Publications - Researchfield: Biochemistry, Bioinformatics And Life Sciences
2024
[83] Free energy landscape of the PI3Kα C-terminal activation (, , and ), In Computational and Structural Biotechnology Journal, volume 23, . [bibtex] [url] [doi]
[82] Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators (, , , and ), In Journal of Chemical Information and Modeling, volume 64, . [bibtex] [url] [doi]
[81] Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A3 Receptor (, and ), In The Journal of Physical Chemistry B, volume 128, . [bibtex] [url] [doi]
[80] Disentangling the riddle of systemic lupus erythematosus with antiphospholipid syndrome: blood transcriptome analysis reveals a less-pronounced IFN-signature and distinct molecular profiles in venous versus arterial events (, , , , , , , , , , , , and ), In Annals of the Rheumatic Diseases, BMJ Publishing Group Ltd, . [bibtex] [url] [doi]
[79] Molecular basis for the disease-modifying effects of belimumab in systemic lupus erythematosus and molecular predictors of early response: blood transcriptome analysis implicates the innate immunity and DNA damage response pathways (, , , , , , , , , , , , , , , and ), In Annals of the Rheumatic Diseases, BMJ Publishing Group Ltd, . [bibtex] [url] [doi]
[78] Beneficial Effects of Sideritis clandestina Extracts and Sideridiol against Amyloid β Toxicity (, , , , , , , , , , , , and ), In Antioxidants, volume 13, . [bibtex] [url] [doi]
2023
[77] Transcriptomic and proteomic profiling reveals distinct pathogenic features of peripheral non-classical monocytes in systemic lupus erythematosus (, , , , , , and ), In Clinical Immunology, volume 255, . [bibtex] [url] [doi]
[76] Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A2A and A1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations (), In Journal of Chemical Information and Modeling, volume 63, . [bibtex] [url] [doi]
[75] Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications (, , , , , , and ), In Journal of Chemical Theory and Computation, volume 19, . [bibtex] [url] [doi]
[74] Synthesis and Testing of Analogs of the Tuberculosis Drug Candidate SQ109 against Bacteria and Protozoa: Identification of Lead Compounds against Mycobacterium abscessus and Malaria Parasites (), In ACS Infectious Diseases, volume 9, . [bibtex] [url] [doi]
[73] Structure of amino acid sequence-reversed wtRop protei: insights from atomistic molecular dynamics simulations (, , , and ), In Journal of Biomolecular Structure and Dynamics, volume 0, . [bibtex] [url] [doi]
[72] A Multilevel Study of Eupatorin and Scutellarein as Anti-Amyloid Agents in Alzheimer’s Disease (, , , , , , , , , and ), In Biomedicines, volume 11, . [bibtex] [url] [doi]
[71] Bacterial Lectin FimH and Its Aggregation Hot-Spots: An Alternative Strategy against Uropathogenic Escherichia coli (), In Pharmaceutics, volume 15, . [bibtex] [url] [doi]
2022
[70] Clusterin in Alzheimer's disease: An amyloidogenic inhibitor of amyloid formation? (, , , , , , and ), In Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, volume 1868, . [bibtex] [url] [doi]
[69] Recognition motifs for Importin 4 [(L)PPRS(G/P)P] and Importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation (, , , , , , , , , and ), In Computational and Structural Biotechnology Journal, . [bibtex] [url] [doi]
[68] Identification of hydrated phases in ALPO4-5, and explanation of their effect on the water sorption and dynamics (), In Microporous and Mesoporous Materials, volume 329, . [bibtex] [url] [doi]
[67] Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations (), In Journal of Chemical Information and Modeling, volume 62, . [bibtex] [url] [doi]
[66] Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering (), In Journal of Chemical Theory and Computation, volume 18, . [bibtex] [url] [doi]
[65] Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability (), In The Journal of Physical Chemistry B, volume 126, . [bibtex] [url] [doi]
[64] Discovery of a High Affinity Adenosine A1/A3 Receptor Antagonist with a Novel 7-Amino-pyrazolo[3,4-d]pyridazine Scaffold (, , , , , , , , , , and ), In ACS Medicinal Chemistry Letters, volume 0, . [bibtex] [url] [doi]
[63] Effects of the structure of lipid-based agents in their complexation with a single stranded mRNA fragment: a computational study (), In Soft Matter, The Royal Society of Chemistry, . [bibtex] [url] [doi]
[62] Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning (), In Briefings in Bioinformatics, . [bibtex] [url] [doi]
[61] DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design ( and ), In Bioinformatics, volume 38, . [bibtex] [url] [doi]
[60] Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis (), In Annals of the Rheumatic Diseases, volume 81, . [bibtex] [url] [doi]
