Department of Cell and Molecular Biology

Publications

  • Manzetti, Sergio

    Addendum: Solvation energies of butylparaben, benzo[a]pyrene diol epoxide, perfluorooctanesulfonic acid and DEHP in complex with DNA bases.

    Part of Chemical Research in Toxicology, 2018.

  • Ekholm, Victor; Vazdar, Mario; Mason, Philip E.; Bialik, Erik et al.

    Anomalous surface behavior of hydrated guanidinium ions due to ion pairing

    Part of Journal of Chemical Physics, 2018.

  • Behzadi, Hadi; Manzetti, Sergio; Darghai, Mayram; Roonasi, Payman et al.

    Application of calculated NMR parameters, aromaticity indices and wavefunction properties for evaluation of corrosion inhibition efficiency of pyrazine inhibitors

    Part of Journal of Molecular Structure, p. 34-40, 2018.

  • Manzetti, Sergio

    Applied quantum physics for novel quantum computation approaches: an update

    Part of Computational Mathematics and Modeling, p. 244-252, 2018.

  • Manzetti, Sergio

    Bonding of Butylparaben, Bis(2-ethylhexyl)-phthalate, and Perfluorooctanesulfonic Acid to DNA: Comparison with Benzo[a]pyrene Shows Low Probability for Strong Noncovalent DNA Intercalation.

    Part of Chemical Research in Toxicology, p. 22-36, 2018.

  • Socan, Jaka; Kazemi, Masoud; Isaksen, Geir Villy; Brandsdal, Bjorn Olav et al.

    Catalytic Adaptation of Psychrophilic Elastase

    Part of Biochemistry, p. 2984-2993, 2018.

  • Ge, Xueliang; Mandava, Chandra Sekhar; Lind, Christoffer; Åqvist, Johan et al.

    Complementary charge-based interaction between the ribosomal-stalk protein L7/12 and IF2 is the key to rapid subunit association

    Part of Proceedings of the National Academy of Sciences of the United States of America, p. 4649-4654, 2018.

  • Barrozo, Alexandre; Liao, Qinghua; Esguerra, Mauricio; Marloie, Gael et al.

    Computer simulations of the catalytic mechanism of wild-type and mutant beta-phosphoglucomutase

    Part of Organic and biomolecular chemistry, p. 2060-2073, 2018.

  • Bashardanesh, Zahedeh; Lötstedt, Per

    Efficient Green's function reaction dynamics (GFRD) simulations for diffusion-limited, reversible reactions

    Part of Journal of Computational Physics, p. 78-99, 2018.

  • Zhang, Haiyang; Yin, Chunhua; Jiang, Yang; van der Spoel, David et al.

    Force Field Benchmark of Amino Acids: I. Hydration and Diffusion in Different Water Models

    Part of Journal of Chemical Information and Modeling, p. 1037-1052, 2018.

  • Rudling, Axel; Orro, Adolfo; Carlsson, Jens

    Prediction of Ordered Water Molecules in Protein Binding Sites from Molecular Dynamics Simulations: The Impact of Ligand Binding on Hydration Networks

    Part of Journal of Chemical Information and Modeling, p. 350-361, 2018.

  • Bauer, Paul; Barrozo, Alexandre; Purg, Miha; Amrein, Beat Anton et al.

    Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations

    Part of SoftwareX, 2018.

  • Manzetti, Sergio

    Quantum chemical calculations of the active site of the solute-binding protein PsaA from Streptococcus pneumoniae explain electronic selectivity of metal binding

    Part of Structural Chemistry, p. 393-401, 2018.

  • Reddy Vanga, Sudarsana; Sävmarker, Jonas; Ng, Leelee; Larhed, Mats et al.

    Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Aryl Sulfonamides

    Part of ACS OMEGA, p. 4509 4509-4521 4521, 2018.

  • Ghahremanpour, Mohammad M.; van Maaren, Paul J.; Van Der Spoel, David

    The Alexandria library, a quantum-chemical database of molecular properties for force field development

    Part of Scientific Data, 2018.

  • Marcellini, Moreno; Nasedkin, Alexandr; Zietz, Burkhard; Petersson, Jonas et al.

    Transient isomers in the photodissociation of bromoiodomethane

    Part of Journal of Chemical Physics, 2018.

  • Dabrowski, Michal J.; Draminski, Michal; Diamanti, Klev; Stepniak, Karolina et al.

    Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival

    Part of Scientific Reports, 2018.

