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Johan Aqvist

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Concepts & Ideas

Occupations

Activities & Behaviors

Computer Simulation

Chemicals & Drugs

Phenomena

Living Beings

Plasmodium falciparum

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Co-Publications
Name
13
Luzhkov, Victor
10
Hallberg, Anders
9
Kolmodin, Karin
9
Brandsdal, Bjørn
8
Carlsson, Jens
8
Warshel, Arieh
7
Nervall, Martin
7
Tapia, Orlando
7
Feierberg, Isabella
7
Marelius, J
6
Almlöf, Martin
6
Bjelic, Sinisa
5
Ersmark, Karolina
5
Gutierrez de teran, Hugo
4
Smalås, Arne

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Publications

TOP 3
Orrling Kristina M; Marzahn Melissa R; Gutiérrez-de-Terán Hugo; Aqvist Johan; Dunn Ben M; Larhed Mats
alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases.
Carlsson Jens; Aqvist Johan
Absolute hydration entropies of alkali metal ions from molecular dynamics simulations.
Johansson Denny G A; Wallin Göran; Sandberg Anders; Macao Bertil; Aqvist Johan; Härd Torleif
Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction.

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All Publications

2009: Orrling Kristina M; Marzahn Melissa R; Gutiérrez-de-Terán Hugo; Aqvist Johan; Dunn Ben M; Larhed Mats
alpha-Substituted norstatines as the transition-state mimic in inhibitors of multiple digestive vacuole malaria aspartic proteases.
Bioorganic & medicinal chemistry 2009;17(16):5933-49.
2009: Carlsson Jens; Aqvist Johan
Absolute hydration entropies of alkali metal ions from molecular dynamics simulations.
The journal of physical chemistry. B 2009;113(30):10255-60.
2009: Johansson Denny G A; Wallin Göran; Sandberg Anders; Macao Bertil; Aqvist Johan; Härd Torleif
Protein autoproteolysis: conformational strain linked to the rate of peptide cleavage by the pH dependence of the N --> O acyl shift reaction.
Journal of the American Chemical Society 2009;131(27):9475-7.
2009: Andér Martin; Aqvist Johan
Does glutamine methylation affect the intrinsic conformation of the universally conserved GGQ motif in ribosomal release factors?
Biochemistry 2009;48(15):3483-9.
2008: Almlöf Martin; Kristensen Emma M E; Siegbahn Hans; Aqvist Johan
Molecular dynamics study of heparin based coatings.
Biomaterials 2008;29(33):4463-9.
2008: Bjelic Sinisa; Brandsdal Bjørn O; Aqvist Johan
Cold adaptation of enzyme reaction rates.
Biochemistry 2008;47(38):10049-57.
2008: Carlsson Jens; Boukharta Lars; Aqvist Johan
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.
Journal of medicinal chemistry 2008;51(9):2648-56.
2008: Nervall Martin; Hanspers Peter; Carlsson Jens; Boukharta Lars; Aqvist Johan
Predicting binding modes from free energy calculations.
Journal of medicinal chemistry 2008;51(9):2657-67.
2008: Trobro Stefan; Aqvist Johan
Role of ribosomal protein L27 in peptidyl transfer.
Biochemistry 2008;47(17):4898-906.
2008: Andér Martin; Luzhkov Victor B; Aqvist Johan
Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state--docking and computer simulations of a homology model.
Biophysical journal 2008;94(3):820-31.
2007: Trobro Stefan; Aqvist Johan
A model for how ribosomal release factors induce peptidyl-tRNA cleavage in termination of protein synthesis.
Molecular cell 2007;27(5):758-66.
2007: Bjelic S; Nervall M; Gutiérrez-de-Terán H; Ersmark K; Hallberg A; Aqvist J
Computational inhibitor design against malaria plasmepsins.
Cellular and molecular life sciences : CMLS 2007;64(17):2285-305.
2007: Henriksson Lena M; Unge Torsten; Carlsson Jens; Aqvist Johan; Mowbray Sherry L; Jones T Alwyn
Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis.
The Journal of biological chemistry 2007;282(27):19905-16.
2007: Thomaeus Ann; Carlsson Jens; Aqvist Johan; Widersten Mikael
Active site of epoxide hydrolases revisited: a noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate.
Biochemistry 2007;46(9):2466-79.
2007: Warshel Arieh; Sharma Pankaz K; Chu Zhen T; Aqvist Johan
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.
Biochemistry 2007;46(6):1466-76.
2007: Almlöf Martin; Andér Martin; Aqvist Johan
Energetics of codon-anticodon recognition on the small ribosomal subunit.
