3723, (2003)

Luzhkov, V.B., Nilsson, J., Århem, P., Åqvist, J. Computational Modeling of the Open-State Kv1.5 Ion Channel Block by Bupivacaine. Biochim. Biophys. Acta1652, 35, (2003)

Luzhkov, V.B., Österberg, F., Åqvist J. Structure-Activity Relationship for Extracellular Block of K+ Channels by Tetraalkylammonium Ions. FEBS Lett.554, 159, (2003)

2002

Åqvist, J., Luzhkov, V.B., Brandsdal, B.O. Ligand Binding Affinities from MD Simulations. Acc. Chem. Res.35, 358, (2002)

Kolmodin, K., Luzhkov, V.B., Åqvist, J. Computational Study of the Influence of Solvent on 16O/18O Equilibrium Isotope Effects in Phosphate Deprotonation Reactions. J. Am. Chem. Soc.124, 10130, (2002)

Feierberg, I., Åqvist, J. Computational Modeling of Enzymatic Keto-Enol Isomerization Reactions. Theor. Chem. Acc108, 71, (2002)

Feierberg, I., Åqvist, J. The Catalytic Power of Ketosteroid Isomerase Investigated by Computer Simulation. Biochemistry41, 15728, (2002)

Luzhkov, V.B., Österberg, F., Acharya, P., Chattopadhyaya, J., Åqvist, J. Computational and NMR Study of Quaternary Ammonium Ion Conformations in Solution. Phys. Chem. Chem. Phys.4, 4640, (2002)

2001

Ljungberg, K.B., Marelius, J., Musil, D., Svensson, P., Nordén B., Åqvist, J. Computational Modelling of Inhibitor Binding to Human Thrombin. Eur. J. Pharm. Sci.12, 441, (2001)

Kolmodin, K., Luzhkov, V., Åqvist, J. Computational Enzymology: Protein Tyrosine Phosphatase Reactions. In Theoretical Biochemistry - Processes and Properties of Biological Systems I (L.A. Eriksson, ed.), Elsevier, Amsterdam, p.253 (2001)

Marelius, J., Ljungberg, K.B., Åqvist, J. Sensitivity of an Empirical Affinity Scoring Function to Changes in Receptor-Ligand Complex Conformations. Eur. J. Pharm. Sci.14, 87, (2001)

Åqvist, J., Marelius, J. The Linear Interaction Energy Method for Computation of Ligand Binding Affinities. In Free Energy Calculations in Rational Drug Design (M.R. Redd. & M.D. Erion, eds.), Kluwer, New York, p. 171 (2001)

Åqvist, J., Marelius, J. The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies. J. Combin. Chem. High Throughput Screening4, 613, (2001)

Graffner-Nordberg, M., Kolmodin, K. Ohlsson, S., Andersson, P., Åqvist, J., Queener, S.F., Hallberg, A. Design, Synthesis, Computational Prediction and Biological Evaluation of Ester Soft Drugs as Inhibitors of Dihydrofolate Reductase from Pneumocystis Carinii. J. Med. Chem.44, 2391, (2001)

Luzhkov, V.B., Åqvist, J. Mechanisms of Tetraethylammonium Ion Block in the KcsA Potassium Channel. FEBS Lett.495, 191, (2001)

Brandsdal, B.O., Åqvist, J., Smalås, A.O. Computational Analysis of Binding of P1-Variants to Trypsin. Protein Sci.10, 1584, (2001)

Luzhkov, V.B., Åqvist, J. K+/Na+ Selectivity of the KcsA Potassium Channel from Microscopic Free Energy Perturbation Calculations. Biochim. Biophys. Acta1548, 194, (2001)

Brandsdal, B.O., Smalås, A.O., Åqvist, J. Electrostatic Effects Play a Central Role in Cold Adaptation of Trypsin. FEBS Lett.499, 171, (2001)

Kolmodin, K., Åqvist, J. The Catalytic Mechanism of Protein Tyrosine Phosphatases Revisited. FEBS Lett.498, 208, (2001)

Luzhkov, V.B. Empirical Valence Bond Study of Radical Reactions: Hydrogen Atom Transfer in Peroxidation of Phenol. Chem. Phys. Lett.345, 34, (2001)

2000

Åqvist, J., Luzhkov, V. Ion Permeation Mechanism of the K+ Channel. Nature404, 881, (2000)

Kolmodin, K., Åqvist, J. Prediction of a Ligand Induced Conformational Change in the Catalytic Core of Cdc25A. FEBS Lett.465, 8, (2000)

Feierberg, I., Luzhkov, V., Åqvist, J. Computer Simulation of Primary Kinetic Isotope Effects in the Proposed Rate Limiting Step of the Glyoxalase I Reaction. J. Biol. Chem.275, 22657, (2000)

