Institute of Neurosciences and Medicine (INM)

Computational Biomedicine (INM-9)

Publications of IAS-5/INM-9 in 2021

Journal Article Lešnik, S. ; Bertalan, É. ; Bren, U. ; Bondar, A.-N. (Corresponding author)FZJ*
Opioid Receptors and Protonation-Coupled Binding of Opioid Drugs
International journal of molecular sciences 22(24), 13353 - (2021) [10.3390/ijms222413353]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bertalan, É. ; Lesca, E. ; Schertler, G. F. X. ; Bondar, A.-N. (Corresponding author)FZJ*
C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins
Journal of chemical information and modeling 61(11), 5692 - 5707 (2021) [10.1021/acs.jcim.1c00827]2021 Files BibTeX | EndNote: XML, Text | RIS

Journal Article Toledo, M. A. S. ; Gatz, M. ; Sontag, S. ; Gleixner, K. V. ; Eisenwort, G. ; Feldberg, K. ; Hamouda, A. E. I. ; Kluge, F. ; Guareschi, R.FZJ* ; Rossetti, G. (Corresponding author)FZJ* ; Sechi, A. S. ; Dufva, O. M. J. ; Mustjoki, S. M. ; Maurer, A. ; Schüler, H. M. ; Goetzke, R. ; Braunschweig, T. ; Kaiser, A. ; Panse, J. ; Jawhar, M. ; Reiter, A. ; Hilberg, F. ; Ettmayer, P. ; Wagner, W. ; Koschmieder, S. ; Brümmendorf, T. H. ; Valent, P. ; Chatain, N. ; Zenke, M.
Nintedanib targets KIT D816V neoplastic cells derived from induced pluripotent stem cells of systemic mastocytosis
Blood 137(15), 2070 - 2084 (2021) [10.1182/blood.2019004509]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sorokina, O. (Corresponding author)Extern* ; Mclean, C. (Corresponding author)Extern* ; Croning, M. D. R.Extern* ; Heil, K. F.Extern* ; Wysocka, E.Extern* ; He, X.Extern* ; Sterratt, D.Extern* ; Grant, S. G. N.Extern* ; Simpson, T. I.Extern* ; Armstrong, J. D.FZJ*
A unified resource and configurable model of the synapse proteome and its role in disease
Scientific reports 11(1), 9967 (2021) [10.1038/s41598-021-88945-7]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sena, D. M. (Corresponding author)Extern* ; Cong, X.Extern* ; Giorgetti, A. (Corresponding author)FZJ*
Ligand based conformational space studies of the μ-opioid receptor
Biochimica et biophysica acta / General subjects 1865(3), 129838 - (2021) [10.1016/j.bbagen.2020.129838]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Micheli, P.Extern* ; Ribeiro, R. (Corresponding author)FZJ* ; Giorgetti, A. (Corresponding author)FZJ*
A Mechanistic Model of NMDA and AMPA Receptor-Mediated Synaptic Transmission in Individual Hippocampal CA3-CA1 Synapses: A Computational Multiscale Approach
International journal of molecular sciences 22(4), 1536 - (2021) [10.3390/ijms22041536]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maggi, L. (Corresponding author)FZJ*
How super-localization affects vibrational energy exchange process in proteins
Physica / A 562, 125325 - (2021) [10.1016/j.physa.2020.125325]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Kuzikov, M. (Corresponding author)Extern* ; Costanzi, E.Extern* ; Reinshagen, J.Extern* ; Esposito, F.Extern* ; Vangeel, L.Extern* ; Wolf, M.Extern* ; Ellinger, B.Extern* ; Claussen, C.Extern* ; Geisslinger, G.Extern* ; Corona, A. ; Iaconis, D.Extern* ; Talarico, C.Extern* ; Manelfi, C.Extern* ; Cannalire, R.Extern* ; Rossetti, G.FZJ* ; Gossen, J.FZJ* ; Albani, S.FZJ* ; Musiani, F.Extern* ; Herzog, K.Extern* ; Ye, Y.Extern* ; Giabbai, B.Extern* ; Demitri, N.Extern* ; Jochmans, D.Extern* ; Jonghe, S. D.Extern* ; Rymenants, J.Extern* ; Summa, V. ; Tramontano, E.Extern* ; Beccari, A. R.Extern* ; Leyssen, P.Extern* ; Storici, P.Extern* ; Neyts, J.Extern* ; Gribbon, P.Extern* ; Zaliani, A.Extern*
