Publications

Rudling A , Gustafsson R, Almlöf I, Homan E, Scobie M, Warpman Berglund U, Helleday T, Stenmark P & Carlsson J (2017) Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space. J Med Chem, Article ASAP

Männel B, Jaiteh M, Zeifman A, Randakova A, Möller D, Hübner H, Gmeiner P & Carlsson J (2017) Structure-Guided Screening for Functionally Selective D2 Dopamine Receptor Ligands from a Virtual Chemical Library. ACS Chem. Biol., Article ASAP

Petersen J, Wright SC, Rodríguez D, Matricon P, Lahav N, Vromen A, Assaf Friedler, Strömqvist J, Wennmalm S, Carlsson J & Schulte G (2017) Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling. Nature Communications 8, 226

Matricon P, Ranganathan A,  Warnick E, Gao ZG, Rudling A,  Lambertucci C,  Marucci G, Ezzati A, Jaiteh M, Dal Ben D, Jacobson KA & Carlsson J (2017) Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A 2A adenosine receptor binding site. Scientific Reports, 7:6398

Strakovaa K, Matricon P, Yokota C, Arthofer E, Bernatik O, Rodrí­guez D, Arenas E, Carlsson J, Bryja V, Schulte G (2017) The tyrosine Y250 2.39 in Frizzled 4 defines a conserved motif important for structural integrity of the receptor and recruitment of Disheveled. Cellular Signalling, 38:85-96

Ranganathan A, Rodrí­guez D, Carlsson J (2017) Structure-Based Discovery of GPCR Ligands from Crystal Structures and Homology Models. Topics in Medicinal Chemistry, pp 1-35.

Borroto-Escuela D, Carlsson J, Ambrogini P, Narváez M, Wydra K, Tarakanov A, Li X, Millón C, Ferraro L, Cuppini R, Tanganelli S, Liu F, Filip M, Diaz-Cabiale Z, Fuxe K (2017) Understanding the Role of GPCR Heteroreceptor Complexes in Modulating the Brain Networks in Health and Disease. Frontiers in Cellular Neuroscience, 11, 1.

Ranganathan A, Heine P, Rudling A, Plückthun A, Kummer L, Carlsson J  (2016) Ligand discovery for a peptide-binding GPCR by structure-based screening of fragment- and lead-like chemical libraries. ACS Chem. Biol., 12:735–745

Rodrí­guez D, Chakraborty S, Warnick E, Crane S, Gao ZG, O’Connor R, Jacobson KA and Carlsson J (2016) Structure-Based Screening of Uncharted Chemical Space for Atypical Adenosine Receptor Agonists. ACS Chem. Biol., 11:2763-2772

Ranganathan A, Stoddart LA, Hill SJ and Carlsson J (2015) Fragment-based discovery of subtype selective adenosine receptor ligands from homology models. J Med Chem, 58:9578-9590

Lam VM, Rodríguez D, Zhang T, Koh EJ, Carlsson J and Salahpour A (2015) Discovery of Trace Amine-Associated Receptor 1 Ligands by Molecular Docking Screening against a Homology Model. Med. Chem. Comm., 6:2216-2223

Rodrí­guez D, Ranganathan A, and Carlsson J (2015) Discovery of GPCR Ligands by Molecular Docking Screening: Novel Opportunities Provided by Crystal Structures. Curr Top Med Chem, 2484-2503.

Rodrí­guez D, Gao ZG, Moss SM,  Jacobson KA., and Carlsson J (2015) Molecular docking screening using agonist-bound GPCR structures: Probing the A2A adenosine receptor. J Chem Inf Model, 54:2004-2021.

Ranganathan A, Dror RO, and Carlsson J (2014) Insights into the Role of Asp79 2.50 in beta 2 Adrenergic Receptor Activation from Molecular Dynamics Simulations. Biochemistry, 53:7283-7296.

Rodrí­guez D, Ranganathan A, and Carlsson J (2014) Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. J Chem Inf Model, 54:2004-2021.

Kufareva I, Katritch V, Rodrí­guez D, Ranganathan A, Carlsson J & other GPCR Dock 2013 Participants; Stevens, R. C.; Abagyan, R. (2014) Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges. Structure, 22:1120-1139.

