Publications
ALLODD Project results will be disseminated via scientific publications, conference presentations and posters.
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Scientific Publications
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Conferences
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Presentations
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Lefebre J., Falk T., Ning Y., Rademacher C., 2024
Secondary sites of the C-type lectin-like fold.
Chem. Eur. J.
https://doi.org/10.1002/chem.202400660
Nerín-Fonz F., Cournia Z., 2024
Machine learning approaches in predicting allosteric sites.
Curr. Opin. Struct. Biol.
https://doi.org/10.1016/j.sbi.2024.102774
Secondary sites of the C-type lectin-like fold.
Chem. Eur. J.
https://doi.org/10.1002/chem.202400660
Nerín-Fonz F., Cournia Z., 2024
Machine learning approaches in predicting allosteric sites.
Curr. Opin. Struct. Biol.
https://doi.org/10.1016/j.sbi.2024.102774
Kleinau G., Ali A.H., Wiechert F., Szczepek M., Schmidt A., Spahn C.M.T., Liebscher I., Schöneberg T., Scheerer P., 2023
Intramolecular activity regulation of adhesion GPCRs in light of recent structural and evolutionary information.
Pharmacol. Res.
https://doi.org/10.1016/j.phrs.2023.106971
Intramolecular activity regulation of adhesion GPCRs in light of recent structural and evolutionary information.
Pharmacol. Res.
https://doi.org/10.1016/j.phrs.2023.106971
Papadourakis M., Sinenka H., Matricon P., Hénin J., Brannigan G., Pérez-Benito L., Pande V., van Vlijmen H., de Graaf C., Deflorian F., Tresadern G., Cecchini M., Cournia Z., 2023
Alchemical Free Energy Calculations on Membrane-Associated Proteins.
J. Chem. Theory. Comput.
https://doi.org/10.1021/acs.jctc.3c00365
Alchemical Free Energy Calculations on Membrane-Associated Proteins.
J. Chem. Theory. Comput.
https://doi.org/10.1021/acs.jctc.3c00365
Giesecke Y., Asimi V., Stulberg V., Kleinau G., Scheerer P., Koksch B., Grötzinger C., 2023
Is the Neuropeptide PEN a Ligand of GPR83?
Int. J. Mol. Sci.
https://doi.org/10.3390/ijms242015117
Is the Neuropeptide PEN a Ligand of GPR83?
Int. J. Mol. Sci.
https://doi.org/10.3390/ijms242015117
Kücükdisli M., Bel-Abed H., Cirillo D., Lo W.T., Efrém N.L., Horatscheck A., Perepelittchenko L., Prokofeva P., Ehret T.A.L., Radetzki S., Neuenschwander M., Specker E., Médard G., Müller S., Wilhelm S., Kuster B., von Kries J.P., Haucke V., Nazaré M., 2023
Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition.
J. Med. Chem.
https://doi.org/10.1021/acs.jmedchem.3c01319
Structural Basis for Highly Selective Class II Alpha Phosphoinositide-3-Kinase Inhibition.
J. Med. Chem.
https://doi.org/10.1021/acs.jmedchem.3c01319
Goßen J., Ribeiro R.P., Bier D., Neumaier B., Carloni P., Giorgetti A., Rossetti G., 2023
AI-based identification of therapeutic agents targeting GPCRs: introducing ligand type classifiers and systems biology.
Chem. Sci.
https://doi.org/10.1039/D3SC02352D
AI-based identification of therapeutic agents targeting GPCRs: introducing ligand type classifiers and systems biology.
Chem. Sci.
https://doi.org/10.1039/D3SC02352D
Leusmann S., Ménová P., Shanin E., Titz A., Rademacher C., 2023
Glycomimetics for the inhibition and modulation of lectins.
Chem. Soc. Rev.
https://doi.org/10.1039/d2cs00954d
Glycomimetics for the inhibition and modulation of lectins.
Chem. Soc. Rev.
https://doi.org/10.1039/d2cs00954d
Bajusz D., Pándy-Szekeres G., Takács Á., de Araujo E.D., Keserű G.M., 2023
SH2db, an information system for the SH2 domain.
Nucleic Acids Res.
https://doi.org/10.1093/nar/gkad420
SH2db, an information system for the SH2 domain.
Nucleic Acids Res.
https://doi.org/10.1093/nar/gkad420
Smirnova J., Loerke J., Kleinau G., Schmidt A., Bürger J., Meyer E.H., Mielke T., Scheerer P., Bock R., Spahn C.M.T., Zoschke R., 2023
Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.
