Publications

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Luttens, Andreas; Gullberg, Hjalmar; Abdurakhmanov, Eldar; Vo, Duy Duc et al.

Part of Journal of the American Chemical Society, p. 2905-2920, 2022.

DOI for Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses Download full text (pdf) of Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction

Begnini, Fabio; Geschwindner, Stefan; Johansson, Patrik; Wissler, Lisa et al.

Part of Journal of Medicinal Chemistry, p. 3473-3517, 2022.

DOI for Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction Download full text (pdf) of Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction

The mGlu₅ Receptor Protomer-Mediated Dopamine D₂ Receptor Trans-Inhibition Is Dependent on the Adenosine A_2A Receptor Protomer: Implications for Parkinson's Disease

Romero-Fernandez, Wilber; Taura, Jaume J.; Crans, Rene A. J.; Lopez-Cano, Marc et al.

Part of Molecular Neurobiology, p. 5955-5969, 2022.

DOI for The mGlu₅ Receptor Protomer-Mediated Dopamine D₂ Receptor Trans-Inhibition Is Dependent on the Adenosine A_2A Receptor Protomer: Implications for Parkinson's Disease Download full text (pdf) of The mGlu₅ Receptor Protomer-Mediated Dopamine D₂ Receptor Trans-Inhibition Is Dependent on the Adenosine A_2A Receptor Protomer: Implications for Parkinson's Disease

Ligand design by targeting a binding site water

Matricon, Pierre; Suresh, R. Rama; Gao, Zhan-Guo; Panel, Nicolas et al.

Part of Chemical Science, p. 960-968, 2021.

DOI for Ligand design by targeting a binding site water

Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

Fleetwood, Oliver; Carlsson, Jens; Delemotte, Lucie

Part of eLIFE, 2021.

DOI for Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling Download full text (pdf) of Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Kapla, Jon; Rodriguez Espigares, Ismael; Ballante, Flavio; Selent, Jana et al.

Part of PloS Computational Biology, 2021.

DOI for Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? Download full text (pdf) of Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

Fragment-based design of selective GPCR ligands guided by free energy simulations

Matricon, Pierre; Vo, Duc Duy; Gao, Zhan-Guo; Kihlberg, Jan et al.

Part of Chemical Communications, p. 12305-12308, 2021.

DOI for Fragment-based design of selective GPCR ligands guided by free energy simulations Download full text (pdf) of Fragment-based design of selective GPCR ligands guided by free energy simulations

A practical guide to large-scale docking

Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun et al.

Part of Nature Protocols, p. 4799-4832, 2021.

DOI for A practical guide to large-scale docking

Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

Draper-Joyce, Christopher J.; Bhola, Rebecca; Wang, Jinan; Bhattarai, Apurba et al.

Part of Nature, p. 571-576, 2021.

DOI for Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

Kampen, Stefanie; Vo, Duc Duy; Zhang, Xiaoqun; Panel, Nicolas et al.

Part of Angewandte Chemie International Edition, p. 18022-18030, 2021.

DOI for Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology Download full text (pdf) of Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

Docking Finds GPCR Ligands in Dark Chemical Matter

Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas et al.

Part of Journal of Medicinal Chemistry, p. 613-620, 2020.

DOI for Docking Finds GPCR Ligands in Dark Chemical Matter

Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

Jaiteh, Mariama; Rodríguez-Espigares, Ismael; Selent, Jana; Carlsson, Jens

Part of PloS Computational Biology, 2020.

DOI for Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity Download full text (pdf) of Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

GPCRmd uncovers the dynamics of the 3D-GPCRome

Rodriguez-Espigares, Ismael; Torrens-Fontanals, Mariona; Tiemann, Johanna K. S.; Aranda-Garcia, David et al.

Part of Nature Methods, p. 777-787, 2020.

DOI for GPCRmd uncovers the dynamics of the 3D-GPCRome

Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches

Fleetwood, Oliver; Matricon, Pierre; Carlsson, Jens; Delemotte, Lucie

Part of Biochemistry, p. 880-891, 2020.

DOI for Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches Download full text (pdf) of Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches

The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling

Sommer, Martha E.; Selent, Jana; Carlsson, Jens; De Graaf, Chris et al.

Part of ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE, p. 361-370, 2020.

DOI for The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling Download full text (pdf) of The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling

A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection

Wright, Shane C.; Kozielewicz, Pawel; Kowalski-Jahn, Maria; Petersen, Julian et al.

Part of Nature Communications, 2019.

DOI for A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection Download full text (pdf) of A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection

Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

Rudling, Axel; Orro, Adolfo; Carlsson, Jens

Part of Journal of Chemical Information and Modeling, p. 350-361, 2018.

DOI for Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

Scavenging of superoxide by a membrane-bound superoxide oxidase

Lundgren, Camilla A. K.; Sjostrand, Dan; Biner, Olivier; Bennett, Matthew et al.

Part of Nature Chemical Biology, p. 788-793, 2018.

DOI for Scavenging of superoxide by a membrane-bound superoxide oxidase

Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats

Borroto-Escuela, Dasiel O.; Wydra, Karolina; Li, Xiang; Rodriguez, David et al.

Part of Molecular Neurobiology, p. 7038-7048, 2018.