[59] Combined – whole blood and skin fibroblasts- transcriptomic analysis in Psoriatic Arthritis reveals molecular signatures of activity, resistance and early response to treatment (), In Frontiers in Immunology, volume 13, . [bibtex] [url] [doi]
[58] Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin (), In Molecules, volume 27, . [bibtex] [url] [doi]
2021
[57] The sequence [EKRKI(E/R)(K/L/R/S/T)] is a nuclear localization signal for importin 7 binding (NLS7) (), In Biochimica et Biophysica Acta (BBA) - General Subjects, volume 1865, . [bibtex] [url] [doi]
[56] Interplay of cholesterol, membrane bilayers and the AT1R: A cholesterol consensus motif on AT1R is revealed (, , , , and ), In Computational and Structural Biotechnology Journal, volume 19, . [bibtex] [url] [doi]
[55] Context-dependent Cryptic Roles of Specific Residues in Substrate Selectivity of the UapA Purine Transporter (, , , and ), In Journal of Molecular Biology, volume 433, . [bibtex] [url] [doi]
[54] FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations (), In J. Chem. Inf. Model., volume 61, . [bibtex] [url] [doi]
[53] Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers (, and ), In Journal of Chemical Information and Modeling, . [bibtex] [url] [doi]
[52] Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments (), In J. Chem. Theory Comput., volume 17, . [bibtex] [url] [doi]
[51] The effect of S427F mutation on RXRα activity depends on its dimeric partner (), In Chem. Sci., . [bibtex] [url] [doi]
[50] Hydration thermodynamics of cytosolic phospholipase A2 GIVA predict its membrane-associated parts and its highly hydrated binding site, In Journal of Biomolecular Structure and Dynamics, Taylor & Francis, volume 39, . [bibtex] [url] [doi]
[49] Computational insights on the molecular mechanisms across breast cancer progression combining gene differential expression and co-expression (, , , and ), In 2021 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI), . [bibtex] [url] [doi]
[48] Structure and Thermal Stability of wtRop and RM6 Proteins through All-Atom Molecular Dynamics Simulations and Experiments (), In International Journal of Molecular Sciences, volume 22, . [bibtex] [url] [doi]
[47] Discovery of Selective Inhibitor Leads by Targeting an Allosteric Site in Insulin-Regulated Aminopeptidase (), In Pharmaceuticals, volume 14, . [bibtex] [url] [doi]
2020
[46] ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compoundsfacilitating both drug discovery and repurposing (), In Bioinformatics, volume , . [bibtex] [pdf] [doi]
[45] The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations (), In Journal of Computer-Aided Molecular Design, volume , . [bibtex] [url] [doi]
[44] Coating of magnetic nanoparticles affects their interactions with model cell membranes (), In Biochimica et Biophysica Acta (BBA) - General Subjects, volume 1864, . [bibtex] [url] [doi]
[43] Exploring the role of the membrane bilayer in the recognition of candesartan by its GPCR AT1 receptor (), In Biochimica et Biophysica Acta (BBA) - Biomembranes, volume 1862, . [bibtex] [url] [doi]
[42] The boundary lipid around DMPC-spanning influenza A M2 transmembrane domain channels: Its structure and potential for drug accommodation (), In Biochimica et Biophysica Acta (BBA)- Biomembranes, volume 1862, . [bibtex] [url] [doi]
[41] Allostery in membrane proteins (), In Current Opinion in Structural Biology, volume 62, . [bibtex] [url] [doi]
[40] Chemical Probes for Blocking of Influenza A M2 Wild-type and S31N Channels (), In ACS Chemical Biology, volume 15, . [bibtex] [url] [doi]
[39] Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments (), In ACS Pharmacology & Translational Science, volume 3, . [bibtex] [url]
[38] Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors (), In ACS Pharmacology & Translational Science, volume 3, . [bibtex] [url] [doi]
[37] Pharmacological characterisation of novel adenosine A3 receptor antagonists (), In Nature Scientific Reports, volume 10, . [bibtex] [url] [doi]
[36] Unravelling the effect of the E545K mutation on PI3Kα kinase ( and ), In Chemical Science, volume , . [bibtex] [url] [doi]
[35] Complexation of single stranded RNA with an ionizable lipid: an all-atom molecular dynamics simulation study (), In Soft Matter, volume 16, . [bibtex] [url] [doi]
[34] Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus (), In Annals of the Rheumatic Diseases, volume 79, . [bibtex] [url] [doi]
[33] Assessing the Direct Binding of Ark-Like E3 RING Ligases to Ubiquitin and Its Implication on Their Protein Interaction Network (), In Molecules, volume 25, . [bibtex] [url] [doi]
2019
[32] Quantification of DNA double-strand breaks using Geant4-DNA (), In Medical Physics, volume 46, . [bibtex] [url] [doi]
[31] Size-specific dose estimations for pediatric chest, abdomen/pelvis and head CT scans with the use of GATE (, , , , and ), In Physica Medica, volume 65, . [bibtex] [url] [doi]