Nat. Plants.
https://doi.org/10.1038/s41477-023-01407-y
Structure of the actively translating plant 80S ribosome at 2.2 Å resolution.
Nat. Plants.
https://doi.org/10.1038/s41477-023-01407-y
Barreto Gomes D.E., Galentino K., Sisquellas M., Monari L., Bouysset C., Cecchini M., 2023.
ChemFlow─From 2D Chemical Libraries to Protein–Ligand Binding Free Energies.
J. Chem. Inf. Model.
https://doi.org/10.1021/acs.jcim.2c00919
ChemFlow─From 2D Chemical Libraries to Protein–Ligand Binding Free Energies.
J. Chem. Inf. Model.
https://doi.org/10.1021/acs.jcim.2c00919
Höpfner F., Paisdzior S., Reininghaus N., Sohail I., Scheerer P., Annibale P., Biebermann H., Kühnen P., 2022.
Evaluation of Pharmacological Rescue of Melanocortin-4 Receptor Nonsense Mutations by Aminoglycoside.
Life.
https://doi.org/10.3390/life12111793
Evaluation of Pharmacological Rescue of Melanocortin-4 Receptor Nonsense Mutations by Aminoglycoside.
Life.
https://doi.org/10.3390/life12111793
Kotzampasi D.M., Premeti K., Papafotika A., Syropoulou V., Christoforidis S., Cournia Z., Leondaritis G., 2022.
The orchestrated signaling by PI3Kα and PTEN at the membrane interface.
Comput. Struct. Biotechnol. J.
https://doi.org/10.1016/j.csbj.2022.10.007
The orchestrated signaling by PI3Kα and PTEN at the membrane interface.
Comput. Struct. Biotechnol. J.
https://doi.org/10.1016/j.csbj.2022.10.007
Zhang H., Modenutti C., Nekkanti Y.P.K., Denis M., Bermejo I.A., Lefèbre J., Che K., Kim D., Kagelmacher M., Kurzbach D., Nazaré M., Rademacher C., 2022.
Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin.
ACS Chem. Biol.
https://doi.org/10.1021/acschembio.2c00626
Identification of the Allosteric Binding Site for Thiazolopyrimidine on the C-Type Lectin Langerin.
ACS Chem. Biol.
https://doi.org/10.1021/acschembio.2c00626
Schulze A.S., Kleinau G., Krakowsky R., Rochmann D., Das R., Worth C.L., Krumbholz P., Scheerer P., Stäubert C., 2022.
Evolutionary analyses reveal immune cell receptor GPR84 as a conserved receptor for bacteria-derived molecules.
iScience.
https://doi.org/10.1016/j.isci.2022.105087
Evolutionary analyses reveal immune cell receptor GPR84 as a conserved receptor for bacteria-derived molecules.
iScience.
https://doi.org/10.1016/j.isci.2022.105087
Reininghaus N., Paisdzior S., Höpfner F., Jyrch S., Cetindag C., Scheerer P., Kühnen P., Biebermann H., 2022.
A Setmelanotide-like Effect at MC4R Is Achieved by MC4R Dimer Separation.
Biomolecules.
https://doi.org/10.3390/biom12081119
A Setmelanotide-like Effect at MC4R Is Achieved by MC4R Dimer Separation.
Biomolecules.
https://doi.org/10.3390/biom12081119
Nemec K., Schihada H., Kleinau G., Zabel U., Grushevskyi E.O., Scheerer P., Lohse M.J., Maiellaro I., 2022.
Functional modulation of PTH1R activation and signaling by RAMP2.
Proc. Natl. Acad. Sci. U.S.A.
https://doi.org/10.1073/pnas.2122037119
Functional modulation of PTH1R activation and signaling by RAMP2.
Proc. Natl. Acad. Sci. U.S.A.
https://doi.org/10.1073/pnas.2122037119
Speck D., Kleinau G., Szczepek M., Kwiatkowski D., Catar R., Philippe A., Scheerer P., 2022.
Angiotensin and Endothelin Receptor Structures With Implications for Signaling Regulation and Pharmacological Targeting.
Front. Endocrinol.
https://doi.org/10.3389/fendo.2022.880002
Angiotensin and Endothelin Receptor Structures With Implications for Signaling Regulation and Pharmacological Targeting.
Front. Endocrinol.
https://doi.org/10.3389/fendo.2022.880002
Philippe A., Kleinau G., Gruner J., Wu S., Postpieszala D., Speck D., Heidecke H., Dowell S., Riemekasten G., Hildebrand P., Kamhieh-Milz J., Catar R., Szczepek M., Dragun D., Scheerer P., 2022.
Molecular Effects of Auto-Antibodies on Angiotensin II Type 1 Receptor Signaling and Cell Proliferation.