Biochemistry 2007;46(1):200-9.
2006: Carlsson Jens; Aqvist Johan
Calculations of solute and solvent entropies from molecular dynamics simulations.
Physical chemistry chemical physics : PCCP 2006;8(46):5385-95.
2006: Gutiérrez-de-Terán Hugo; Nervall Martin; Dunn Ben M; Clemente Jose C; Aqvist Johan
Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor.
FEBS letters 2006;580(25):5910-6.
2006: Luzhkov Victor B; Almlöf Martin; Nervall Martin; Aqvist Johan
Computational study of the binding affinity and selectivity of the bacterial ammonium transporter AmtB.
Biochemistry 2006;45(36):10807-14.
2006: Gutiérrez-de-Terán Hugo; Nervall Martin; Ersmark Karolina; Liu Peng; Janka Linda K; Dunn Ben; Hallberg Anders; Aqvist Johan
Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum.
Biochemistry 2006;45(35):10529-41.
2006: Brandsdal Bjørn O; Smalås Arne O; Aqvist Johan
Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin.
Proteins 2006;64(3):740-8.
2006: Carlsson Jens; Andér Martin; Nervall Martin; Aqvist Johan
Continuum solvation models in the linear interaction energy method.
The journal of physical chemistry. B 2006;110(24):12034-41.
2006: Bjelic Sinisa; Aqvist Johan
Catalysis and linear free energy relationships in aspartic proteases.
Biochemistry 2006;45(25):7709-23.
2006: Trobro Stefan; Aqvist Johan
Analysis of predictions for the catalytic mechanism of ribosomal peptidyl transfer.
Biochemistry 2006;45(23):7049-56.
2006: Almlöf Martin; Aqvist Johan; Smalås Arne O; Brandsdal Bjørn O
Probing the effect of point mutations at protein-protein interfaces with free energy calculations.
Biophysical journal 2006;90(2):433-42.
2005: Ersmark Karolina; Nervall Martin; Hamelink Elizabeth; Janka Linda K; Clemente Jose C; Dunn Ben M; Blackman Michael J; Samuelsson Bertil; Aqvist Johan; Hallberg Anders
Synthesis of malarial plasmepsin inhibitors and prediction of binding modes by molecular dynamics simulations.
Journal of medicinal chemistry 2005;48(19):6090-106.
2005: Trobro Stefan; Aqvist Johan
Mechanism of peptide bond synthesis on the ribosome.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(35):12395-400.
2005: Zavialov Anton V; Tischenko Vladimir M; Fooks Laura J; Brandsdal Bjørn O; Aqvist Johan; Zav'yalov Vladimir P; Macintyre Sheila; Knight Stefan D
Resolving the energy paradox of chaperone/usher-mediated fibre assembly.
The Biochemical journal 2005;389(Pt 3):685-94.
2005: Osterberg Fredrik; Aqvist Johan
Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods.
FEBS letters 2005;579(13):2939-44.
2005: Carlsson Jens; Aqvist Johan
Absolute and relative entropies from computer simulation with applications to ligand binding.
The journal of physical chemistry. B 2005;109(13):6448-56.
2005: Luzhkov V B; Aqvist J
Ions and blockers in potassium channels: insights from free energy simulations.
Biochimica et biophysica acta 2005;1747(1):109-20.
2004: Bjelic Sinisa; Aqvist Johan
Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site.
Biochemistry 2004;43(46):14521-8.
2004: Almlöf Martin; Brandsdal Bjørn O; Aqvist Johan
Binding affinity prediction with different force fields: examination of the linear interaction energy method.
Journal of computational chemistry 2004;25(10):1242-54.
2004: Gutiérrez-de-Terán Hugo; Pastor Manuel; Centeno Nuria B; Aqvist Johan; Sanz Ferran
Comparative analysis of putative agonist-binding modes in the human A1 adenosine receptor.
Chembiochem : a European journal of chemical biology 2004;5(6):841-9.
2004: Graffner-Nordberg Malin; Kolmodin Karin; Aqvist Johan; Queener Sherry F; Hallberg Anders
Design, synthesis, and computational affinity prediction of ester soft drugs as inhibitors of dihydrofolate reductase from Pneumocystis carinii.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2004;22(1):43-54.
2004: Ersmark Karolina; Feierberg Isabella; Bjelic Sinisa; Hamelink Elizabeth; Hackett Fiona; Blackman Michael J; Hultén Johan; Samuelsson Bertil; Aqvist Johan; Hallberg Anders
Potent inhibitors of the Plasmodium falciparum enzymes plasmepsin I and II devoid of cathepsin D inhibitory activity.
Journal of medicinal chemistry 2004;47(1):110-22.