Identification of Inhibitors of SARS-CoV-2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen
ACS pharmacology & translational science 4(3), 1096 - 1110 (2021) [10.1021/acsptsci.0c00216]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Korn, P.Extern* ; Classen, A.Extern* ; Murthy, S.Extern* ; Guareschi, R. ; Maksimainen, M. M.Extern* ; Lippok, B. E.Extern* ; Galera-Prat, A.Extern* ; Sowa, S. T.Extern* ; Voigt, C.Extern* ; Rossetti, G.FZJ* ; Lehtiö, L.Extern* ; Bolm, C.Extern* ; Lüscher, B. (Corresponding author)Extern*
Evaluation of 3‐ and 4‐Phenoxybenzamides as Selective Inhibitors of the Mono‐ADP‐Ribosyltransferase PARP10
ChemistryOpen 10(10), 939 - 948 (2021) [10.1002/open.202100087]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Giannos, T.Extern* ; Lešnik, S.Extern* ; Bren, U.Extern* ; Hodošček, M.Extern* ; Domratcheva, T.Extern* ; Bondar, A.-N. (Corresponding author)FZJ*
CHARMM Force-Field Parameters for Morphine, Heroin, and Oliceridine, and Conformational Dynamics of Opioid Drugs
Journal of chemical information and modeling 61(8), 3964 - 3977 (2021) [10.1021/acs.jcim.1c00667]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Domínguez-Mendoza, E. A. ; Galván-Ciprés, Y. ; Martínez-Miranda, J. ; Miranda-González, C. ; Colín-Lozano, B. ; Hernández-Núñez, E.Extern* ; Hernández-Bolio, G. I.Extern* ; Palomino-Hernández, O.FZJ* ; Navarrete-Vazquez, G. (Corresponding author)Extern*
Design, Synthesis, and In Silico Multitarget Pharmacological Simulations of Acid Bioisosteres with a Validated In Vivo Antihyperglycemic Effect
Molecules 26(4), 799 - (2021) [10.3390/molecules26040799]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L.FZJ* ; Gori, M.Extern* ; Pettini, M. (Corresponding author)Extern*
Topology and Phase Transitions: A First Analytical Step towards the Definition of Sufficient Conditions
Entropy 23(11), 1414 - (2021) [10.3390/e23111414]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L.FZJ* ; Gori, M.Extern* ; Pettini, G.Extern* ; Pettini, M. (Corresponding author)Extern*
Hamiltonian chaos and differential geometry of configuration space–time
Physica / D 422, 132909 - (2021) [10.1016/j.physd.2021.132909]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Berdnikova, D. V.Extern* ; Carloni, P.FZJ* ; Krauß, S. (Corresponding author)Extern* ; Rossetti, G. (Corresponding author)FZJ*
Role and Perspective of Molecular Simulation-Based Investigation of RNA–Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding
Molecules 26(11), 3384 - (2021) [10.3390/molecules26113384]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ansari, N.Extern* ; Rizzi, V.Extern* ; Carloni, P.FZJ* ; Parrinello, M. (Corresponding author)Extern*
Water-Triggered, Irreversible Conformational Change of SARS-CoV-2 Main Protease on Passing from the Solid State to Aqueous Solution
Journal of the American Chemical Society 143(33), 12930 - 12934 (2021) [10.1021/jacs.1c05301]2021 Files BibTeX | EndNote: XML, Text | RIS