IJMS.
https://doi.org/10.3390/ijms23073984
Molecular Effects of Auto-Antibodies on Angiotensin II Type 1 Receptor Signaling and Cell Proliferation.
IJMS.
https://doi.org/10.3390/ijms23073984
BRFAA, Francho Nerín Fonz [ESR1]
F. Nerín-Fonz, Z. Cournia. Review of machine learning methods for investigating protein
allostery. Biomedicine, Bioinformatics & Biotechnology Forum: Fostering Collaboration in
Industry & Academia, Athens, Greece, 15-17 September 2023
UNIVIE, Jonathan Lefèbre [ESR2]
J. Lefèbre, J. Pipart, A. Volkamer, C. Rademacher. Conservation of Allosteric Secondary Binding
Sites Across Human C-type Lectins. Eurocarb21, Paris, France, 9-13 July 2023
University of Barcelona, Ozge Ergun [ESR4]
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, 12th Congress on Electronic Structure Principles and Applications ESPA, Vigo, Spain, 21-24 June 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Computational Chemistry GRC, Castelldefels, Spain, 17-22 July 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Institut de Química Teòrica i Computacional (IQTC) Meeting, Barcelona, Spain, 19-20 July 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Jornada de Recerca de la Facultat de Farmàcia i Ciències de l’Alimentació, Barcelona, Spain, 19 October 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, 1a Reunio de Química Teòrica i Computacional (RQTC), Barcelona, Spain, 30-31 January 2023
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Förster Resonance Energy Transfer Applied to Drug Design, The International Congress of Quantum Chemistry (ICQC), Bratislava, Slovakia, 26 June-1 July 2023
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Förster Resonance Energy Transfer Applied to Drug Design, EuChemS CompChem, Thessaloniki, Greece, 27-31 August 2023
Charite, Sigrid Pedersen [ESR6]
S. Pedersen, D. Speck, M. Gallandi, P. Scheerer, Structural Elucidation of Activity Regulation at GPCRs Involved in Metabolism and Immune Responses, SFB1423 Structural Dynamics of GPCR Activation and Signalling (Vanderbilt-Leipzig University Partnership), Klosterhotel Nimbschen, Grimma, Germany, 07-08 May 2024
Nxera, Sonja Peter [ESR10]
Peter S, de Graaf C, Chen I, Computational elucidation of GPCR allosteric modulators, Strasbourg Summer School in Chemoinformatics, University of Strasbourg, 28th June 2022
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, ACSMEDI-EFMC Medicinal Chemistry Frontiers 2023, Boston, USA, 12th June 2023
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, Ninth Joint Sheffield Conference on Chemoinformatics, Sheffield, UK, 20th June 2023
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, ESMEC, Urbino, Italy, 4th July 2023
UNISTRA, Hryhory Sinenka [ESR11]
Sinenka H, Cecchini M, Rational design of agonists, antagonists and allosteric modulators of synaptic receptors: work in progress, Strasbourg Spring Science Days UMR 7177, University of Strasbourg, April 15 & 16 2024.
Merck, Léxane Fournier [ESR12]
L. Fournier, L. Toleikis, H. Kolmar, S. Becker. A Streamlined Approach to Identify Allosteric Single-Domain Antibodies, PEGS Europe: Protein & Antibody Engineering Summit, Lisbon, Portugal, 14-16 November 2023
L. Fournier, H. Kolmar, S. Becker. Discovery of Novel Potent Allosteric Heavy-chain Antibodies Inhibiting EGFR. Festival of Biologics USA, San Diego, 15-17 April 2024
L. Fournier, H. Kolmar, S. Becker. Discovery of Novel Potent Allosteric Heavy-chain Antibodies Inhibiting EGFR. Antibody Engineering and Therapeutics Europe, London, 4-6 Jun. 2024
UNIURB, David Sotillo Núñez [ESR14]
D. Sotillo-Núñez, G. Bottegoni. Automatic protocol to build, equilibrate and simulate Protein – membrane systems, ESMEC, Urbino, Italy, 4th July 2023
F. Nerín-Fonz, Z. Cournia. Review of machine learning methods for investigating protein
allostery. Biomedicine, Bioinformatics & Biotechnology Forum: Fostering Collaboration in
Industry & Academia, Athens, Greece, 15-17 September 2023
UNIVIE, Jonathan Lefèbre [ESR2]
J. Lefèbre, J. Pipart, A. Volkamer, C. Rademacher. Conservation of Allosteric Secondary Binding
Sites Across Human C-type Lectins. Eurocarb21, Paris, France, 9-13 July 2023