DOI for Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats Download full text (pdf) of Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats

Structure-guided discovery of adenosine receptor ligands

Carlsson, Jens

Part of Purinergic Signalling Purinergic Signalling, p. S51-S51, 2018.

DOI for Structure-guided discovery of adenosine receptor ligands

FZD(5) is a G alpha(q)-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs

Wright, Shane C.; Canizal, Maria Consuelo Alonso; Benkel, Tobias; Simon, Katharina et al.

Part of Science Signaling, 2018.

DOI for FZD(5) is a G alpha(q)-coupled receptor that exhibits the functional hallmarks of prototypical GPCRs

Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer

Borroto-Escuela, Dasiel O.; Rodriguez, David; Romero Fernandez, Wilber; Kapla, Jon et al.

Part of Frontiers in Pharmacology, 2018.

DOI for Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer Download full text (pdf) of Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer

Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease

Jaiteh, Mariama; Zeifman, Alexey; Saarinen, Marcus; Svenningsson, Per et al.

Part of Journal of Medicinal Chemistry, p. 5269-5278, 2018.

DOI for Docking Screens for Dual Inhibitors of Disparate Drug Targets for Parkinson's Disease

Structure-based screening for GPCR ligands from fragment and lead-like chemical space

Carlsson, Jens

Part of Abstracts of Papers of the American Chemical Society, 2018.

Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling

Kennedy, Amanda; Ballante, Flavio; Johansson, Johan; Milligan, Graeme et al.

Part of ACS Pharmacology & Translational Science, p. 119-133, 2018.

DOI for Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling Download full text (pdf) of Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

Petersen, Julian; Wright, Shane C.; Rodriguez, David; Matricon, Pierre et al.

Part of Nature Communications, 2017.

DOI for Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling Download full text (pdf) of Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries

Ranganathan, Anirudh; Heine, Philipp; Rudling, Axel; Pluckthun, Andreas et al.

Part of ACS Chemical Biology, p. 735-745, 2017.

DOI for Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries

Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space

Rudling, Axel; Gustafsson, Robert; Almlof, Ingrid; Homan, Evert et al.

Part of Journal of Medicinal Chemistry, p. 8160-8169, 2017.

DOI for Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space

Structure-Guided Screening for Functionally Selective D-2 Dopamine Receptor Ligands from a Virtual Chemical Library

Mannel, Barbara; Jaiteh, Mariama; Zeifman, Alexey; Randakova, Alena et al.

Part of ACS Chemical Biology, p. 2652-2661, 2017.

DOI for Structure-Guided Screening for Functionally Selective D-2 Dopamine Receptor Ligands from a Virtual Chemical Library

The tyrosine Y250(2.39) in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled

Strakova, Katerina; Matricon, Pierre; Yokota, Chika; Arthofer, Elisa et al.

Part of Cellular Signalling, p. 85-96, 2017.

DOI for The tyrosine Y250(2.39) in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled

Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site

Matricon, Pierre; Ranganathan, Anirudh; Warnick, Eugene; Gao, Zhan-Guo et al.

Part of Scientific Reports, 2017.

DOI for Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site Download full text (pdf) of Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site

Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists

Rodriguez, David; Chakraborty, Saibal; Warnick, Eugene; Crane, Steven et al.

Part of ACS Chemical Biology, p. 2763-2772, 2016.

DOI for Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists

Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

Lam, V. M.; Rodriguez, D.; Zhang, T.; Koh, E. J. et al.

Part of MedChemComm, p. 2216-2223, 2015.

DOI for Discovery of trace amine-associated receptor 1 ligands by molecular docking screening against a homology model

Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

Ranganathan, Anirudh; Stoddart, Leigh A.; Hill, Stephen J.; Carlsson, Jens

Part of Journal of Medicinal Chemistry, p. 9578-9590, 2015.

DOI for Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models

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

Wallin, Göran; Nervall, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 380-395, 2009.

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

Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Journal of Physical Chemistry B, p. 10255-10260, 2009.

DOI for Absolute hydration entropies of alkali metal ions from molecular dynamics simulations

Predicting Binding Modes from Free Energy Calculations

Nervall, Martin; Hanspers, Peter; Carlsson, Jens; Boukharta, Lars et al.

Part of Journal of Medicinal Chemistry, p. 2657-2667, 2008.

DOI for Predicting Binding Modes from Free Energy Calculations

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

Henriksson, Lena M.; Unge, Torsten; Carlsson, Jens; Åqvist, Johan et al.

Part of Journal of Biological Chemistry, p. 19905-19916, 2007.

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

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

Thomaeus, Ann; Carlsson, Jens; Åqvist, Johan; Widersten, Mikael

Part of Biochemistry, p. 2466-2479, 2007.

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

Improving the accuracy of the linear interaction energy method for solvation free energies

Almlöf, Martin; Carlsson, Jens; Åqvist, Johan

Part of Journal of Chemical Theory and Computation, p. 2162-2175, 2007.

DOI for Improving the accuracy of the linear interaction energy method for solvation free energies

Calculations of solute and solvent entropies from molecular dynamics simulations

Carlsson, Jens; Åqvist, Johan

Part of Physical Chemistry, Chemical Physics - PCCP, p. 5385-5395, 2006.

DOI for Calculations of solute and solvent entropies from molecular dynamics simulations