@article {265,
title = {CABS-fold: server for the de novo and consensus-based prediction of protein structure},
journal = {Nucleic Acids Research},
volume = {41},
year = {2013},
pages = {W406-W411},
abstract = {The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous CASP competitions (Critical Assessment of techniques for protein Structure Prediction) as one of the leading approaches for de novo\< and template-based modeling. Except for template data, fragmentary distance restraints can also be incorporated into the modeling process. The web server output is a coarse-grained trajectory of generated conformations, its Jmol representation and predicted models in all-atom resolution (together with accompanying analysis). CABS-fold can be freely accessed at http://biocomp.chem.uw.edu.pl/CABSfold},
keywords = {coarse-grained modeling, homology modeling, protein structure prediction},
doi = {10.1093/nar/gkt462},
author = {Maciej Blaszczyk and Michal Jamroz and Sebastian Kmiecik and Andrzej Koli{\'n}ski}
}
@article {Gniewek2011,
title = {How noise in force fields can affect the structural refinement of protein models?},
journal = {Proteins},
volume = {80},
year = {2012},
pages = {335{\textendash}341},
abstract = {Structural refinement of predicted models of biological macromolecules using atomistic or coarse-grained molecular force fields having various degree of error is investigated. The goal of this analysis is to estimate what is the probability for designing an effective structural refinement based on computations of conformational energies using force field, and starting from a structure predicted from the sequence (using template-based or template-free modeling), and refining it to bring the structure into closer proximity to the native state. It is widely believed that it should be possible to develop such a successful structure refinement algorithm by applying an iterative procedure with stochastic sampling and appropriate energy function, which assesses the quality (correctness) of protein decoys. Here, an analysis of noise in an artificially introduced scoring function is investigated for a model of an ideal sampling scheme, where the underlying distribution of RMSDs is assumed to be Gaussian. Sampling of the conformational space is performed by random generation of RMSD values. We demonstrate that whenever the random noise in a force field exceeds some level, it is impossible to obtain reliable structural refinement. The magnitude of the noise, above which a structural refinement, on average is impossible, depends strongly on the quality of sampling scheme and a size of the protein. Finally, possible strategies to overcome the intrinsic limitations in the force fields for impacting the development of successful refinement algorithms are discussed. Proteins 2011;. {\textcopyright} 2011 Wiley Periodicals, Inc.},
keywords = {force field, knowledge-based potentials, normal modes analysis, protein structure prediction, protein structure refinement, white noise},
issn = {1097-0134},
doi = {10.1002/prot.23240},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22223184},
author = {Pawel Gniewek and Andrzej Koli{\'n}ski and Robert L. Jernigan and Andrzej Kloczkowski}
}
@article {Pokarowski2007,
title = {Ideal amino acid exchange forms for approximating substitution matrices},
journal = {Proteins: Structure, Function, Bioinformatics},
volume = {69},
year = {2007},
pages = {379{\textendash}393},
abstract = {We have analyzed 29 published substitution matrices (SMs) and five statistical protein contact potentials (CPs) for comparison. We find that popular, {\textquoteleft}classical{\textquoteright} SMs obtained mainly from sequence alignments of globular proteins are mostly correlated by at least a value of 0.9. The BLOSUM62 is the central element of this group. A second group includes SMs derived from alignments of remote homologs or transmembrane proteins. These matrices correlate better with classical SMs (0.8) than among themselves (0.7). A third group consists of intermediate links between SMs and CPs - matrices and potentials that exhibit mutual correlations of at least 0.8. Next, we show that SMs can be approximated with a correlation of 0.9 by expressions c0 + xixj + yiyj + zizj, 1<= i, j <= 20, where c0 is a constant and the vectors (xi), (yi), (zi) correlate highly with hydrophobicity, molecular volume and coil preferences of amino acids, respectively. The present paper is the continuation of our work (Pokarowski et al., Proteins 2005;59:49{\textendash}57), where similar approximation were used to derive ideal amino acid interaction forms from CPs. Both approximations allow us to understand general trends in amino acid similarity and can help improve multiple sequence alignments using the fast Fourier transform (MAFFT), fast threading or another methods based on alignments of physicochemical profiles of protein sequences. The use of this approximation in sequence alignments instead of a classical SM yields results that differ by less than 5\%. Intermediate links between SMs and CPs, new formulas for approximating these matrices, and the highly significant dependence of classical SMs on coil preferences are new findings.},
keywords = {protein contact potentials, protein structure prediction, Sequence Alignment, substitution matrices},
doi = {10.1002/prot},
url = {http://onlinelibrary.wiley.com/doi/10.1002/prot.21509/full},
author = {Piotr Pokarowski and Andrzej Kloczkowski and Szymon Nowakowski and Maria Pokarowska and Robert L. Jernigan and Andrzej Koli{\'n}ski}
}
@article {Kmiecik2007,
title = {Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field},
journal = {BMC Structural Biology},
volume = {7},
year = {2007},
month = {jan},
pages = {43},
abstract = {BACKGROUND: Although experimental methods for determining protein structure are providing high resolution structures, they cannot keep the pace at which amino acid sequences are resolved on the scale of entire genomes. For a considerable fraction of proteins whose structures will not be determined experimentally, computational methods can provide valuable information. The value of structural models in biological research depends critically on their quality. Development of high-accuracy computational methods that reliably generate near-experimental quality structural models is an important, unsolved problem in the protein structure modeling.