Poster (After Call) de Bruyn, E. (Corresponding author)FZJ*RWTH* ; Zimmermann, O.FZJ* ; Grohe, M.RWTH* ; Rossetti, G.FZJ*RWTH*
Modelling Ion-Residue Interaction in Implicit Solvation for Intrinsically Disordered Proteins
2021INM & IBI Retreat 2021, RWTH AachenJülich, RWTH Aachen, Germany, 5 Oct 2021 - 6 Oct 20212021-10-052021-10-06 Fulltext BibTeX | EndNote: XML, Text | RIS

Poster (After Call) Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Winkler, R. G.FZJ* ; Naegele, G.FZJ*
Quasi-two-dimensional diffusion of interacting protein monomers and dimers: A MPC simulation study
202111th LIQUID MATTER CONFERENCE 2020/2021, Prague/OnlinePrague/Online, Czech Republic, 19 Jul 2021 - 23 Jul 20212021-07-192021-07-23 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Nin-Hill, A. ; Mueller, N. P. F.FZJ* ; Molteni, C. ; Rovira, C. ; Alfonso-Prieto, M. (Corresponding author)FZJ*
Photopharmacology of Ion Channels through the Light of the Computational Microscope
International journal of molecular sciences 22(21), 12072 - (2021) [10.3390/ijms222112072] special issue: "Light-Controlled Modulation and Analysis of Neuronal Functions"2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Costanzi, E. ; Kuzikov, M. ; Esposito, F. ; Albani, S.FZJ* ; Demitri, N. ; Giabbai, B. ; Camasta, M. ; Tramontano, E. ; Rossetti, G. (Corresponding author)FZJ* ; Zaliani, A. ; Storici, P. (Corresponding author)
Structural and Biochemical Analysis of the Dual Inhibition of MG-132 against SARS-CoV-2 Main Protease (Mpro/3CLpro) and Human Cathepsin-L
International journal of molecular sciences 22(21), 11779 - (2021) [10.3390/ijms222111779]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Rossetti, G. (Corresponding author)FZJ* ; Capelli, R.FZJ* ; Li, J. ; Carloni, P.FZJ* ; Zhao, Q.FZJ*
An Enhanced Sampling Approach to the Induced Fit Docking Problem in Protein-Ligand Binding: the case of mono-ADPribosylationhydrolases inhibitors
Journal of chemical theory and computation 17(12), 7899–7911 (2021) [10.1021/acs.jctc.1c00649]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Di Cairano, L. (Corresponding author)FZJ* ; Stamm, B. (Corresponding author)RWTH* ; Calandrini, V. (Corresponding author)FZJ*
Subdiffusive-Brownian crossover in membrane proteins: a Generalized Langevin Equation-based approach
Biophysical journal 120(21), 4722-4737 (2021) [10.1016/j.bpj.2021.09.033]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Parrinello, M. (Corresponding author) ; Rizzi, A.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Targeted Free Energy Perturbation Revisited: Accurate Free Energies from Mapped Reference Potentials
The journal of physical chemistry letters 12(39), 9449–9454 (2021) [10.1021/acs.jpclett.1c02135]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Tan, Z. (Corresponding author)FZJ* ; Calandrini, V.FZJ* ; Dhont, J. K. G.FZJ* ; Nägele, G.FZJ* ; Winkler, R. G.FZJ*
Hydrodynamics of immiscible binary fluids with viscosity contrast: a multiparticle collision dynamics approach
Soft matter 17(34), 7978 - 7990 (2021) [10.1039/D1SM00541C]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Zuo, K. ; Marjault, H.-B. ; Bren, K. L. ; Rossetti, G.FZJ* ; Nechushtai, R. ; Carloni, P. (Corresponding author)FZJ*
The two redox states of the human NEET proteins’ [2Fe–2S] clusters
Journal of biological inorganic chemistry 26, 763–774 (2021) [10.1007/s00775-021-01890-8]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Alfonso-Prieto, M. (Corresponding author)FZJ*
Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose
The journal of membrane biology 254(4), 343-352 (2021) [10.1007/s00232-021-00182-1]2021 Files Fulltext Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Chiariello, M. G. (Corresponding author)FZJ* ; Alfonso-Prieto, M.FZJ* ; Ippoliti, E.FZJ* ; Fahlke, C. (Corresponding author)FZJ* ; Carloni, P. (Corresponding author)FZJ*
Mechanisms Underlying Proton Release in CLC-type F – /H + Antiporters
The journal of physical chemistry letters 12(18), 4415 - 4420 (2021) [10.1021/acs.jpclett.1c00361]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Bolnykh, V.FZJ* ; Rossetti, G.FZJ* ; Rothlisberger, U. ; Carloni, P. (Corresponding author)FZJ*
Expanding the boundaries of ligand–target modeling by exascale calculations