Graffner-Nordberg, M., Marelius, J., Ohlsson, S., Persson, Å., Swedberg, G., Andersson, P., Andersson, S.E., Åqvist, J., Hallberg, A. Computational Predictions of Binding Affinities to Dihydrofolate Reductase: Synthesis and Biological Evaluation of Methotrexate Analogues. J. Med. Chem.43, 3852, (2000)

Vagedes, P., Rabenstein, B., Åqvist, J., Marelius, J., Knapp, E.-W. The Deacylation Step of Acetylcholine Esterase: Computer Simulation Studies. J. Am. Chem. Soc.122, 12254, (2000)

Luzhkov, V., Åqvist, J. A Computational Study of Ion Binding and Protonation States in the KcsA Potassium Channel. Biochim. Biophys. Acta1481, 360, (2000)

1999

Kolmodin, K., Hansson, T., Danielsson, J., Åqvist, J. Molecular Dynamics Simulations of Substrate Dephosphorylation by Low Molecular Weight Protein Tyrosine Phosphatase. ACS Symp. Ser.721, 370, (1999)

Åqvist, J., Kolmodin, K., Florian, J., Warshel, A. Mechanistic Alternatives in Phosphate Ester Hydrolysis. Chemistry & Biology6, R71, (1999)

Kolmodin, K., Åqvist, J. Computational Modelling of Catalysis and Binding in Low Molecular Weight Protein Tyrosine Phosphatase. Int. J. Quantum Chem.73, 147, (1999)

Kolmodin, K., Nordlund, P., Åqvist, J. Mechanism of Substrate Dephosphorylation in low Mr Protein Tyrosine Phosphatase. Proteins36, 370, (1999)

Marelius, J., Kolmodin, K., Feierberg, I., Åqvist, J. Q: An MD Program for Free Energy Calculations and Empirical Valence Bond Simulations in Biomolecular Systems. J. Mol. Graph. Model.16, 213, (1999)

Feierberg, I., Cameron, A.D., Åqvist, J. Energetics of the Proposed Rate-Determining Step of the Glyoxalase I Reaction. FEBS Lett.453, 90, (1999)

Åqvist, J. Long-Range Electrostatic Effects on Peptide Folding. FEBS Lett.457, 414, (1999)

Kolmodin, K., Åqvist, J. Computational Modelling of the Rate-Limiting Step in Low Molecular Weight Protein Tyrosine Phosphatase. FEBS Lett.456, 301, (1999)

Luzhkov, V., Åqvist, J. Free Energy Perturbation Calculations of Binding and Transition State Energies: Hydrolysis of Phenyl Esters by beta-Cyclodextrin. Chem. Phys. Lett.302, 267, (1999)

1998

Hansson, T., Marelius, J., Åqvist, J. Ligand Binding Affinity Prediction by Linear Interaction Energy Methods. J. Comput.-Aided Mol. Design12, 27, (1998)

Marelius, J., Graffner Nordberg, M., Hansson, T., Hallberg, A., Åqvist, J. Computation of Affinity and Selectivity: Binding of 2,4-Diaminopteridine and 2,4-Diaminoquinazoline Inhibitors to Dihydrofolate Reductases. J. Comput.-Aided Mol. Design12, 119, (1998)

Marelius, J., Hansson, T., Åqvist, J. Calculation of Ligand Binding Free Energies from Molecular Dynamics Simulations. Int. J. Quantum Chem.69, 77, (1998)

Åqvist, J., Hansson, T. Analysis of Electrostatic Potential Truncation Schemes in Simulations of Polar Solvents. J. Phys. Chem.102, 3837, (1998)

Florian, J., Åqvist, J., Warshel, A. On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution. J. Am. Chem. Soc.120, 11524, (1998)

Luzhkov, V., Åqvist, J. Computer Simulation of Phenyl Ester Cleavage by beta-Cyclodextrin in Solution. J. Am. Chem. Soc.120, 6131, (1998)

1997

Åqvist, J. Modelling of Proton Transfer Reactions in Enzymes. In Computational Approaches to Biochemical Reactivity (G. Naray-Szabo & A. Warshel, eds.) p.341, Kluwer, Dordrecht (1997)

Hansson, T., Nordlund, P., Åqvist, J. Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase. J. Mol. Biol.265, 118, (1997)

Hultén, J., Bonham, N.M., Nillroth, U., Hansson, T., Zuccarello, G., Bouzide, A., Åqvist, J., Classon, B., Danielsson, H., Karlén, A., Kvarnström, I., Samuelsson, B., Hallberg, A. Cyclic HIV-1 Protease Inhibitors Derived from Mannitol. Synthesis, Inhibitory Potency and Computational Predictions of Binding Affinities. J. Med. Chem.40, 885, (1997)