Rodrí­guez D, Brea J, Loza M I, Carlsson J (2014) Structure-based Discovery of Selective Serotonin 5-HT1B Receptor Ligands. Structure , 22:1140-1151.

Chen D, Ranganathan A, Ijzerman AP, Siegal G, Carlsson J (2013) Complementarity between in silico and biophysical screening approaches in fragment-based lead discovery against the A2A adenosine receptor. J Chem Inf Model 53(10):2701-14.

Heusser SA, Howard RJ, Borghese CM, Cullins MA, Broemstrup T, Lee US, Lindahl E, Carlsson J, Harris RA (2013) Functional validation of virtual screening for novel agents with general anesthetic action at ligand-gated ion channels. Mol Pharmacol 84:670-678.

Johansson A, Högbom M, Carlsson J, Gennis RB, Brzezinski P (2013) The role of aspartate 132 at the orifice of a proton pathway in Cytochrome c Oxidase. Proc Natl Acad Sci 110:8912-8917.

Benod C*, Carlsson J*, Uthayaruban R, Hwang P, Irwin JJ, Doak AK, Shoichet BK, Sablin EB, and Fletterick RJ (2013) Structure-based discovery of antagonists of nuclear receptor LRH-1, J Biol Chem 288:19830-44.

Johansson A, Carlsson J, Högbom M, Hosler JP, Gennis RB, and Brzezinski P (2013) Proton uptake and pKa changes in the uncoupled Asn139Cys variant of Cytochrome c Oxidase. Biochemistry 52:827-836.

Carlsson J, ToshDK, Phan K, Gao ZG, Jacobson KA (2012) Structure-activity relationships and molecular modeling of 1,2,4-triazoles as adenosine receptor  antagonists. ACS Med Chem Lett, 3:715-720.

Carlsson J, Coleman RG, SetolaV, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, and Shoichet, BK (2011) Ligand discovery from a Dopamine D3 receptor homology model and crystal Structure. Nature Chemical Biology 7:769-778.

Kufareva I, Rueda M, Katritch V, Carlsson J and other participants of GPCR Dock 2010, Stevens R, Abagyan R. (2011) Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment, Structure, 19:1108-1126.

Carlsson J, Yoo L, Gao GZ, Irwin JI, Shoichet BK, and Jacobson KA (2010) Structure-based discovery of A2A adenosine receptor ligands. J Med Chem 53:3748-3755.

Carlsson J and Åqvist J (2009) Absolute hydration entropies of alkali metal ions from molecular dynamics simulations. J Phys Chem B 113:10255-10260.

Wallin G, Nervall M, Carlsson J, Boukharta L, and Åqvist J (2009) Charges for large scale binding free energy calculations with the linear interaction energy method. J. Chem. Theory Comput. 5:381-295.

Carlsson J, Boukharta L, and Åqvist J (2008) 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 51:2648-2656.

Nervall M, Hanspers P, Carlsson J, Boukharta L, and Åqvist J (2008) Predicting binding modes from free energy calculations. J Med Chem 51:2657-2667.

Henriksson LM, Unge T, Carlsson J, Åqvist J, Mowbray SL, and Jones TA (2007) Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis. J Biol Chem 282:19905-19916.

Almlöf M, Carlsson J, and Åqvist J (2007) Improving the accuracy of the linear interaction energy method for solvation free energies. J Chem Theory Comput 3:2162-2175.

Thomaeus A, Carlsson J, Åqvist J, and Widersten M (2007) Active site of epoxide hydrolases revisited: A noncanonical residue in potato StEH1 promotes both formation and breakdown of the alkylenzyme intermediate. Biochemistry 46:2466-2479.

Carlsson J, and Åqvist J (2006) Calculations of solute and solvent entropies from molecular dynamics simulations. Phys Chem Chem Phys 8:5385-5395.

Carlsson J, Ander M, Nervall M, and Åqvist J (2006) Continuum solvation models in the linear interaction energy method. J Phys Chem B 110:12034-12041.

Carlsson J, and Åqvist J (2005) Absolute and relative entropies from computer simulation with applications to ligand binding. J Phys Chem B 109:6448-6456.

Simonson T, Carlsson J, and Case DA (2004) Proton binding to proteins: pKa calculations with explicit and implicit solvent models. J Am Chem Soc 126:4167-4180.