Publikationer

  • Raehtz, Kevin D.; Barrenäs, Fredrik; Xu, Cuiling; Busman-Sahay, Kathleen et al.

    African green monkeys avoid SIV disease progression by preventing intestinal dysfunction and maintaining mucosal barrier integrity

    Ingår i PLoS Pathogens, 2020.

    Open access
  • Henschel, Henning; Van der Spoel, David

    An Intuitively Understandable Quality Measure for Theoretical Vibrational Spectra

    Ingår i Journal of Physical Chemistry Letters, s. 5471-5475, 2020.

    Open access
  • Rheinbay, Esther; Nielsen, Morten Muhlig; Abascal, Federico; Wala, Jeremiah A. et al.

    Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

    Ingår i Nature, s. 102-111, 2020.

    Open access
  • Manzetti, Sergio; Trounev, Alexander

    Analytical Solutions for a Supersymmetric Wave‐Equation for Quasiparticles in a Quantum System

    Ingår i Advanced Theory and Simulations, 2020.

  • Carlevaro-Fita, Joana; Lanzos, Andres; Feuerbach, Lars; Hong, Chen et al.

    Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis

    Ingår i COMMUNICATIONS BIOLOGY, 2020.

    Open access
  • Socan, Jaka; Purg, Miha; Åqvist, Johan

    Computer simulations explain the anomalous temperature optimum in a cold-adapted enzyme

    Ingår i Nature Communications, 2020.

    Open access
  • Ballante, Flavio; Rudling, Axel; Zeifman, Alexey; Luttens, Andreas et al.

    Docking Finds GPCR Ligands in Dark Chemical Matter

    Ingår i Journal of Medicinal Chemistry, s. 613-620, 2020.

  • Manzetti, Sergio; Trounev, Alexander

    Electromagnetic Vorticity in a Square-Well Crystal System Described by a Supersymmetric Wave-Equation

    Ingår i ADVANCED THEORY AND SIMULATIONS, 2020.

  • Fleetwood, Oliver; Matricon, Pierre; Carlsson, Jens; Delemotte, Lucie

    Energy Landscapes Reveal Agonist Control of G Protein-Coupled Receptor Activation via Microswitches

    Ingår i Biochemistry, s. 880-891, 2020.

    Open access
  • Gorini, Giacomo; Fourati, Slim; Vaccari, Monica; Rahman, Mohammad Arif et al.

    Engagement of monocytes, NK cells, and CD4(+) Th1 cells by ALVAC-SIV vaccination results in a decreased risk of SIVmac251 vaginal acquisition

    Ingår i PLoS Pathogens, 2020.

    Open access
  • Vasile, Silvana; Hallberg, Anders; Sallander, Jessica; Hallberg, Mathias et al.

    Evolution of Angiotensin Peptides and Peptidomimetics as Angiotensin II Receptor Type 2 (AT2) Receptor Agonists

    Ingår i Biomolecules, 2020.

    Open access
  • Wang, Xuesong; Jespers, Willem; Bongers, Brandon J.; Jansen, Maria C. C. Habben et al.

    Full length article Characterization of cancer -related somatic mutations in the adenosine A 2B receptor

    Ingår i European Journal of Pharmacology, 2020.

  • Cabrera, Carin C.; Ekstrom, Mattias; Linde, Cecilia; Persson, Hans et al.

    Increased iron absorption in patients with chronic heart failure and iron deficiency

    Ingår i Journal of Cardiac Failure, s. 440-443, 2020.

    Open access
  • Diamanti, Klev; Visvanathar, Robin; Pereira, Maria J.; Cavalli, Marco et al.

    Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes

    Ingår i Scientific Reports, 2020.

    Open access
  • Barlow, Nicholas; Reddy Vanga, Sudarsana; Sävmarker, Jonas; Sandström, Anja et al.

    Macrocyclic Peptidomimetics as Inhibitors of Insulin-Regulated Aminopeptidase (IRAP)

    Ingår i RSC Medicinal chemistry, s. 234-244, 2020.

  • Bortot, Leandro Oliveira; Bashardanesh, Zahedeh; Van der Spoel, David

    Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation

    Ingår i Journal of Chemical Information and Modeling, s. 322-331, 2020.