  • El Maatougui, Abdelaziz; Yanez, Matilde; Crespo, Abel; Fraiz, Nuria et al.

    3-Oxopyridazin-5-yl-Chalcone Hybrids: Potent Antiplatelet Agents That Prevent Glycoprotein IIb/IIIa Activation

    Part of CHEMISTRYSELECT, p. 4920 4920-4933 4933, 2017.

  • Lind, Christoffer; Esguerra, Mauricio; Åqvist, Johan

    A close-up view of codon selection in eukaryotic initiation

    Part of RNA Biology, p. 815-819, 2017.

  • Petersen, Julian; Wright, Shane C.; Rodriguez, David; Matricon, Pierre et al.

    Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

    Part of Nature Communications, 2017.

  • Polanski, Andrzej; Szczesna, Agnieszka; Garbulowski, Mateusz; Kimmel, Marek et al.

    Coalescence computations for large samples drawn from populations of time-varying sizes

    Part of PLoS ONE, 2017.

  • Åqvist, Johan

    Cold Adaptation of Triosephosphate Isomerase

    Part of Biochemistry, p. 4169-4176, 2017.

  • Azuaje, Jhonny; Jespers, Willem; Yaziji, Vicente; Mallo, Ana et al.

    Effect of Nitrogen Atom Substitution in A(3) Adenosine Receptor Binding: N-(4,6-Diarylpyridin-2-yl)acetamides as Potent and Selective Antagonists

    Part of Journal of Medicinal Chemistry, p. 7502-7511, 2017.

  • Carbajales, Carlos; Azuaje, Jhonny; Oliveira, Ana; Loza, Maria I. et al.

    Enantiospecific Recognition at the A(2B) Adenosine Receptor by Alkyl 2-Cyanoimino-4-substituted-6-methyl-1,2,3,4-tetrahydropyrimidine-5-carboxylates

    Part of Journal of Medicinal Chemistry, p. 3372-3382, 2017.

  • Ruffier, Magali; Kähäri, Andreas; Komorowska, Monika; Keenan, Stephen et al.

    Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

    Part of Database, 2017.

  • Marinho, Ricardo R. T.; Walz, Marie-Madeleine; Ekholm, Victor; Ohrwall, Gunnar et al.

    Ethanol Solvation in Water Studied on a Molecular Scale by Photoelectron Spectroscopy

    Part of Journal of Physical Chemistry B, p. 7916-7923, 2017.

  • Crespo, Abel; El Maatougui, Abdelaziz; Azuaje, Jhonny; Escalante, Luz et al.

    Exploring the influence of the substituent at position 4 in a series of 3,4-dihydropyrimidin-2(1H)-one A(2B) adenosine receptor antagonists

    Part of Chemistry of Heterocyclic Compounds, p. 316-321, 2017.

  • Matricon, Pierre; Ranganathan, Anirudh; Warnick, Eugene; Gao, Zhan-Guo et al.

    Fragment optimization for GPCRs by molecular dynamics free energy calculations: Probing druggable subpockets of the A(2A) adenosine receptor binding site

    Part of Scientific Reports, 2017.

  • Rudling, Axel; Gustafsson, Robert; Almlof, Ingrid; Homan, Evert et al.

    Fragment-Based Discovery and Optimization of Enzyme Inhibitors by Docking of Commercial Chemical Space

    Part of Journal of Medicinal Chemistry, p. 8160-8169, 2017.

  • Zhang, Haiyang; Jiang, Yang; Yan, Hai; Yin, Chunhua et al.

    Free-Energy Calculations of Ionic Hydration Consistent with the Experimental Hydration Free Energy of the Proton

    Part of Journal of Physical Chemistry Letters, p. 2705-2712, 2017.

  • Ranganathan, Anirudh; Heine, Philipp; Rudling, Axel; Pluckthun, Andreas et al.

    Ligand Discovery for a Peptide-Binding GPCR by Structure-Based Screening of Fragment- and Lead-Like Chemical Libraries

    Part of ACS Chemical Biology, p. 735-745, 2017.

  • Lehmann, Laura C.; Hewitt, Graeme; Aibara, Shintaro; Leitner, Alexander et al.

    Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

    Part of Molecular Cell, p. 847-859.e7, 2017.

  • dos Santos Soares, Ricardo de Oliveira; Bortot, Leandro Oliveira; van Der Spoel, David; Caliri, Antonio et al.

