Andrzej Kolinski
Primary tabs
Pages
Importance of Secondary Structure Data in Large Scale Protein Modeling using Low-Resolution SURPASS MethodMethods in Molecular Biology, in press , 2023.
Integrative modeling of diverse protein-peptide systems using CABS-dockPLoS Comput Biol. 5;19(7), e1011275, 2023.
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.
Flexible docking of peptides to proteins using CABS-dockProtein Science, 29:211-222 , 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 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.
Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold AssemblyJournal of Chemical Theory and Computation 14 (4), 2277–2287, 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.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological ComplexesMolecules 23(8), 1995, 2018.
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction ToolMethods in Molecular Biology 1484, 7-24, 2017.
Highly flexible protein-peptide docking using CABS-dockMethods in Molecular Biology 1561, 69-94, 2017.
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.
One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS ModelMethods in Molecular Biology 1484, 83-113, 2017.