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Publications 2017

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(Corresponding author) ; (Corresponding author) ; ; ; ;
Unifying view of mechanical and functional hotspots across class A GPCRs
PLoS Computational Biology 13(2), e1005381 - () [10.1371/journal.pcbi.1005381] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Structural prediction of the interaction of the tumor suppressor p27$^{KIP1}$ with cyclin A/CDK2 identifies a novel catalytically relevant determinant
BMC bioinformatics 18(1), 15 () [10.1186/s12859-016-1411-0] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Proton Dynamics in Protein Mass Spectrometry
The journal of physical chemistry letters 8(6), 1105 - 1112 () [10.1021/acs.jpclett.7b00127]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation
Biomedicines 5(1), 9 () [10.3390/biomedicines5010009] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions
Journal of biological physics 13(2), 185-195 () [10.1007/s10867-017-9443-x]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Structural heterogeneity of the $μ$-opioid receptor’s conformational ensemble in the apo state
Scientific reports 7, 45761 () [10.1038/srep45761] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Unbinding Kinetics of a p38 MAP Kinase Type II Inhibitor from Metadynamics Simulations
Journal of the American Chemical Society 139(13), 4780 - 4788 () [10.1021/jacs.6b12950]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Sulfoximines as ATR inhibitors: Analogs of VE-821
Bioorganic & medicinal chemistry letters 27(12), 2659 - 2662 () [10.1016/j.bmcl.2017.04.026]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Copper(II) and the pathological H50Q α-synuclein mutant: Environment meets genetics
Communicative & integrative biology 10(1), e1270484 - () [10.1080/19420889.2016.1270484] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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The conserved macrodomains of the non-structural proteins of Chikungunya virus and other pathogenic positive strand RNA viruses function as mono-ADP-ribosylhydrolases
Scientific reports 7, 41746 - () [10.1038/srep41746] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Hypomorphic mutations in POLR3A are a frequent cause of sporadic and recessive spastic ataxia.
Brain 140(6), 1561 - 1578 () [10.1093/brain/awx095]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Origin of proton affinity to membrane/water interfaces
Scientific reports 7(1), 4553 () [10.1038/s41598-017-04675-9] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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A covalent PIN1 inhibitor selectively targets cancer cells by a dual mechanism of action
Nature Communications 8, 15772 - () [10.1038/ncomms15772] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Lid domain plasticity and lipid flexibility modulate enzyme specificity in human monoacylglycerol lipase
Biochimica et biophysica acta / Molecular and cell biology of lipids 1862(5), 441 - 451 () [10.1016/j.bbalip.2017.01.002]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations
Journal of chemical theory and computation 13(1), 180 - 190 () [10.1021/acs.jctc.6b00981]  GO OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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; (Corresponding author)
Meshing molecular surfaces based on analytical implicit representation
Journal of molecular graphics and modelling 71, 200 - 210 () [10.1016/j.jmgm.2016.11.008]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Multi-scale simulations of membrane proteins: The case of bitter taste receptors
Journal of science 2(1), 15 - 21 () [10.1016/j.jsamd.2017.03.001]  GO OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition
Chem 3(1), 92 - 109 () [10.1016/j.chempr.2017.05.016]  GO OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Pharmacophore Identification and Scaffold Exploration to Discover Novel, Potent, and Chemically Stable Inhibitors of Acid Ceramidase in Melanoma Cells
Journal of medicinal chemistry 60(13), 5800 - 5815 () [10.1021/acs.jmedchem.7b00472]  GO OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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(First author) ; (First author) ; (Corresponding author) ; (Corresponding author) ; ; (Last author)
Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis
Frontiers in molecular biosciences 4, 63 () [10.3389/fmolb.2017.00063] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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; (Corresponding author)
Structural Modeling of Human Prion Protein's Point Mutations
Prion Protein / Rossetti, Giulia ; : Elsevier, 2017, ; ISSN: 18771173 ; ISBN: 9780128112267 ; doi:10.1016/bs.pmbts.2017.07.001 Amsterdam [u.a.] : Elsevier, Progress in Molecular Biology and Translational Science 150, 105 - 122 () [10.1016/bs.pmbts.2017.07.001] BibTeX | EndNote: XML, Text | RIS

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Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme
Journal of chemical theory and computation 13(11), 5647–5657 () [10.1021/acs.jctc.7b00508] OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release
The journal of physical chemistry <Washington, DC> / B 121(47), 10648–10656 () [10.1021/acs.jpcb.7b10584] Embargoed OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Novel xanthone-polyamine conjugates as catalytic inhibitors of human topoisomerase IIα
Bioorganic & medicinal chemistry letters 27(20), 4687 - 4693 () [10.1016/j.bmcl.2017.09.011]  GO  Download fulltext Files BibTeX | EndNote: XML, Text | RIS

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Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis
ACS central science 3(9), 949 - 960 () [10.1021/acscentsci.7b00211]  GO OpenAccess  Download fulltext Files  Download fulltextFulltext by OpenAccess repository BibTeX | EndNote: XML, Text | RIS

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Recent advances in dynamic docking for drug discovery
Wiley interdisciplinary reviews / Computational Molecular Science 7(6), e1320 - () [10.1002/wcms.1320] BibTeX | EndNote: XML, Text | RIS

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(Editor) ; (Corresponding author) ; (Corresponding author) ; (Corresponding author)
Chapter 12. Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targets
Computational Tools for Chemical Biology / Martín-Santamaría, Sonsoles (Editor) ; Cambridge : Royal Society of Chemistry, 2017, ; ISBN: ; doi:10.1039/9781788010139 Cambridge : Royal Society of Chemistry 317 - 348 () [10.1039/9781788010139-00317]  Download fulltext Files BibTeX | EndNote: XML, Text | RIS


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