Publikationer

  • Miranda-Pastoriza, Dario; Bernardez, Rodrigo; Azuaje, Jhonny; Prieto-Diaz, Ruben et al.

    Exploring Non-orthosteric Interactions with a Series of Potent and Selective A(3) Antagonists

    Ingår i ACS Medicinal Chemistry Letters, s. 243-249, 2022.

    Open access
  • Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Cabuk, Ugur; Younes, Sara et al.

    Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment

    Ingår i Cancers, 2022.

    Open access
  • Pham, Em Canh; Truong, Tuyen Ngoc; Dong, Nguyen Hanh; Vo, Duc Duy et al.

    Synthesis of a Series of Novel 2-Amino-5-substituted 1,3,4-oxadiazole and 1,3,4-thiadiazole Derivatives as Potential Anticancer, Antifungal and Antibacterial Agents

    Ingår i Medicinal chemistry, s. 558-573, 2022.

  • Koenekoop, Lucien; van der Ent, Florian; Purg, Miha; Åqvist, Johan

    The Activation Parameters of a Cold-Adapted Short Chain Dehydrogenase Are Insensitive to Enzyme Oligomerization

    Ingår i Biochemistry, s. 514-522, 2022.

  • Stratmann, Svea; Yones, Sara A.; Garbulowski, Mateusz; Sun, Jitong et al.

    Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression

    Ingår i Blood Advances SUPPLEMENTAL INFORMATION FOR: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression SUPPLEMENTARY MATERIAL: Transcriptomic analysis reveals pro-inflammatory signatures associated with acute myeloid leukemia progression, s. 152-164, 2022.

    Open access
  • Luttens, Andreas; Gullberg, Hjalmar; Abdurakhmanov, Eldar; Vo, Duy Duc et al.

    Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

    Ingår i Journal of the American Chemical Society, s. 2905-2920, 2022.

    Open access
  • Majellaro, María; Jespers, Willem; Crespo, Abel; Núñez, María J. et al.

    3,4-Dihydropyrimidin-2(1H)-ones as Antagonists of the Human A2B Adenosine Receptor: Optimization, Structure–Activity Relationship Studies, and Enantiospecific Recognition

    Ingår i Journal of Medicinal Chemistry, s. 458-480, 2021.

  • Manzetti, Sergio; Trounev, Alexander

    A Korteweg-DeVries type model for helical soliton solutions for quantum and continuum phenomena

    Ingår i International Journal of Modern Physics C, 2021.

  • Bender, Brian J.; Gahbauer, Stefan; Luttens, Andreas; Lyu, Jiankun et al.

    A practical guide to large-scale docking

    Ingår i Nature Protocols, s. 4799-4832, 2021.

  • Gapsys, Vytautas; Yildirim, Ahmet; Aldeghi, Matteo; Khalak, Yuriy et al.

    Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches

    Ingår i Communications Chemistry, 2021.

    Open access
  • Le, Thanh Thanh; Le, Phung Thi Kim; Dam, Hai Thi Thanh; Vo, Duc Duy et al.

    Anticancer Activity of New 1,2,3-Triazole-Amino Acid Conjugates

    Ingår i Molbank, 2021.

    Open access
  • Kapla, Jon; Rodriguez Espigares, Ismael; Ballante, Flavio; Selent, Jana et al.

    Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models?

    Ingår i PloS Computational Biology, 2021.

    Open access
  • Brooks, Charles L., III; Case, David A.; Plimpton, Steve; Roux, Benoit et al.

    Classical molecular dynamics

    Ingår i Journal of Chemical Physics, 2021.

  • Thysell, Elin; Köhn, Linda; Semenas, Julius; Järemo, Helena et al.

    Clinical and biological relevance of the transcriptomic-based prostate cancer metastasis subtypes MetA-C.

    Ingår i Molecular Oncology, 2021.

  • Jespers, Willem; Heitman, Laura H.; IJzerman, Adriaan P.; Sotelo, Eddy et al.

    Deciphering conformational selectivity in the A(2A) adenosine G protein-coupled receptor by free energy simulations

    Ingår i PloS Computational Biology, 2021.

