Publikationer

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.

Ingår i Journal of the American Chemical Society, s. 2905-2920, 2022.

DOI för Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses Ladda ner fulltext (pdf) av 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.

Ingår i Journal of Medicinal Chemistry, s. 3473-3517, 2022.

DOI för Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction Ladda ner fulltext (pdf) av Importance of Binding Site Hydration and Flexibility Revealed When Optimizing a Macrocyclic Inhibitor of the Keap1-Nrf2 Protein-Protein Interaction

Ligand design by targeting a binding site water

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

Ingår i Chemical Science, s. 960-968, 2021.

DOI för 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

Ingår i eLIFE, 2021.

DOI för Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling Ladda ner fulltext (pdf) av 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.

Ingår i PloS Computational Biology, 2021.

DOI för Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? Ladda ner fulltext (pdf) av 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.

Ingår i Chemical Communications, s. 12305-12308, 2021.

DOI för Fragment-based design of selective GPCR ligands guided by free energy simulations Ladda ner fulltext (pdf) av 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.

Ingår i Nature Protocols, s. 4799-4832, 2021.

DOI för 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.

Ingår i Nature, s. 571-576, 2021.

DOI för 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.

Ingår i Angewandte Chemie International Edition, s. 18022-18030, 2021.

DOI för Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology Ladda ner fulltext (pdf) av 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.

Ingår i Journal of Medicinal Chemistry, s. 613-620, 2020.

DOI för 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

Ingår i PloS Computational Biology, 2020.

DOI för Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity Ladda ner fulltext (pdf) av 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.

Ingår i Nature Methods, s. 777-787, 2020.

DOI för 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

Ingår i Biochemistry, s. 880-891, 2020.

DOI för Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches Ladda ner fulltext (pdf) av 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.

Ingår i ACS PHARMACOLOGY & TRANSLATIONAL SCIENCE, s. 361-370, 2020.

DOI för The European Research Network on Signal Transduction (ERNEST): Toward a Multidimensional Holistic Understanding of G Protein-Coupled Receptor Signaling Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2019.

DOI för A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection Ladda ner fulltext (pdf) av 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

Ingår i Journal of Chemical Information and Modeling, s. 350-361, 2018.

DOI för 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.

Ingår i Nature Chemical Biology, s. 788-793, 2018.

DOI för 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.

Ingår i Molecular Neurobiology, s. 7038-7048, 2018.

DOI för Disruption of A2AR-D2R Heteroreceptor Complexes After A2AR Transmembrane 5 Peptide Administration Enhances Cocaine Self-Administration in Rats Ladda ner fulltext (pdf) av 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

Ingår i Purinergic Signalling Purinergic Signalling, s. S51-S51, 2018.

DOI för 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.

Ingår i Science Signaling, 2018.

DOI för 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.

Ingår i Frontiers in Pharmacology, 2018.

DOI för Mapping the Interface of a GPCR Dimer: A Structural Model of the A(2A) Adenosine and D-2 Dopamine Receptor Heteromer Ladda ner fulltext (pdf) av 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.

Ingår i Journal of Medicinal Chemistry, s. 5269-5278, 2018.

DOI för 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

Ingår i 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.

Ingår i ACS Pharmacology & Translational Science, s. 119-133, 2018.

DOI för Structural Characterization of Agonist Binding to Protease-Activated Receptor 2 through Mutagenesis and Computational Modeling Ladda ner fulltext (pdf) av 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.

Ingår i Nature Communications, 2017.

DOI för Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling Ladda ner fulltext (pdf) av 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.

Ingår i ACS Chemical Biology, s. 735-745, 2017.

DOI för 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.

Ingår i Journal of Medicinal Chemistry, s. 8160-8169, 2017.

DOI för 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.

Ingår i ACS Chemical Biology, s. 2652-2661, 2017.

DOI för 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.

Ingår i Cellular Signalling, s. 85-96, 2017.

DOI för 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.

Ingår i Scientific Reports, 2017.

DOI för Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site Ladda ner fulltext (pdf) av 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.

Ingår i ACS Chemical Biology, s. 2763-2772, 2016.

DOI för 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.

Ingår i MedChemComm, s. 2216-2223, 2015.

DOI för 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

Ingår i Journal of Medicinal Chemistry, s. 9578-9590, 2015.

DOI för 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

Ingår i Journal of Chemical Theory and Computation, s. 380-395, 2009.

DOI för 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

Ingår i Journal of Physical Chemistry B, s. 10255-10260, 2009.

DOI för 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.

Ingår i Journal of Medicinal Chemistry, s. 2657-2667, 2008.

DOI för 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.

Ingår i Journal of Biological Chemistry, s. 19905-19916, 2007.

DOI för 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

Ingår i Biochemistry, s. 2466-2479, 2007.

DOI för 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

Ingår i Journal of Chemical Theory and Computation, s. 2162-2175, 2007.

DOI för 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

Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 5385-5395, 2006.

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