Selected publications from the Åqvist group
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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) [abstract]
Andér, M, Åqvist, J Does Glutamine Methylation Affect the Intrinsic Conformation of the Universally Conserved GGQ Motif in Ribosomal Release Factors? Biochemistry 48, 3483, (2009) [abstract]
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) [abstract]
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) [abstract]
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)
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. Biochemistry 46, 1466, (2007)
Almlöf, M., Andér, M., Åqvist, J. Energetics of Codon-Anticodon Recognition on the Small Ribosomal Subunit. Biochemistry 46, 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. Biochemistry 46, 2466, (2007)
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) [abstract]
Trobro, S., Åqvist, J. A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis Mol. Cell 27, 758, (2007)
Brandsdal, B.O., Smalås, A.O., Åqvist, J. Free Energy Calculations Show that Acidic P1 Variants Undergo Large pKa Shifts Upon Binding to Trypsin. Proteins 64, 740, (2006)
Luzhkov, V., Almlöf, M., Nervall, M., Åqvist, J. Computational Study of Binding Affinity and Selectivity of the Bacterial Ammonium Transporter AmtB. Biochemistry 45, 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. B 110, 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. Biochemistry 45, 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. Biochemistry 45, 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. Biochemistry 45, 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)
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. B 109, 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. Acta 1747, 109, (2005)
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. ChemBioChem 5, 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. Biochemistry 43, 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)
Feierberg, I., Åqvist, J. Correction: The Catalytic Power of Ketosteroid Isomerase Investigated by Computer Simulation. Biochemistry 42, 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. Acta 1652, 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)
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. Acc 108, 71, (2002)
Feierberg, I., Åqvist, J. The Catalytic Power of Ketosteroid Isomerase Investigated by Computer Simulation. Biochemistry 41, 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)
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 Screening 4, 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. Acta 1548, 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)
Åqvist, J., Luzhkov, V. Ion Permeation Mechanism of the K+ Channel. Nature 404, 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. Acta 1481, 360, (2000)
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 & Biology 6, 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. Proteins 36, 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)
Hansson, T., Marelius, J., Åqvist, J. Ligand Binding Affinity Prediction by Linear Interaction Energy Methods. J. Comput.-Aided Mol. Design 12, 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. Design 12, 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)
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. Proteins 28, 143, (1997)
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)
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)
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)
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. Methods 26, 241, (1993)
Åqvist, J., Warshel, A. Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches. Chemical Reviews 93, 2523, (1993)
Åqvist, J., Tapia, O. A Molecular Model for the Retinol Binding Protein-Prealbumin Complex. J. Mol. Graph 10, 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)
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)
Åqvist, J., Tapia, O. Molecular Dynamics Simulation of the Solution Structure of the C-Terminal Fragment of L7/L12 Ribosomal Protein. Biopolymers 30, 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)
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. Biochemistry 28, 4680, (1989)
Warshel, A., Åqvist, J. Electrostatic Correlation of Structure and Function in Proteins. Chemica Scripta 29A, 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)
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 Tidskrift 14, 46, (1987)
Åqvist, J. A Simple Way to Calculate the Axis of an alpha-helix. Computers & Chemistry 10, 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)
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)
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)