[30] Delving into the amyloidogenic core of human leukocyte chemotactic factor 2 (, , , , and ), In Journal of Structural Biology, . [bibtex] [url] [doi]
[29] The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields (, and ), In Journal of Computational Chemistry, volume 40, . [bibtex] [url] [doi]
[28] Insights to the Binding of a Selective Adenosine A3 Receptor Antagonist Using Molecular Dynamic Simulations, MM-PBSA and MM-GBSA Free Energy Calculations, and Mutagenesis (, , , , , and ), In Journal of Chemical Information and Modeling, volume 59, . [bibtex] [url] [doi]
[27] Structural Characterization of Agonist Binding to an A3 Adenosine Receptor through Biomolecular Simulations and Mutagenesis Experiments (, , , , and ), In Journal of Medicinal Chemistry, volume 62, . [bibtex] [url] [doi]
[26] Structural Basis for Allosteric Regulation in the Major Antenna Trimer of Photosystem II (), In J. Phys. Chem. B, volume 123, . [bibtex] [url] [doi]
[25] Chimera patterns and subthreshold oscillations in two-dimensional networks of fractally coupled leaky integrate-and-fire neurons (), In PHYSICAL REVIEW E, volume 99, . [bibtex] [url] [doi]
[24] GPU Implementation of Neural-Network Simulations Based on Adaptive-Exponential Models (, , , , and ), In 2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE), . [bibtex] [url] [doi]
[23] Chimera States With 2D Deterministic and Random Fractal Connectivity (), In Front. Appl. Math. Stat., volume 5, . [bibtex] [url] [doi]
[22] Shear Rheology of Unentangled and Marginally Entangled Ring Polymer Melts from Large-Scale Nonequilibrium Molecular Dynamics Simulations (, , and ), In Polymers, volume 11, . [bibtex] [url] [doi]
[21] Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1) ( and ), In Journal of Computer-Aided Molecular Design, volume 33, . [bibtex] [url] [doi]
[20] Biodegradation of Cellulose in Laboratory-Scale Bioreactors: Experimental and Numerical Studies (, and ), In Journal of Polymers and the Environment, . [bibtex] [url] [doi]
2018
[19] αCGRP, another amyloidogenic member of the CGRP family (, , , , , and ), In Journal of Structural Biology, volume 203, . [bibtex] [url] [doi]
[18] Entropic fluctuations in DNA sequences (), In Physica A, volume 493, . [bibtex] [url] [doi]
[17] Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode (, , , , , , , and ), In Journal of Chemical Information and Modeling, volume 58, . [bibtex] [url] [doi]
[16] Three-dimensional chimera patterns in networks of spiking neuron oscillators (), In PHYSICAL REVIEW E, volume 97, . [bibtex] [url] [doi]
[15] Synchronization patterns in LIF neuron networks: mergingnonlocal and diagonal connectivity (), In Eur. Phys. J. B, volume 91, . [bibtex] [url] [doi]
[14] Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations. (, , and ), In Sci Rep, volume 8, . [bibtex] [url] [doi]
2017
[13] Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications (), In Scientific Reports, volume 7, . [bibtex] [url] [doi]
[12] Tracking the amyloidogenic core of IAPP amyloid fibrils: Insights from micro-Raman spectroscopy (, , , , , and ), In Journal of Structural Biology, volume 199, . [bibtex] [url] [doi]
[11] Chimera patterns in two-dimensional networks of coupled neurons (), In Physical Review E, volume 95, . [bibtex] [url] [doi]
[10] Chimeras in leaky integrate-and-fire neural networks:effects of reflecting connectivities (), In Eur. Phys. J. B, volume 90, . [bibtex] [url] [doi]
[9] Informed walks: whispering hints to gene hunters inside networks’ jungle (), In BMC systems biology, volume 11, . [bibtex] [url] [doi]
[8] Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2 (), In Journal of Computer-Aided Molecular Design, . [bibtex] [url] [doi]
2016
[7] DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators (, , , , , , , , , and ), In Nucleic Acids Research, volume 44, . [bibtex] [url] [doi]
[6] DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts (, , , , , , , , , and ), In Nucleic Acids Research, volume 44, . [bibtex] [url] [doi]
[5] DIANA-mirExTra v2.0: Uncovering microRNAs and transcription factors with crucial roles in NGS expression data (), In Nucleic Acids Research, volume 44, . [bibtex] [url] [doi]
[4] Multi-chimera states and transitions in the Leaky Integrate-and-Fire model with nonlocaland hierarchical connectivity (), In Eur. Phys. J. Special Topics, volume 225, . [bibtex] [url] [doi]
[3] A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils (), In Journal of Computer-Aided Molecular Design, volume 30, . [bibtex] [url] [doi]
[2] Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions (), In Journal of Computer-Aided Molecular Design, volume 30, . [bibtex] [url] [doi]
[1] Fractal and multifractal analysis of PET/CT images of metastatic melanoma before and after treatment with ipilimumab (), In EJNMMI Research, volume 6, . [bibtex] [url] [doi]