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Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubilityNucleic Acids Research 47, W300-W307, 2019.
CABS-flex 2.0: a web server for fast simulations of flexibility of protein structuresNucleic Acids Research, gky356 , 2018.
Aggrescan3D standalone package for structure-based prediction of protein aggregation propertiesBioinformatics btz143, , 2019.
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding siteNucleic Acids Research 43 (W1), W419-W424, 2015.
A protocol for CABS-dock protein–peptide docking driven by side-chain contact informationBioMedical Engineering OnLine, 16:73 , 2017.
Mechanism of Folding and Binding of an Intrinsically Disordered Protein as Revealed by Ab Initio SimulationsJournal of Chemical Theory and Computation 10, 2224–2231, 2014.
CABS-flex standalone: a simulation environment for fast modeling of protein flexibilityBioinformatics bty685, 2018.
Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequencesThe Journal of Steroid Biochemistry and Molecular Biology 103, 357–60, 2007.
Theoretical study of molecular mechanism of binding TRAP220 coactivator to Retinoid X Receptor alpha, activated by 9-cis retinoic acidThe Journal of Steroid Biochemistry and Molecular Biology 121, 124–9, 2010.
Flexible protein-peptide docking using CABS-dock with knowledge about the binding siteProceedings of the International Work-conference on Bioinformatics and BIOmedical engineering (IWWBIO) in Granada, Spain, 195-201, arXiv:1605.09269 , 2016.
Molar Excess Enthalpies and Volumes of Mixtures of 2,4,6-trimethylopyridyne with some Aliphatic AlcoholsPolish Journal of Chemistry 54, 1995, 1980.
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.
A numerical investigation into possible mechanisms by that the A629P mutant of ATP7A causes Menkes DiseasePhys Chem Chem Phys 12, 11390-7, 2010.
The GOR Method of Protein Secondary Structure Prediction, and its Application as Protein Aggregation Prediction ToolMethods in Molecular Biology 1484, 7-24, 2017.
Role of Resultant Dipole Moment in Mechanical Dissociation of Biological ComplexesMolecules 23(8), 1995, 2018.
Velocity scaling for optimizing replica exchange molecular dynamicsThe Journal of Chemical Physics 134, 044124, 2011.
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.
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.
Folding Simulations of the A and B Domains of Protein GThe Journal of Physical Chemistry B 116, 6645-6653, 2012.
Mechanical unfolding of DDFLN4 studied by the coarse-grained knowledge-based CABS modelTASK Quarterly 18, 373–378, 2014.