@article {554, title = {Computational reconstruction of atomistic protein structures from coarse-grained models}, journal = {Computational and Structural Biotechnology Journal}, volume = {18}, year = {2020}, pages = {162-176}, abstract = {Three-dimensional protein structures, whether determined experimentally or theoretically, are often too low resolution. In this mini-review, we outline the computational methods for protein structure reconstruction from incomplete coarse-grained to all atomistic models. Typical reconstruction schemes can be divided into four major steps. Usually, the first step is reconstruction of the protein backbone chain starting from the C-alpha trace. This is followed by side-chains rebuilding based on protein backbone geometry. Subsequently, hydrogen atoms can be reconstructed. Finally, the resulting all-atom models may require structure optimization. Many methods are available to perform each of these tasks. We discuss the available tools and their potential applications in integrative modeling pipelines that can transfer coarse-grained information from computational predictions, or experiment, to all atomistic structures.}, keywords = {coarse-grained modeling, protein modeling, protein reconstruction, structure prediction, structure refinement}, issn = {2001-0370}, doi = {https://doi.org/10.1016/j.csbj.2019.12.007}, url = {http://www.sciencedirect.com/science/article/pii/S2001037019305537}, author = {Aleksandra E. Badaczewska-Dawid and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @article {553, title = {Flexible docking of peptides to proteins using CABS-dock}, journal = {Protein Science, 29:211-222}, year = {2020}, abstract = {Molecular docking of peptides to proteins can be a useful tool in the exploration of the possible peptide binding sites and poses. CABS-dock is a method for protein{\textendash}peptide docking that features significant conformational flexibility of both the peptide and the protein molecules during the peptide search for a binding site. The CABS-dock has been made available as a web server and a standalone package. The web server is an easy to use tool with a simple web interface. The standalone package is a command-line program dedicated to professional users. It offers a number of advanced features, analysis tools and support for large-sized systems. In this article, we outline the current status of the CABS-dock method, its recent developments, applications, and challenges ahead.}, keywords = {molecular modeling, peptide drugs, peptide therapeutics, protein{\textendash}peptide complex, protein{\textendash}peptide interactions, structure prediction}, doi = {10.1002/pro.3771}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/pro.3771}, author = {Mateusz Kurcinski and Aleksandra E. Badaczewska-Dawid and Michal Kolinski and Andrzej Koli{\'n}ski and Sebastian Kmiecik} } @article {279, title = {Protein Folding with a Reduced Model and Inaccurate Short-Range Restraints}, journal = {Macromolecular Theory and Simulations}, volume = {14}, year = {2005}, pages = {444{\textendash}451}, abstract = {Summary: A reduced high-coordination lattice protein model and the Replica Exchange Monte Carlo sampling were employed in de novo folding simulations of a set of representative small proteins. Three distinct situations were analyzed. In the first series of simulations, the folding was controlled purely by the generic force field of the model. In the second, a bias was introduced towards the theoretically predicted secondary structure. Finally, we superimposed soft restraints towards the native-like local conformation of the backbone. The short-range restraints used in these simulations are based on approximate values of ϕ and ψ dihedral angles, which may simulate restraints derived from inaccurate experimental measurements. Incorporating such data into the reduced model required developing a procedure, which transforms the ϕ and ψ coordinates into coordinates of the protein alpha carbon trace. It has been shown that such limited data are sufficient for de novo determination of three-dimensional structures of small and topologically not too complex proteins.}, keywords = {dihedral angles, Monte Carlo simulation, Proteins, reduced models, structure prediction}, doi = {10.1002/mats.200500020}, url = {http://dx.doi.org/10.1002/mats.200500020}, author = {Dorota Plewczynska and Andrzej Koli{\'n}ski} } @article {Skolnick2000a, title = {Derivation of protein-specific pair potentials based on weak sequence fragment similarity}, journal = {Proteins: Structure, Function, Bioinformatics}, volume = {38}, year = {2000}, pages = {3{\textendash}16}, abstract = {A method is presented for the derivation of knowledge-based pair potentials that corrects for the various compositions of different proteins. The resulting statistical pair potential is more specific than that derived from previous approaches as assessed by gapless threading results. Additionally, a methodology is presented that interpolates between statistical potentials when no homologous examples to the protein of interest are in the structural database used to derive the potential, to a Go-like potential (in which native interactions are favorable and all nonnative interactions are not) when homologous proteins are present. For cases in which no protein exceeds 30\% sequence identity, pairs of weakly homologous interacting fragments are employed to enhance the specificity of the potential. In gapless threading, the mean z score increases from -10.4 for the best statistical pair potential to -12.8 when the local sequence similarity, fragment-based pair potentials are used. Examination of the ab initio structure prediction of four representative globular proteins consistently reveals a qualitative improvement in the yield of structures in the 4 to 6 A rmsd from native range when the fragment-based pair potential is used relative to that when the quasichemical pair potential is employed. This suggests that such protein-specific potentials provide a significant advantage relative to generic quasichemical potentials.}, keywords = {knowledge-based potentials, potential deriva-, Sequence Analysis, structure prediction, Tertiary, tion}, url = {http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0134(20000101)38:1\%3C3::AID-PROT2\%3E3.0.CO;2-S/full}, author = {Jeffrey Skolnick and Andrzej Koli{\'n}ski and Angel Ortiz} } @proceedings {Vieth1996a, title = {Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.}, journal = {Proceeding of I-st Pacific Symposium on Biocomputing}, year = {1996}, pages = {653{\textendash}662}, abstract = {A methodology for predicting coiled coil quaternary structure and for the dissection of the interactions responsible for the global fold is described. Application is made to the equilibrium between different oligomeric species of the wild type GCN4 leucine zipper and seven of its mutants that were studied by Harbury et al. Over the entire experimental concentration range, agreement with experiment is found in five cases, while in two other cases, agreement is found over a portion of the concentration range. These simulations suggest that the degree of chain association is determined by the balance between specific side chain packing preferences and the entropy reduction associated with side chain burial in higher order multimers.}, keywords = {be addressed, gcn4 leucine zipper, multimeric equilibrium, protein folding simulations, Quaternary, quaternary structure stability, structure prediction}, url = {http://ukpmc.ac.uk/abstract/MED/9390265}, author = {Michal Vieth and Andrzej Koli{\'n}ski and Charles L. Brooks III and Jeffrey Skolnick and L. Hunter and T. E. Klein} }