University of Barcelona, Ozge Ergun [ESR4]
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, 12th Congress on Electronic Structure Principles and Applications ESPA, Vigo, Spain, 21-24 June 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Computational Chemistry GRC, Castelldefels, Spain, 17-22 July 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Institut de Química Teòrica i Computacional (IQTC) Meeting, Barcelona, Spain, 19-20 July 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, Jornada de Recerca de la Facultat de Farmàcia i Ciències de l’Alimentació, Barcelona, Spain, 19 October 2022
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Characterizing Drug Binding Through Förster Resonance Energy Transfer, 1a Reunio de Química Teòrica i Computacional (RQTC), Barcelona, Spain, 30-31 January 2023
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Förster Resonance Energy Transfer Applied to Drug Design, The International Congress of Quantum Chemistry (ICQC), Bratislava, Slovakia, 26 June-1 July 2023
O. Ergun, M. Castell, X. Barril, C. Galdeano, C. Curutchet, Förster Resonance Energy Transfer Applied to Drug Design, EuChemS CompChem, Thessaloniki, Greece, 27-31 August 2023
Charite, Sigrid Pedersen [ESR6]
S. Pedersen, D. Speck, M. Gallandi, P. Scheerer, Structural Elucidation of Activity Regulation at GPCRs Involved in Metabolism and Immune Responses, SFB1423 Structural Dynamics of GPCR Activation and Signalling (Vanderbilt-Leipzig University Partnership), Klosterhotel Nimbschen, Grimma, Germany, 07-08 May 2024
Nxera, Sonja Peter [ESR10]
Peter S, de Graaf C, Chen I, Computational elucidation of GPCR allosteric modulators, Strasbourg Summer School in Chemoinformatics, University of Strasbourg, 28th June 2022
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, ACSMEDI-EFMC Medicinal Chemistry Frontiers 2023, Boston, USA, 12th June 2023
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, Ninth Joint Sheffield Conference on Chemoinformatics, Sheffield, UK, 20th June 2023
Peter S, Bender B, Thomas M, Palló A, Bajusz D, Ferenczy G, Keserű G, O’Boyle N, Bottegoni G, Chen I, de Graaf C, Navigating the Orthosteric and Allosteric GPCR Pocketome for Structure-Based Drug Discovery, ESMEC, Urbino, Italy, 4th July 2023
UNISTRA, Hryhory Sinenka [ESR11]
Sinenka H, Cecchini M, Rational design of agonists, antagonists and allosteric modulators of synaptic receptors: work in progress, Strasbourg Spring Science Days UMR 7177, University of Strasbourg, April 15 & 16 2024.
Merck, Léxane Fournier [ESR12]
L. Fournier, L. Toleikis, H. Kolmar, S. Becker. A Streamlined Approach to Identify Allosteric Single-Domain Antibodies, PEGS Europe: Protein & Antibody Engineering Summit, Lisbon, Portugal, 14-16 November 2023
L. Fournier, H. Kolmar, S. Becker. Discovery of Novel Potent Allosteric Heavy-chain Antibodies Inhibiting EGFR. Festival of Biologics USA, San Diego, 15-17 April 2024
L. Fournier, H. Kolmar, S. Becker. Discovery of Novel Potent Allosteric Heavy-chain Antibodies Inhibiting EGFR. Antibody Engineering and Therapeutics Europe, London, 4-6 Jun. 2024
UNIURB, David Sotillo Núñez [ESR14]
D. Sotillo-Núñez, G. Bottegoni. Automatic protocol to build, equilibrate and simulate Protein – membrane systems, ESMEC, Urbino, Italy, 4th July 2023
Cryo-EM for Drug Development – The Melanocortin 4 receptor (MC4R) case,
Patrick Scheerer, Charité – Universitätsmedizin Berlin, Germany,
Opening Symposium Core Facility for Cryo-Electron Microscopy of Berlin, Sep 15, 2023
Patrick Scheerer, Charité – Universitätsmedizin Berlin, Germany,
Opening Symposium Core Facility for Cryo-Electron Microscopy of Berlin, Sep 15, 2023
High Throughput and Deep Chemical Proteomics for Confident Drug Target Deconvolution and MoA elucidation in Cell Lines and in Primary Cultures,
Massimiliano Gaetani, Karolinska Institutet, Stockholm, Sweden
Janeiro-na-Madeira Winter Summer School 2022, Jan 16-21, 2022
Massimiliano Gaetani, Karolinska Institutet, Stockholm, Sweden
Janeiro-na-Madeira Winter Summer School 2022, Jan 16-21, 2022
This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 956314.
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