Sebastian Kmiecik
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Molecular Dynamics Scoring of Protein–Peptide Models Derived from Coarse-Grained DockingMolecules 26(11), , 2021.
Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulationsInternational Journal of Molecular Sciences 22(14), , 2021.
Computational reconstruction of atomistic protein structures from coarse-grained modelsComputational and Structural Biotechnology Journal 18, 162-176, 2020.
Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulationInternational Journal of Biological Macromolecules 149, 1151-1160, 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.
Isoxazole-containing 5′ mRNA cap analogues as inhibitors of the translation initiation processBioorganic Chemistry 96, 103583, 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.
Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubilityNucleic Acids Research 47, W300-W307, 2019.
Aggrescan3D standalone package for structure-based prediction of protein aggregation propertiesBioinformatics btz143, , 2019.
Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force FieldsInternational Journal of Molecular Sciences 20, , 2019.
Protein Dynamics Simulations Using Coarse-Grained ModelsComputational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes: From Bioinformatics to Molecular Quantum Mechanics 61–87, 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.
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresNucleic Acids Research, gky356 , 2018.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityBioinformatics bty685, 2018.
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.
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.
Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network ModelsInternational Journal of Molecular Sciences 19, , 2018.
Protein–peptide docking using CABS-dock and contact informationBriefings in Bioinformatics bby080, 2018.