Publications
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Importance of Secondary Structure Data in Large Scale Protein Modeling using Low-Resolution SURPASS MethodMethods in Molecular Biology, in press , 2023.
Computational reconstruction of atomistic protein structures from coarse-grained modelsComputational and Structural Biotechnology Journal 18, 162-176, 2020.
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinementBriefings in Bioinformatics , 2020.
Flexible docking of peptides to proteins using CABS-dockProtein Science, 29:211-222 , 2020.
Phosphorylation of the N-terminal domain of ribosomal P-stalk protein uL10 governs its association with the ribosomeFEBS Letters 594, 3002-3019, 2020.
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex StructuresProtein Structure Prediction 273–287, 2020.
Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASSProtein Structure Prediction 337–353, 2020.
Explicit-Solvent All-Atom Molecular Dynamics of Peptide AggregationComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 541–558, 2019.
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsInternational Journal of Molecular Sciences 20, , 2019.
Protein Structure Prediction Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 27–59, 2019.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityMolecular Pharmaceutics 15, 3846-3859, 2018.
Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studiesEuropean Journal of Medicinal Chemistry 156, 631 - 640, 2018.
In silico analysis of cytochrome P450 monooxygenases in chronic granulomatous infectious fungus Sporothrix schenckii: Special focus on CYP51.Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1866(1), 166-177, 2018.
Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational studyThe Journal of Chemical Physics 148, 215106, 2018.
Protein–peptide docking using CABS-dock and contact informationBriefings in Bioinformatics bby080, 2018.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological ComplexesMolecules 23(8), 1995, 2018.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological ComplexesMolecules 23(8), 1995, 2018.
Synthesis, structural and antimicrobial studies of type II topoisomerase-targeted copper(II) complexes of 1,3-disubstituted thiourea ligandsJournal of Inorganic Biochemistry 182, 61 - 70, 2018.
Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motifBioMedical Engineering OnLine, 16:71 , 2017.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible modelPhysical Chemistry Chemical Physics 19, 2990-9, 2017.
Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible modelPhysical Chemistry Chemical Physics 19, 2990-9, 2017.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationBioMedical Engineering OnLine, 16:73 , 2017.