2003: Luzhkov Victor B; Osterberg Fredrik; Aqvist Johan
Structure-activity relationship for extracellular block of K+ channels by tetraalkylammonium ions.
FEBS letters 2003;554(1-2):159-64.
2003: Luzhkov Victor B; Nilsson Johanna; Arhem Peter; Aqvist Johan
Computational modelling of the open-state Kv 1.5 ion channel block by bupivacaine.
Biochimica et biophysica acta 2003;1652(1):35-51.
2003: Ersmark Karolina; Feierberg Isabella; Bjelic Sinisa; Hultén Johan; Samuelsson Bertil; Aqvist Johan; Hallberg Anders
C2-symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions.
Bioorganic & medicinal chemistry 2003;11(17):3723-33.
2003: Brandsdal Bjørn O; Osterberg Fredrik; Almlöf Martin; Feierberg Isabella; Luzhkov Victor B; Aqvist Johan
Free energy calculations and ligand binding.
Advances in protein chemistry 2003;66():123-58.
2002: Feierberg Isabella; Aqvist Johan
The catalytic power of ketosteroid isomerase investigated by computer simulation.
Biochemistry 2002;41(52):15728-35.
2002: Kolmodin Karin; Luzhkov Victor B; Aqvist Johan
Computational study of the influence of solvent on (16)O/(18)O equilibrium isotope effects in phosphate deprotonation reactions.
Journal of the American Chemical Society 2002;124(34):10130-5.
2002: Aqvist Johan; Luzhkov Victor B; Brandsdal Bjørn O
Ligand binding affinities from MD simulations.
Accounts of chemical research 2002;35(6):358-65.
2001: Aqvist J; Marelius J
The linear interaction energy method for predicting ligand binding free energies.
Combinatorial chemistry & high throughput screening 2001;4(8):613-26.
2001: Luzhkov V B; Aqvist J
K(+)/Na(+) selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations.
Biochimica et biophysica acta 2001;1548(2):194-202.
2001: Brandsdal B O; Aqvist J; Smalås A O
Computational analysis of binding of P1 variants to trypsin.
Protein science : a publication of the Protein Society 2001;10(8):1584-95.
2001: Marelius J; Ljungberg K B; Aqvist J
Sensitivity of an empirical affinity scoring function to changes in receptor-ligand complex conformations.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2001;14(1):87-95.
2001: Graffner-Nordberg M; Kolmodin K; Aqvist 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.
Journal of medicinal chemistry 2001;44(15):2391-402.
2001: Brandsdal B O; Smalås A O; Aqvist J
Electrostatic effects play a central role in cold adaptation of trypsin.
FEBS letters 2001;499(1-2):171-5.
2001: Kolmodin K; Aqvist J
The catalytic mechanism of protein tyrosine phosphatases revisited.
FEBS letters 2001;498(2-3):208-13.
2001: Luzhkov V B; Aqvist J
Mechanisms of tetraethylammonium ion block in the KcsA potassium channel.
FEBS letters 2001;495(3):191-6.
2001: Ljungberg K B; Marelius J; Musil D; Svensson P; Norden B; Aqvist J
Computational modelling of inhibitor binding to human thrombin.
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences 2001;12(4):441-6.
2000: Graffner-Nordberg M; Marelius J; Ohlsson S; Persson A; Swedberg G; Andersson P; Andersson S E; Aqvist J; Hallberg A
Computational predictions of binding affinities to dihydrofolate reductase: synthesis and biological evaluation of methotrexate analogues.
Journal of medicinal chemistry 2000;43(21):3852-61.
2000: Luzhkov V B; Aqvist J
A computational study of ion binding and protonation states in the KcsA potassium channel.
Biochimica et biophysica acta 2000;1481(2):360-70.
2000: Feierberg I; Luzhkov V; Aqvist J
Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.
The Journal of biological chemistry 2000;275(30):22657-62.
2000: Aqvist J; Luzhkov V
Ion permeation mechanism of the potassium channel.
Nature 2000;404(6780):881-4.
2000: Kolmodin K; Aqvist J
Prediction of a ligand-induced conformational change in the catalytic core of Cdc25A.
FEBS letters 2000;465(1):8-11.
1999: Aqvist J
Long-range electrostatic effects on peptide folding.
FEBS letters 1999;457(3):414-8.
1999: Kolmodin K; Aqvist J
Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase.
FEBS letters 1999;456(2):301-5.
1999: Kolmodin K; Nordlund P; Aqvist J
Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase.
Proteins 1999;36(3):370-9.
1999: Feierberg I; Cameron A D; Aqvist J