  • Mallo-Abreu, Ana; Prieto-Diaz, Ruben; Jespers, Willem; Azuaje, Jhonny et al.

    Nitrogen-Walk Approach to Explore Bioisosteric Replacements in a Series of Potent A(2B) Adenosine Receptor Antagonists

    Ingår i Journal of Medicinal Chemistry, s. 7721-7739, 2020.

  • Campbell, Peter J.; Diamanti, Klev; Komorowski, Jan; Umer, Husen Muhammad et al.

    Pan-cancer analysis of whole genomes

    Ingår i Nature, s. 82-93, 2020.

    Open access
  • Jaiteh, Mariama; Rodríguez-Espigares, Ismael; Selent, Jana; Carlsson, Jens

    Performance of virtual screening against GPCR homology models: Impact of template selection and treatment of binding site plasticity

    Ingår i PloS Computational Biology, 2020.

    Open access
  • Engen, Karin; Reddy Vanga, Sudarsana; Lundbäck, Thomas; Agalo, Faith et al.

    Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors

    Ingår i ChemistryOpen, s. 325-337, 2020.

    Open access
  • Henschel, Henning; Andersson, Alfred T.; Jespers, Willem; Ghahremanpour, Mohammad Mehdi et al.

    Theoretical Infrared Spectra: Quantitative Similarity Measures and Force Fields

    Ingår i Journal of Chemical Theory and Computation, s. 3307-3315, 2020.

    Open access
  • Kamerlin, Natasha; Delcey, Mickaël G; Manzetti, Sergio; Van der Spoel, David

    Toward a Computational Ecotoxicity Assay

    Ingår i Journal of Chemical Information and Modeling, s. 3792-3803, 2020.

  • Etemadikhah, Mitra; Niazi, Adnan; Wetterberg, Lennart; Feuk, Lars

    Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes

    Ingår i Scientific Reports, 2020.

    Open access
  • Wright, Shane C.; Kozielewicz, Pawel; Kowalski-Jahn, Maria; Petersen, Julian et al.

    A conserved molecular switch in Class F receptors regulates receptor activation and pathway selection

    Ingår i Nature Communications, 2019.

    Open access
  • Isaksson, Rebecka; Lindman, Jens; Wannberg, Johan; Sallander, Jessica et al.

    A Series of Analogues to the AT2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode

    Ingår i ChemistryOpen, s. 114-125, 2019.

    Open access
  • Borroto-Escuela, Dasiel O.; Narváez, Manuel; Romero Fernández, Wilber; Pinton, Luca et al.

    Acute Cocaine Enhances Dopamine D2R Recognition and Signaling and Counteracts D2R Internalization in Sigma1R-D2R Heteroreceptor Complexes

    Ingår i Molecular Neurobiology, s. 7045-7055, 2019.

    Open access
  • Cavalli, Marco; Baltzer, Nicholas; Umer, Husen Muhammad; Grau, Jan et al.

    Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases

    Ingår i Scientific Reports, 2019.

    Open access
  • Moghadam, Behrooz Torabi; Etemadikhah, Mitra; Rajkowska, Grazyna; Stocluneier, Craig et al.

    Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods

    Ingår i Journal of Psychiatric Research, s. 41-47, 2019.

  • Rajan, Meenu Rohini; Sotak, Matus; Barrenäs, Fredrik; Shen, Tong et al.

    Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum

    Ingår i Scientific Reports, 2019.

    Open access
  • Walz, Marie-Madeleine; Van der Spoel, David

    Direct Link between Structure, Dynamics, and Thermodynamics in Molten Salts

    Ingår i The Journal of Physical Chemistry C, s. 25596-25602, 2019.

  • Lind, Christoffer; Esguerra, Mauricio; Jespers, Willem; Satpati, Priyadarshi et al.

    Free energy calculations of RNA interactions

    Ingår i Methods, s. 85-95, 2019.

  • Jandova, Zuzana; Jespers, Willem; Sotelo, Eddy; Gutiérrez-de-Terán, Hugo et al.

    Free-Energy Calculations for Bioisosteric Modifications of A(3) Adenosine Receptor Antagonists

    Ingår i International Journal of Molecular Sciences, 2019.

    Open access
  • Shebanits, Kateryna; Vasile, Silvana; Xu, Bo; Gutiérrez-de-Terán, Hugo et al.