Åqvist, J. Comment: On the Sensitivity to Changes in Water-Protein Interaction Parameters. Proteins28, 143, (1997)

1996

Åqvist, J., Fothergill, M. Computer Simulation of the Triosephosphate Isomerase Catalyzed Reaction. J. Biol. Chem.271, 10010, (1996)

Åqvist, J. Calculation of Absolute Binding Free Energies for Charged Ligands and the Effects of Long-Range Electrostatic Interactions. J. Comput. Chem.17, 1587, (1996)

Åqvist, J., Hansson, T. On the Validity of Electrostatic Linear Response in Polar Solvents. J. Phys. Chem.100, 9512, (1996)

1995

Åqvist, J., Mowbray, S.L. Sugar Recognition by a Glucose/Galactose Receptor: Evaluation of Binding Energetics from Molecular Dynamics Simulations. J. Biol. Chem.270, 9978, (1995)

Hansson, T., Åqvist, J. Estimation of Binding Free Energies for HIV Proteinase Inhibitors by Molecular Dynamics Simulations. Protein Eng.8, 1137, (1995)

Åqvist, J. Book review: Metalloenzymes Involving Amino Acid-Residue and Related Radicals. Q. Rev. Biol.70, 505., (1995)

1994

Åqvist, J., Medina, C., Samuelsson, J.-E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design. Protein Eng.7, 385, (1994)

Åqvist, J. Comment on Transferability of Ion Models. J. Phys. Chem.98, 8253, (1994)

1993

Åqvist, J., Warshel, A. Molecular Recognition in the Catalytic Action of Metalloenzymes. In Principles of Molecular Recognition (A.D. Buckingham, A.C. Lego., & S.M. Roberts, eds.), p. 108, Chapman & Hall (1993)

Åqvist, J., Fothergill, M., Warshel, A. Computer Simulation of the CO2/HCO3- Interconversion Step in Human Carbonic Anhydrase I. J. Am. Chem. Soc.115, 631, (1993)

Åqvist, J. Book review: Computer Modeling of Chemical Reactions in Enzymes and Solution. J. Biochem. Biophys. Methods26, 241, (1993)

Åqvist, J., Warshel, A. Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches. Chemical Reviews93, 2523, (1993)

1992

Åqvist, J., Tapia, O. A Molecular Model for the Retinol Binding Protein-Prealbumin Complex. J. Mol. Graph10, 120, (1992)

Eisenman, G., Alvarez, O., Åqvist, J. Free Energy Perturbation Simulations of Cation Binding to Valinomycin. J. Inclusion Phenom. Molec. Recog. Chem.12, 23, (1992)

Åqvist, J., Warshel, A. Computer Simulation of the Initial Proton Transfer Step in Human Carbonic Anhydrase I. J. Mol. Biol.224, 7, (1992)

Åqvist, J. Modelling of Ion-Ligand Interactions in Solutions and Biomolecules. J. Mol. Struct. (Theochem)256, 135, (1992)

Åqvist, J., Eisenman, G., Alvarez, O. Ion-Selective Properties of a Small Ionophore in Methanol Studied by Free Energy Perturbation Simulations. J. Phys. Chem.96, 10019, (1992)

Warshel, A., Hwang, J.K., Åqvist, J. Computer Simulations of Enzymatic Reactions: Examination of Linear Free Energy Relationships and Quantum Mechanical Corrections in the Initial Proton Transfer Step of Carbonic Anhydrase. Faraday Discuss.93, 225, (1992)

Åqvist, J. Comment on Models for Electrostatic Effects in Proteins. Protein Eng.5, 469, (1992)

Åqvist, J., Alvarez, O., Eisenman, G. Computer Modelling of Ion Binding Sites in Proteins. In Membrane Proteins: Structures, Interactions and Models (A. Pullman, J. Jortner, & B. Pullman, eds.) p. 367. Kluwer, Dordrecht (1992)

1991

Åqvist, J., Luecke, H., Quiocho, F.A., Warshel, A. Dipoles Localized at Helix Termini of Proteins Stabilize Charges. Proc. Natl. Acad. Sci. U.S.A.88, 2026, (1991)

Warshel, A., Åqvist, J. Electrostatic Energy and Macromolecular Function. Ann. Rev. Biophys. Biophys. Chem.20, 267, (1991)

Eisenman, G., Åqvist, J., Alvarez, O. Free Energies Underlying Ion Binding and Transport in Protein Channels: Free Energy Perturbation Simulations of Ion Binding and Selectivity for Valinomycin. J. Chem. Soc. Faraday Trans.87, 2099, (1991)

Åqvist, J. Free Energy Perturbation Study of Metal Ion Catalyzed Proton Transfer in Water. J. Phys. Chem.95, 4587, (1991)

1990

Åqvist, J., Tapia, O. Molecular Dynamics Simulation of the Solution Structure of the C-Terminal Fragment of L7/L12 Ribosomal Protein. Biopolymers30, 205, (1990)