    Open access
  • Cruz-Lopez, Olga; Ner, Matilde; Nerin-Fonz, Francho; Jimenez-Martinez, Yaiza et al.

    Design, synthesis, HER2 inhibition and anticancer evaluation of new substituted 1,5-dihydro-4,1-benzoxazepines

    Ingår i Journal of enzyme inhibition and medicinal chemistry (Print), s. 1553-1563, 2021.

    Open access
  • Matricon, Pierre; Vo, Duc Duy; Gao, Zhan-Guo; Kihlberg, Jan et al.

    Fragment-based design of selective GPCR ligands guided by free energy simulations

    Ingår i Chemical Communications, s. 12305-12308, 2021.

    Open access
  • Umer, Husen Muhammad; Smolinska, Karolina; Komorowski, Jan; Wadelius, Claes

    Functional annotation of noncoding mutations in cancer

    Ingår i Life Science Alliance, 2021.

    Open access
  • Stratmann, Svea; Yones, Sara A.; Mayrhofer, Markus; Norgren, Nina et al.

    Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets

    Ingår i Blood Advances SUPPLEMENTAL INFORMATION FOR: Genomic characterization of adult and pediatric relapsed acute myeloid leukemia reveals novel therapeutic targets, s. 900-912, 2021.

  • Nencetti, Susanna; Cuffaro, Doretta; Nuti, Elisa; Ciccone, Lidia et al.

    Identification of histone deacetylase inhibitors with (arylidene)aminoxy scaffold active in uveal melanoma cell lines

    Ingår i Journal of enzyme inhibition and medicinal chemistry (Print), s. 34-47, 2021.

    Open access
  • Fleetwood, Oliver; Carlsson, Jens; Delemotte, Lucie

    Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling

    Ingår i eLIFE, 2021.

    Open access
  • Wang, Xuesong; Jespers, Willem; Prieto-Diaz, Ruben; Majellaro, Maria et al.

    Identification of V6.51L as a selectivity hotspot in stereoselective A(2B) adenosine receptor antagonist recognition

    Ingår i Scientific Reports, 2021.

    Open access
  • Barrenäs, Fredrik; Hansen, Scott G.; Law, Lynn; Driscoll, Connor et al.

    Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy

    Ingår i PLoS Pathogens, 2021.

    Open access
  • Garbulowski, Mateusz; Smolinska Garbulowska, Karolina; Diamanti, Klev; Pan, Gang et al.

    Interpretable Machine Learning Reveals Dissimilarities Between Subtypes of Autism Spectrum Disorder

    Ingår i Frontiers in Genetics, 2021.

    Open access
  • Matricon, Pierre; Suresh, R. Rama; Gao, Zhan-Guo; Panel, Nicolas et al.

    Ligand design by targeting a binding site water

    Ingår i Chemical Science, s. 960-968, 2021.

    Open access
  • Stepniak, Karolina; Machnicka, Magdalena A.; Mieczkowski, Jakub; Macioszek, Anna et al.

    Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas

    Ingår i Nature Communications, 2021.

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

    Microscopic origins of conductivity in molten salts unraveled by computer simulations

    Ingår i Communications Chemistry, 2021.

    Open access
  • van der Valk, Tom; Pecnerova, Patricia; Diez-del-Molino, David; Bergström, Anders et al.

    Million-year-old DNA sheds light on the genomic history of mammoths

    Ingår i Nature, s. 265-269, 2021.

  • Pan, Gang; Diamanti, Klev; Cavalli, Marco; Gutierrez, Ariadna Lara et al.

    Multifaceted regulation of hepatic lipid metabolism by YY1

    Ingår i Life Science Alliance, 2021.

    Open access
  • Wannberg, Johan; Gising, Johan; Lindman, Jens; Salander, Jessica et al.

    N-(Methyloxycarbonyl)thiophene sulfonamides as high affinity AT2 receptor ligands

    Ingår i Bioorganic & Medicinal Chemistry, 2021.

  • Sinelnikova, Anna; Van der Spoel, David

    NMR Refinement and Peptide Folding Using the GROMACS Software

    Ingår i Journal of Biomolecular NMR, s. 143-149, 2021.

    Open access
  • Tehrani, Kamaleddin H. M. E.; Wade, Nicola; Mashayekhi, Vida; Bruchle, Nora C. et al.