Wiley interdisciplinary reviews / Computational Molecular Science 11(4), e1535 (2021) [10.1002/wcms.1535]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Korshunova, K.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Ligand Affinities within the Open-Boundary Molecular Mechanics/Coarse-Grained Framework (I): Alchemical Transformations within the Hamiltonian Adaptive Resolution Scheme
The journal of physical chemistry <Washington, DC> / B 125(3), 789 - 797 (2021) [10.1021/acs.jpcb.0c09805]2021 Embargoed OpenAccess Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article D'Arrigo, G. ; Gianquinto, E. ; Rossetti, G. (Corresponding author)FZJ* ; Cruciani, G. ; Lorenzetti, S. ; Spyrakis, F.
Binding of Androgen- and Estrogen-Like Flavonoids to Their Cognate (Non)Nuclear Receptors: A Comparison by Computational Prediction
Molecules 26(6), 1613 - (2021) [10.3390/molecules26061613]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Gossen, J.FZJ* ; Albani, S.FZJ* ; Hanke, A.Extern* ; Joseph, B. P.FZJ* ; Bergh, C.Extern* ; Kuzikov, M.Extern* ; Costanzi, E. ; Manelfi, C. ; Storici, P. ; Gribbon, P. ; Beccari, A. R. ; Talarico, C.Extern* ; Spyrakis, F.Extern* ; Lindahl, E.Extern* ; Zaliani, A.Extern* ; Carloni, P.FZJ* ; Wade, R. C.Extern* ; Musiani, F.Extern* ; Kokh, D. B.Extern* ; Rossetti, G. (Corresponding author)FZJ*
A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics
ACS pharmacology & translational science 4(3), 1079–1095 (2021) [10.1021/acsptsci.0c00215]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Schmitz-Hübsch, T. (Corresponding author) ; Lux, S. ; Bauer, P. ; Brandt, A. U. ; Schlapakow, E. ; Greschus, S. ; Scheel, M. ; Gärtner, H. ; Kirlangic, M. E. ; Gras, V. ; Timmann, D. ; Synofzik, M. ; Giorgetti, A.FZJ* ; Carloni, P.FZJ* ; Shah, N. J.FZJ* ; Schöls, L. ; Kopp, U. ; Bußenius, L. ; Oberwahrenbrock, T. ; Zimmermann, H. ; Pfueller, C. ; Kadas, E. M. ; Rönnefarth, M. ; Grosch, A. S. ; Endres, M. ; Amunts, K.FZJ* ; Friedemann, P. ; Doss, S. ; Minnerop, M. (Corresponding author)FZJ*
Spinocerebellar ataxia type 14: Refining clinico-genetic diagnosis in a rare adult-onset disorder
Annals of Clinical and Translational Neurology 8(4), 774-789 (2021) [10.1002/acn3.51315]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Lai, H. T. T. ; Giorgetti, A.FZJ* ; Rossetti, G.FZJ* ; Nguyen, T. T. ; Carloni, P.FZJ* ; Kranjc Pietrucci, A. (Corresponding author)FZJ*
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations
Molecules 26(5), 1250 - (2021) [10.3390/molecules26051250]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Manelfi, C. ; Gossen, J.FZJ* ; Gervasoni, S. ; Talarico, C. ; Albani, S.FZJ* ; Philipp, B. J. ; Musiani, F. ; Vistoli, G. ; Rossetti, G.FZJ* ; Beccari, A. R. ; Pedretti, A. (Corresponding author)
Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease
Molecules 26(4), 797 - (2021) [10.3390/molecules26040797]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Sitani, D. (Corresponding author)FZJ* ; Giorgetti, A.FZJ* ; Alfonso‐Prieto, M.FZJ* ; Carloni, P. (Corresponding author)FZJ*
Robust Principal Component Analysis‐based Prediction of Protein‐Protein Interaction Hot spots ( RBHS )
Proteins 89(6), 639-647 (2021) [10.1002/prot.26047]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Ferraro, M. ; Moroni, E. ; Ippoliti, E.FZJ* ; Rinaldi, S. ; Sanchez-Martin, C. ; Rasola, A. ; Pavarino, L. F. (Corresponding author) ; Colombo, G. (Corresponding author)
Machine Learning of Allosteric Effects: The Analysis of Ligand-Induced Dynamics to Predict Functional Effects in TRAP1
The journal of physical chemistry <Washington, DC> / B 125(1), 101 - 114 (2021) [10.1021/acs.jpcb.0c09742]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Journal Article Maleeva, G. (Corresponding author) ; Nin-Hill, A. ; Rustler, K. ; Petukhova, E. ; Ponomareva, D. ; Mukhametova, E. ; Gomila-Juaneda, A. ; Wutz, D. ; Alfonso-Prieto, M. (Corresponding author)FZJ* ; König, B. ; Gorostiza, P. ; Bregestovski, P. (Corresponding author)
Subunit-specific photocontrol of glycine receptors by azobenzene-nitrazepam photoswitcher
eNeuro 8(1), ENEURO.0294-20.2020 (2021) [10.1523/ENEURO.0294-20.2020]2021 Files Fulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

Last Modified: 12.06.2024