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1

Ion permeation mechanism of the potassium channel

Åqvist, Johan, Luzhkov, Victor

Journal:

Year:

2000

Language:

english

File:

PDF, 238 KB

english, 2000

2

Ligand Binding Affinities from MD Simulations

Åqvist, Johan, Luzhkov, Victor B., Brandsdal, Bjørn O.

Journal:

Accounts of Chemical Research

Year:

2002

Language:

english

File:

PDF, 396 KB

english, 2002

3

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

Åqvist, Johan, Kamerlin, Shina C. L.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

4

Computation of enzyme cold adaptation

Åqvist, Johan, Isaksen, Geir Villy, Brandsdal, Bjørn Olav

Journal:

Nature Reviews Chemistry

Year:

2017

Language:

english

File:

PDF, 6.37 MB

english, 2017

5

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

Bauer, Paul, Barrozo, Alexandre, Purg, Miha, Amrein, Beat Anton, Esguerra, Mauricio, Wilson, Philippe Barrie, Major, Dan Thomas, Åqvist, Johan, Kamerlin, Shina Caroline Lynn

Journal:

Year:

2018

Language:

english

File:

PDF, 1.34 MB

english, 2018

6

Comment to Daura, X., et al., Proteins 25:89–103, 1996.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 16 KB

english, 1997

7

Mechanism of substrate dephosphorylation in low Mr protein tyrosine phosphatase

Karin Kolmodin, Pär Nordlund, Johan Åqvist

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 244 KB

english, 1999

8

Computational modeling of catalysis and binding in low-molecular-weight protein tyrosine phosphatase

Karin Kolmodin, Johan Åqvist

Journal:

International Journal of Quantum Chemistry

Year:

1999

Language:

english

File:

PDF, 283 KB

english, 1999

9

Molecular dynamics simulation of the solution structure of the C-terminal fragment of L7/L12 ribosomal protein

Johan Åqvist, Orlando Tapia

Journal:

Year:

1990

Language:

english

File:

PDF, 447 KB

english, 1990

10

Comparative Analysis of Putative Agonist-Binding Modes in the Human A1 Adenosine Receptor

Hugo Gutiérrez-de-Terán, Manuel Pastor, Nuria B. Centeno, Johan Åqvist, Ferran Sanz

Journal:

Year:

2004

Language:

english

File:

PDF, 256 KB

english, 2004

11

Computational Modeling of Enzymatic Keto-Enol Isomerization Reactions

Isabella Feierberg, Johan Aqvist

Journal:

Year:

2003

File:

PDF, 51 KB

2003

12

Toward a Consensus Model of the hERG Potassium Channel

Anna Stary, Sören J. Wacker, Lars Boukharta, Ulrich Zachariae, Yasmin Karimi-Nejad, Johan Åqvist, Gert Vriend, Bert L. de Groot

Journal:

Year:

2010

Language:

english

File:

PDF, 1.88 MB

english, 2010

13

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

Martin Almlöf, BjØrn O. Brandsdal, Johan Åqvist

Journal:

Journal of Computational Chemistry

Year:

2004

Language:

english

File:

PDF, 309 KB

english, 2004

14

A simple way to calculate the axis of an α-helix

Journal:

Computers & Chemistry

Year:

1986

Language:

english

File:

PDF, 214 KB

english, 1986

15

A molecular model for the retinol binding protein-transthyretin complex

Johan Åqvist, Orlando Tapia

Journal:

Journal of Molecular Graphics

Year:

1992

Language:

english

File:

PDF, 650 KB

english, 1992

16

Computational modelling of the open-state Kv1.5 ion channel block by bupivacaine

Victor B Luzhkov, Johanna Nilsson, Peter Århem, Johan Åqvist

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2003

Language:

english

File:

PDF, 2.16 MB

english, 2003

17

Macrocyclic inhibitors of the malarial aspartic proteases plasmepsin I, II, and IV

Karolina Ersmark, Martin Nervall, Hugo Gutiérrez-de-Terán, Elizabeth Hamelink, Linda K. Janka, Jose C. Clemente, Ben M. Dunn, Adolf Gogoll, Bertil Samuelsson, Johan Åqvist, Anders Hallberg

Journal:

Bioorganic & Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 1.95 MB

english, 2006

18

Molecular dynamics study of heparin based coatings

Martin Almlöf, Emma M.E. Kristensen, Hans Siegbahn, Johan Åqvist

Journal:

Year:

2008

Language:

english

File:

PDF, 2.21 MB

english, 2008

19

Virtual screening and bioassay study of novel inhibitors for dengue virus mRNA cap (nucleoside-2′O)-methyltransferase

Victor B. Luzhkov, Barbara Selisko, Anneli Nordqvist, Frédéric Peyrane, Etienne Decroly, Karine Alvarez, Anders Karlen, Bruno Canard, Johan Åqvist

Journal:

Bioorganic & Medicinal Chemistry

Year:

2007

Language:

english

File:

PDF, 880 KB

english, 2007

20

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]

Victor B. Luzhkov, Barbara Selisko, Anneli Nordqvist, Frédéric Peyrane, Etienne Decroly, Karine Alvarez, Anders Karlen, Bruno Canard, Johan Åqvist

Journal:

Bioorganic & Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 69 KB

english, 2008

21

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

Kristina M. Orrling, Melissa R. Marzahn, Hugo Gutiérrez-de-Terán, Johan Åqvist, Ben M. Dunn, Mats Larhed

Journal:

Bioorganic & Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 819 KB

english, 2009

22

Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm

Johan Åqvist, Petra Wennerström, Martin Nervall, Sinisa Bjelic, Bjørn O. Brandsdal

Journal:

Chemical Physics Letters

Year:

2004

Language:

english

File:

PDF, 465 KB

english, 2004

23

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

Karolina Ersmark, Isabella Feierberg, Sinisa Bjelic, Johan Hultén, Bertil Samuelsson, Johan Åqvist, Anders Hallberg

Journal:

Bioorganic & Medicinal Chemistry

Year:

2003

Language:

english

File:

PDF, 371 KB

english, 2003

24

Mechanistic alternatives in phosphate monoester hydrolysis: What conclusions can be drawn from available experimental data?

Johan Åqvist, Karin Kolmodin, Jan Florian, Arieh Warshel

Journal:

Chemistry & Biology

Year:

1999

Language:

english

File:

PDF, 1.29 MB

english, 1999

25

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems

John Marelius, Karin Kolmodin, Isabella Feierberg, Johan Åqvist

Journal:

Journal of Molecular Graphics and Modelling

Year:

1998

Language:

english

File:

PDF, 195 KB

english, 1998

26

Free energy perturbation simulations of cation binding to valinomycin

George Eisenman, Osvaldo Alvarez, Johan Aqvist

Journal:

Journal of Inclusion Phenomena and Macrocyclic Chemistry

Year:

1992

Language:

english

File:

PDF, 1.57 MB

english, 1992

27

Computational modeling of enzymatic keto-enol isomerization reactions

Isabella Feierberg, Johan Åqvist

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

2002

Language:

english

File:

PDF, 324 KB

english, 2002

28

Free-energy perturbation calculations of binding and transition-state energies: hydrolysis of phenyl esters by β-cyclodextrin

Victor Luzhkov, Johan Åqvist

Journal:

Chemical Physics Letters

Year:

1999

Language:

english

File:

PDF, 147 KB

english, 1999

29

Phe369(7.38) at human 5-HT7 receptors confers interspecies selectivity to antagonists and partial agonists

Thibault Varin, Hugo Gutiérrez-de-Terán, Marián Castro, José Brea, Frederic Fabis, François Dauphin, Johan Åqvist, Alban Lepailleur, Pilar Perez, Javier Burgueño, José Miguel Vela, Maria Isabel Loza,

Journal:

British Journal of Pharmacology

Year:

2010

Language:

english

File:

PDF, 1.01 MB

english, 2010

30

Principles of stop-codon reading on the ribosome

Sund, Johan, Andér, Martin, Åqvist, Johan

Journal:

Year:

2010

Language:

english

File:

PDF, 641 KB

english, 2010

31

Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases

John Marelius, Malin Graffner-Nordberg, Tomas Hansson, Anders Hallberg, Johan Åqvist

Journal:

Journal of Computer-Aided Molecular Design

Year:

1998

Language:

english

File:

PDF, 138 KB

english, 1998

32

Ligand binding affinity prediction by linear interaction energy methods

Tomas Hansson, John Marelius, Johan Åqvist

Journal:

Journal of Computer-Aided Molecular Design

Year:

1998

Language:

english

File:

PDF, 125 KB

english, 1998

33

A new method for predicting binding affinity in computer-aided drug design

Åqvist, Johan, Medina, Carmen, Samuelsson, Jan-Erik

Journal:

Protein Engineering Design and Selection

Year:

1994

Language:

english

File:

PDF, 646 KB

english, 1994

34

Catalysis and Linear Free Energy Relationships in Aspartic Proteases†

Bjelic, Sinisa, Åqvist, Johan

Journal:

Year:

2006

Language:

english

File:

PDF, 526 KB

english, 2006

35

Synthesis of Malarial Plasmepsin Inhibitors and Prediction of Binding Modes by Molecular Dynamics Simulations

Ersmark, Karolina, Nervall, Martin, Hamelink, Elizabeth, Janka, Linda K., Clemente, Jose C., Dunn, Ben M., Blackman, Michael J., Samuelsson, Bertil, Åqvist, Johan, Hallberg, Anders

Journal:

Journal of Medicinal Chemistry

Year:

2005

Language:

english

File:

PDF, 467 KB

english, 2005

36

Modelling of ion-ligand interactions in solutions and biomolecules

Journal:

Journal of Molecular Structure: THEOCHEM

Year:

1992

Language:

english

File:

PDF, 1.15 MB

english, 1992

37

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

Malin Graffner-Nordberg, Karin Kolmodin, Johan Åqvist, Sherry F Queener, Anders Hallberg

Journal:

European Journal of Pharmaceutical Sciences

Year:

2004

Language:

english

File:

PDF, 222 KB

english, 2004

38

A computational study of ion binding and protonation states in the KcsA potassium channel

Victor B Luzhkov, Johan Åqvist

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

2000

Language:

english

File:

PDF, 1.67 MB

english, 2000

39

K+/Na+ selectivity of the KcsA potassium channel from microscopic free energy perturbation calculations

Victor B Luzhkov, Johan Åqvist

Journal:

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology

Year:

2001

Language:

english

File:

PDF, 658 KB

english, 2001

40

Computational modelling of inhibitor binding to human thrombin

Kajsa B. Ljungberg, John Marelius, Djordje Musil, Peder Svensson, Bo Norden, Johan Åqvist

Journal:

European Journal of Pharmaceutical Sciences

Year:

2001

Language:

english

File:

PDF, 306 KB

english, 2001

41

Sensitivity of an empirical affinity scoring function to changes in receptor–ligand complex conformations

John Marelius, Kajsa B Ljungberg, Johan Åqvist

Journal:

European Journal of Pharmaceutical Sciences

Year:

2001

Language:

english

File:

PDF, 737 KB

english, 2001

42

Potent Inhibitors of the Plasmodium falciparum Enzymes Plasmepsin I and II Devoid of Cathepsin D Inhibitory Activity

Ersmark, Karolina, Feierberg, Isabella, Bjelic, Sinisa, Hamelink, Elizabeth, Hackett, Fiona, Blackman, Michael J., Hultén, Johan, Samuelsson, Bertil, Åqvist, Johan, Hallberg, Anders

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 401 KB

english, 2004

43

The Deacylation Step of Acetylcholinesterase: Computer Simulation Studies

Vagedes, Peter, Rabenstein, Björn, Åqvist, Johan, Marelius, John, Knapp, Ernst-Walter

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 120 KB

english, 2000

44

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

Sushil Kumar Mishra, Johan Sund, Johan Åqvist, Jaroslav Koča

Journal:

Journal of Computational Chemistry

Year:

2012

Language:

english

File:

PDF, 826 KB

english, 2012

45

Energetics of nucleophile activation in a protein tyrosine phosphatase

Thomas Hansson, Pär Nordlund, Johan Åqvist

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 505 KB

english, 1997

46

Computer simulation of the initial proton transfer step in human carbonic anhydrase I

Johan Åqvist, Arieh Warshel

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 2.13 MB

english, 1992

47

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

Fredrik Österberg, Johan Åqvist

Journal:

Year:

2005

Language:

english

File:

PDF, 267 KB

english, 2005

48

Computational analysis of plasmepsin IV bound to an allophenylnorstatine inhibitor

Hugo Gutiérrez-de-Terán, Martin Nervall, Ben M. Dunn, Jose C. Clemente, Johan Åqvist

Journal:

Year:

2006

Language:

english

File:

PDF, 727 KB

english, 2006

49

A Model for How Ribosomal Release Factors Induce Peptidyl-tRNA Cleavage in Termination of Protein Synthesis

Stefan Trobro, Johan Åqvist

Journal:

Year:

2007

Language:

english

File:

PDF, 1.09 MB

english, 2007

50

Mechanisms of tetraethylammonium ion block in the KcsA potassium channel

Victor B Luzhkov, Johan Åqvist

Journal:

Year:

2001

Language:

english

File:

PDF, 799 KB

english, 2001

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