    Novel Cephalosporin Conjugates Display Potent and Selective Inhibition of Imipenemase-Type Metallo-beta-Lactamases

    Ingår i Journal of Medicinal Chemistry, s. 9141-9151, 2021.

    Open access
  • Kutashev, Konstantin O.; Franek, Michal; Diamanti, Klev; Komorowski, Jan et al.

    Nucleolar rDNA folds into condensed foci with a specific combination of epigenetic marks

    Ingår i The Plant Journal, s. 1534-1548, 2021.

  • Chai, Siew Yeen; Gutiérrez-de-Terán, Hugo; Stratikos, Efstratios

    Physiological, Pathological Roles and Pharmacology of Insulin Regulated Aminopeptidase: Editorial

    Ingår i Frontiers in Molecular Biosciences, 2021.

    Open access
  • Draper-Joyce, Christopher J.; Bhola, Rebecca; Wang, Jinan; Bhattarai, Apurba et al.

    Positive allosteric mechanisms of adenosine A(1) receptor-mediated analgesia

    Ingår i Nature, s. 571-576, 2021.

  • Mallo-Abreu, Ana; Reyes-Resina, Irene; Azuaje, Jhonny; Franco, Rafael et al.

    Potent and Subtype-Selective Dopamine D-2 Receptor Biased Partial Agonists Discovered via an Ugi-Based Approach

    Ingår i Journal of Medicinal Chemistry, s. 8710-8726, 2021.

  • Gao, Yongzhi; van Haren, Matthijs J.; Buijs, Ned; Innocenti, Paolo et al.

    Potent Inhibition of Nicotinamide N-Methyltransferase by Alkene-Linked Bisubstrate Mimics Bearing Electron Deficient Aromatics

    Ingår i Journal of Medicinal Chemistry, s. 12938-12963, 2021.

    Open access
  • Garbulowski, Mateusz; Diamanti, Klev; Smolinska, Karolina; Baltzer, Nicholas et al.

    R.ROSETTA: an interpretable machine learning framework

    Ingår i BMC Bioinformatics, 2021.

    Open access
  • Reddy Vanga, Sudarsana; Åqvist, Johan; Gutiérrez-de-Terán, Hugo

    Structural Basis of Inhibition of Human Insulin-Regulated Aminopeptidase (IRAP) by Benzopyran-based Inhibitors

    Ingår i Frontiers in Molecular Biosciences, 2021.

    Open access
  • Guo, Xiaohu; Söderholm, Annika; Kanchugal Puttaswamy, Sandesh; Isaksen, Geir V et al.

    Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family

    Ingår i eLIFE, 2021.

    Open access
  • Kampen, Stefanie; Vo, Duc Duy; Zhang, Xiaoqun; Panel, Nicolas et al.

    Structure-Guided Design of G-Protein-Coupled Receptor Polypharmacology

    Ingår i Angewandte Chemie International Edition, s. 18022-18030, 2021.

    Open access
  • Assis Silva, Flavia Cristina; Lourenco, Tuanan da Costa; Van der Spoel, David; Aparicio, Santiago et al.

    The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

    Ingår i Journal of Chemical Physics, 2021.

  • Machado, Teresa F. G.; Purg, Miha; Åqvist, Johan; da Silva, Rafael G.

    Transition States for Psychrophilic and Mesophilic (R)-3-Hydroxybutyrate Dehydrogenase-Catalyzed Hydride Transfer a Sub-zero Temperatures

    Ingår i Biochemistry, s. 2186-2194, 2021.

  • Paulsson, Johan O.; Rafati, Nima; DiLorenzo, Sebastian; Chen, Yi et al.

    Whole-genome Sequencing of Follicular Thyroid Carcinomas Reveal Recurrent Mutations in MicroRNA Processing Subunit DGCR8

    Ingår i Journal of Clinical Endocrinology and Metabolism, s. 3265-3282, 2021.

    Open access
  • Cavalli, Marco; Diamanti, Klev; Pan, Gang; Spalinskas, Rapolas et al.

    A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

    Ingår i Omics, s. 180-194, 2020.

    Open access
  • 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