Energetics of the proposed rate-determining step of the glyoxalase I reaction.
FEBS letters 1999;453(1-2):90-4.
1999: Aqvist J; Kolmodin K; Florian J; Warshel A
Mechanistic alternatives in phosphate monoester hydrolysis: what conclusions can be drawn from available experimental data?
Chemistry & biology 1999;6(3):R71-80.
1998: Marelius J; Kolmodin K; Feierberg I; Aqvist J
Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.
Journal of molecular graphics & modelling 1998;16(4-6):213-25, 261.
1998: Marelius J; Graffner-Nordberg M; Hansson T; Hallberg A; Aqvist J
Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases.
Journal of computer-aided molecular design 1998;12(2):119-31.
1998: Hansson T; Marelius J; Aqvist J
Ligand binding affinity prediction by linear interaction energy methods.
Journal of computer-aided molecular design 1998;12(1):27-35.
1997: Hultén J; Bonham N M; Nillroth U; Hansson T; Zuccarello G; Bouzide A; Aqvist J; Classon B; Danielson U H; Karlén A; Kvarnström I; Samuelsson B; Hallberg A
Cyclic HIV-1 protease inhibitors derived from mannitol: synthesis, inhibitory potencies, and computational predictions of binding affinities.
Journal of medicinal chemistry 1997;40(6):885-97.
1996: Aqvist J; Fothergill M
Computer simulation of the triosephosphate isomerase catalyzed reaction.
The Journal of biological chemistry 1996;271(17):10010-6.
1995: Hansson T; Aqvist J
Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations.
Protein engineering 1995;8(11):1137-44.
1995: Aqvist J; Mowbray S L
Sugar recognition by a glucose/galactose receptor. Evaluation of binding energetics from molecular dynamics simulations.
The Journal of biological chemistry 1995;270(17):9978-81.
1994: Aqvist J; Medina C; Samuelsson J E
A new method for predicting binding affinity in computer-aided drug design.
Protein engineering 1994;7(3):385-91.
1992: Aqvist J; Tapia O
A molecular model for the retinol binding protein-transthyretin complex.
Journal of molecular graphics 1992;10(2):120-3, 111.
1992: Aqvist J; Warshel A
Computer simulation of the initial proton transfer step in human carbonic anhydrase I.
Journal of molecular biology 1992;224(1):7-14.
1992: Warshel A; Hwang J K; Aqvist 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 discussions 1992;(93):225-38.
1991: Aqvist J; Luecke H; Quiocho F A; Warshel A
Dipoles localized at helix termini of proteins stabilize charges.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(5):2026-30.
1991: Warshel A; Aqvist J
Electrostatic energy and macromolecular function.
Annual review of biophysics and biophysical chemistry 1991;20():267-98.
1989: Warshel A; Aqvist J; Creighton S
Enzymes work by solvation substitution rather than by desolvation.
Proceedings of the National Academy of Sciences of the United States of America 1989;86(15):5820-4.
1989: Aqvist J; Warshel A
Energetics of ion permeation through membrane channels. Solvation of Na+ by gramicidin A.
Biophysical journal 1989;56(1):171-82.
1989: Aqvist J; Warshel A
Calculations of free energy profiles for the staphylococcal nuclease catalyzed reaction.
Biochemistry 1989;28(11):4680-9.
1989: Aqvist 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.
European biophysics journal : EBJ 1989;16(6):327-39.
1989: Tapia O; Aqvist 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.
Progress in clinical and biological research 1989;289():55-64.
1987: Horjales E; Aqvist 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.
Biochemical and biophysical research communications 1987;148(3):954-61.
1986: Aqvist 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.
Journal of molecular biology 1986;192(3):593-603.
1986: Sandblom P; Aqvist 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.
Biochemical and biophysical research communications 1986;139(2):564-70.
1985: Aqvist 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.
Journal of molecular biology 1985;183(3):461-77.
1984: Newcomer M E; Jones T A; Aqvist J; Sundelin J; Eriksson U; Rask L; Peterson P A
The three-dimensional structure of retinol-binding protein.
The EMBO journal 1984;3(7):1451-4.

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