Warshel, A., Åqvist, J. Microscopic Simulations of Chemical Processes in Proteins and the Role of Electrostatic Free Energy. In Theoretical Biochemistry & Molecular Biophysics (D.L. Beveridge & R. Lavery, eds.), p. 257, Adenine Press (1990)

Åqvist, J., Warshel, A. Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effects of Metal Ion Substitutions in Staphylococcal Nuclease. J. Am. Chem. Soc.112, 2860, (1990)

Åqvist, J. Ion-Water Interaction Potentials Derived from Free Energy Perturbation Simulations. J. Phys. Chem.94, 8021, (1990)

Tapia, O., Nilsson, O., Campillo, M., Åqvist, J., Horjales, E. Low Frequency Motions in Protein Secondary Structures. Molecular Dynamics Studies on Carboxy Terminal Fragment of L7/L12 Ribosomal Protein. In Structure & Methods, Vol. 2: DNA Protein Complexes & Proteins (R.H. Sarma & M.H. Sarma, eds.), p. 147, Adenine Press (1990)

1989

Åqvist, J., Leijonmarck, M., Tapia, O. A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein. II. Effects of Intermolecular Interactions on Structure and Dynamics. Eur. Biophys. J.16, 327, (1989)

Tapia, O., Åqvist, J. Molecular Dynamics as a Tool for Structural and Functional Predictions: the Retinol Binding Protein and Chloroplast C-Terminal Fragment of the L12 Ribosomal Protein Cases. Prog. Clin. Biol. Res.289, 55, (1989)

Åqvist, J., Warshel, A. Consistent Calculations of Electrostatic Free Energies in Membrane Channels. The Solvation of Na+ by the Gramicidin Channel. Comm. Mol. Cell. Biophys.6, 91, (1989)

Åqvist, J., Warshel, A. Calculations of Free Energy Profiles for the Staphylococcal Nuclease Catalyzed Reaction. Biochemistry28, 4680, (1989)

Warshel, A., Åqvist, J. Electrostatic Correlation of Structure and Function in Proteins. Chemica Scripta29A, 75, (1989)

Åqvist, J., Warshel, A. Energetics of Ion Permeation through Membrane Channels. The Solvation of Na+ by Gramicidin A. Biophys. J.56, 171, (1989)

Warshel, A., Åqvist, J., Creighton, S. Enzymes Work by Solvation Substitution rather than by Desolvation. Proc. Natl. Acad. Sci. U.S.A.86, 5820, (1989)

1987

Åqvist, J., Tapia, O. Surface Fractality as a Guide for Studying Protein-Protein Interactions. J. Mol. Graph.5, 30, (1987)

Horjales, E., Åqvist, J., Leijonmarck, M., Tapia, O. Aspects of Model Building Applied to the C-Terminal Domain of the L12 Protein from Chloroplast Ribosomes. A Molecular Dynamics Study. Biochem. Biophys. Res. Comm.148, 954, (1987)

Åqvist, J., Tapia, O. Surface Fractality and Protein-Protein Interactions (in Swedish). Kemisk Tidskrift14, 46, (1987)

1986

Åqvist, J. A Simple Way to Calculate the Axis of an alpha-helix. Computers & Chemistry10, 97, (1986)

Sandblom, P., Åqvist, J., Jones, T.A., Newcomer, M.E., van Gunsteren, W.F., Tapia, O. Structural Changes in Retinol Binding Protein Induced by Retinol Removal. A Molecular Dynamics Study. Biochem. Biophys. Res. Comm.139, 564, (1986)

Åqvist, J., Sandblom, P., Jones, T.A., Newcomer, M.E., van Gunsteren, W.F., Tapia, O. Molecular Dynamics Simulations of the Holo and Apo Forms of Retinol Binding Protein. Structural and Dynamical Changes Induced by Retinol Removal. J. Mol. Biol.192, 593, (1986)

1985

Åqvist, J., van Gunsteren, W.F., Leijonmarck, M., Tapia, O. A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein. In Molecular Dynamics and Protein Structure (J. Hermans, ed.), p. 145, Polycrystal Book Service, Western Springs Ill (1985)

Åqvist, J., van Gunsteren, W.F., Leijonmarck, M., Tapia, O. A Molecular Dynamics Study of the C-Terminal Fragment of the L7/L12 Ribosomal Protein: Secondary Structure Motion in a 150 Picosecond Trajectory. J. Mol. Biol.183, 461, (1985)

1984

Newcomer, M.E., Jones, T.A., Åqvist, J., Sundelin, J., Eriksson, U., Rask, L., Peterson, P.A. The Three-Dimensional Structure of Retinol-Binding Protein. EMBO J.3, 1451, (1984)