    Membrane vesiculation induced by proteins of the dengue virus envelope studied by molecular dynamics simulations

    Part of Journal of Physics, 2017.

  • Lind, Christoffer; Oliveira, Ana; Åqvist, Johan

    Origin of the omnipotence of eukaryotic release factor 1

    Part of Nature Communications, 2017.

  • Torabi Moghadam, Behrooz; Zamani, Neda; Komorowski, Jan; Grabherr, Manfred et al.

    PiiL: visualization of DNA methylation and gene expression data in gene pathways

    Part of BMC Genomics, 2017.

  • Shamsudin Khan, Yasmin; Gutiérrez-de-Terán, Hugo; Åqvist, Johan

    Probing the Time Dependency of Cyclooxygenase-1 Inhibitors by Computer Simulations

    Part of Biochemistry, p. 1911-1920, 2017.

  • Manzetti, Sergio; Yakovlev, Alexei

    Quantum chemical study of regular and irregular geometries of MgO nanoclusters: Effects on magnetizability, electronic properties and physical characteristics

    Part of Materials Chemistry and Physics, p. 7-17, 2017.

  • Hamnevik, Emil; Enugala, Thilak Reddy; Maurer, Dirk; Ntuku, Siphosethu et al.

    Relaxation of Nonproductive Binding and Increased Rate of Coenzyme Release in an Alcohol Dehydrogenase Increases Turnover With a Non-Preferred Alcohol Enantiomer

    Part of The FEBS Journal, p. 3895-3914, 2017.

  • Baltzer, Nicholas; Sundström, Karin; Nygård, Jan F.; Dillner, Joakim et al.

    Risk stratification in cervical cancer screening by complete screening history: Applying bioinformatics to a general screening population

    Part of International Journal of Cancer, p. 200-209, 2017.

  • Asp, Michaela; Salmen, Fredrik; Ståhl, Patrik L.; Vickovic, Sanja et al.

    Spatial detection of fetal marker genes expressed at low level in adult human heart tissue

    Part of Scientific Reports, 2017.

  • Manzetti, Sergio; Enrichi, Francesco

    State-of-the-art developments in metal and carbon-based semiconducting nanomaterials: applications and functions in spintronics, nanophotonics, and nanomagnetics

    Part of Advances in Manufacturing, p. 105-119, 2017.

  • Jespers, Willem; Oliveira, Ana; Prieto-Diaz, Ruben; Majellaro, Maria et al.

    Structure-Based Design of Potent and Selective Ligands at the Four Adenosine Receptors

    Part of Molecules, 2017.

  • Mannel, Barbara; Jaiteh, Mariama; Zeifman, Alexey; Randakova, Alena et al.

    Structure-Guided Screening for Functionally Selective D-2 Dopamine Receptor Ligands from a Virtual Chemical Library

    Part of ACS Chemical Biology, p. 2652-2661, 2017.

  • Ameur, Adam; Dahlberg, Johan; Olason, Pall; Vezzi, Francesco et al.

    SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population

    Part of European Journal of Human Genetics, p. 1253-1260, 2017.

  • Bálint, Mónika; Jeszenői, Norbert; Horváth, István; van der Spoel, David et al.

    Systematic exploration of multiple drug binding sites

    Part of Journal of Cheminformatics, 2017.

  • Nohr, Anne Cathrine; Jespers, Willem; Shehata, Mohamed A.; Floryan, Leonard et al.

    The GPR139 reference agonists 1a and 7c, and tryptophan and phenylalanine share a common binding site

    Part of Scientific Reports, 2017.

  • Isaksen, Geir Villy; Åqvist, Johan; Brandsdal, Björn Olav

    Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations

    Part of Biochemistry, p. 306-312, 2017.

  • Manzetti, Sergio; Andersen, Otto

    A molecular dynamics study of nanoparticle-formation from bioethanol-gasoline blend emissions

    Part of Fuel, p. 55-63, 2016.

  • Umer, Husen M.; Cavalli, Marco; Dabrowski, Michal J.; Diamanti, Klev et al.

    A Significant Regulatory Mutation Burden at a High-Affinity Position of the CTCF Motif in Gastrointestinal Cancers

    Part of Human Mutation, p. 904-913, 2016.

  • Diwakarla, Shanti; Nylander, Erik; Grönbladh, Alfhild; Vanga, Sudarsana Reddy et al.

    Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures

    Part of ACS Chemical Neuroscience, p. 1383-1392, 2016.