    Functional characterization in vitro of twelve naturally occurring variants of the human pancreatic polypeptide receptor NPY4R

    Ingår i Neuropeptides, 2019.

    Open access
  • Ge, Xueliang; Oliveira, Ana; Hjort, Karin; Bergfors, Terese et al.

    Inhibition of translation termination by small molecules targeting ribosomal release factors

    Ingår i Scientific Reports, 2019.

    Open access
  • Diamanti, Klev; Cavalli, Marco; Pan, Gang; Pereira, Maria J et al.

    Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

    Ingår i Scientific Reports, 2019.

    Open access
  • Barrenäs, Fredrik; Raehtz, Kevin; Xu, Cuiling; Law, Lynn et al.

    Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control

    Ingår i Nature Communications, 2019.

    Open access
  • Walz, Marie-Madeleine; Van der Spoel, David

    Molten alkali halides - temperature dependence of structure, dynamics and thermodynamics

    Ingår i Physical Chemistry, Chemical Physics - PCCP, s. 18516-18524, 2019.

  • Karlsson, Leif; Michelatto, Debora de Paula; Gori Lusa, Ana Leticia; Mgnani Silva, Camila D'Almeida et al.

    Novel non-classic CYP21A2 variants, including combined alleles, identified in patients with congenital adrenal hyperplasia

    Ingår i Clinical Biochemistry, s. 50-56, 2019.

  • Capuccini, Marco; Larsson, Anders; Carone, Matteo; Novella, Jon Ander et al.

    On-demand virtual research environments using microservices

    Ingår i PeerJ Computer Science, 2019.

    Open access
  • Roos, Katarina; Wu, Chuanjie; Damm, Wolfgang; Reboul, Mark et al.

    OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules

    Ingår i Journal of Chemical Theory and Computation, s. 1863-1874, 2019.

  • Van der Spoel, David; Manzetti, Sergio; Haiyang, Zhang; Klamt, Andreas

    Prediction of Partition Coefficients of Environmental Toxins Using Computational Chemistry Methods

    Ingår i ACS Omega, s. 13772-13781, 2019.

    Open access
  • Kumar, Amit; Åqvist, Johan; Satpati, Priyadarshi

    Principles of tRNA(Ala) Selection by Alanyl-tRNA Synthetase Based on the Critical G3.U70 Base Pair

    Ingår i ACS OMEGA, s. 15539 15539-15548 15548, 2019.

    Open access
  • Jespers, Willem; Esguerra, Mauricio; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

    QligFEP: an automated workflow for small molecule free energy calculations in Q

    Ingår i Journal of Cheminformatics, 2019.

    Open access
  • Jespers, Willem; Isaksen, Geir V; Andberg, Tor A H; Vasile, Silvana et al.

    QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q

    Ingår i Journal of Chemical Theory and Computation, s. 5461-5473, 2019.

  • Yin, Chunhua; Cui, Ziheng; Jiang, Yang; Van der Spoel, David et al.

    Role of Host-Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

    Ingår i The Journal of Physical Chemistry C, s. 17745-17756, 2019.

  • Bashardanesh, Zahedeh; Elf, Johan; Zhang, Haiyang; Van der Spoel, David

    Rotational and Translational Diffusion of Proteins as a Function of Concentration

    Ingår i ACS OMEGA, s. 20654-20664, 2019.

    Open access
  • Cavalli, Marco; Baltzer, Nicholas; Pan, Gang; Walls, Jose Ramon Barcenas et al.

    Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

    Ingår i HUMAN GENOMICS, 2019.

    Open access
  • Manzetti, Sergio; Trounev, Alexander

    Supersymmetric Hamiltonian and Vortex Formation Model in a Quantum Nonlinear System in an Inhomogeneous Electromagnetic Field

    Ingår i Advanced Theory and Simulations, 2019.

  • Walz, Marie-Madeleine; Van der Spoel, David

    Systematically improved melting point prediction: a detailed physical simulation model is required

    Ingår i Chemical Communications, s. 12044-12047, 2019.

    Open access
  • Elofsson, Arne; Hess, Berk; Lindahl, Erik; Onufriev, Alexey et al.

    Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

    Ingår i PloS Computational Biology, 2019.

    Open access