RESULTS: Large sets of structural decoys have been generated using reduced conformational space protein modeling tool CABS. Subsequently, the reduced models were subject to all-atom reconstruction. Then, the resulting detailed models were energy-minimized using state-of-the-art all-atom force field, assuming fixed positions of the alpha carbons. It has been shown that a very short minimization leads to the proper ranking of the quality of the models (distance from the native structure), when the all-atom energy is used as the ranking criterion. Additionally, we performed test on medium and low accuracy decoys built via classical methods of comparative modeling. The test placed our model evaluation procedure among the state-of-the-art protein model assessment methods.
CONCLUSION: These test computations show that a large scale high resolution protein structure prediction is possible, not only for small but also for large protein domains, and that it should be based on a hierarchical approach to the modeling protocol. We employed Molecular Mechanics with fixed alpha carbons to rank-order the all-atom models built on the scaffolds of the reduced models. Our tests show that a physic-based approach, usually considered computationally too demanding for large-scale applications, can be effectively used in such studies.
},
keywords = {Computer Simulation, Models, Molecular, Protein Structure, protein structure prediction, Proteins, Proteins: chemistry, Secondary, Software, Tertiary, Time Factors},
isbn = {1472680774},
issn = {1472-6807},
doi = {10.1186/1472-6807-7-43},
url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933428\&tool=pmcentrez\&rendertype=abstract},
author = {Sebastian Kmiecik and Dominik Gront and Andrzej Koli{\'n}ski}
}
@article {Kolinski2001a,
title = {Structure of proteins: New approach to molecular modeling},
journal = {Polish Journal of Chemistry},
volume = {75},
year = {2001},
pages = {587{\textendash}599},
keywords = {comperative modeling, lattice protein models, loop modeling, Monte Carlo simulations, Protein Folding, protein structure prediction},
url = {http://baztech.icm.edu.pl/baztech/cgi-bin/btgetdoc.cgi?BUJ1-0017-0036},
author = {Andrzej Koli{\'n}ski and Piotr Rotkiewicz and Jeffrey Skolnick}
}
@article {Skolnick1999c,
title = {De novo predictions of the quaternary structure of leucine zippers and other coiled coils},
journal = {International Journal of Quantum Chemistry},
volume = {75},
year = {1999},
pages = {165{\textendash}176},
abstract = {Coiled coils possess a quaternary structure comprised of the side-by-side arrangement of a-helices. Due their inherent structural simplicity, they are ideal model systems for both theoretical and experimental studies. Among the coiled coils are the leucine zippers, which play an important role in the activation of DNA transcription. In contrast to the large amount of available experimental data, an overview of which is
presented, there are very few theoretical studies. To address this need, the status of existing theoretical approaches to predict coiled coil quaternary structure is described. Furthermore, to treat the conformational equilibria inherent in these systems, an extension of entropy sampling Monte Carlo simulations is developed that can treat multimers. Here, the approach is applied to GCN4 leucine zippers in the context of a reduced protein model. Not only is the native conformation successfully predicted, but the model also reproduces the experimentally observed helix content in the denatured state and the observed two-state thermodynamic behavior. Such two-state behavior arises from the dissociation of highly helical dimeric chains to form monomers of low, isolated chain helix content.},
keywords = {coiled coil, lattice protein models, Leucine Zippers, protein structure prediction, quaternary structure prediction},
url = {http://cssb.biology.gatech.edu/skolnick/publications/pdffiles/183.pdf},
author = {Jeffrey Skolnick and Andrzej Koli{\'n}ski and Debasisa Mohanty}
}
@article {Godzik1992a,
title = {A Topology Fingerprint Approach to the Inverse Protein Folding Problem},
journal = {Journal of Molecular Biology},
volume = {227},
year = {1992},
pages = {227{\textendash}238},
abstract = {We describe the most general solution to date of the problem of matching globular protein sequences to the appropriate three-dimensional structures. The screening template, against which sequences are tested, is provided by a protein "structural fingerprint" library based on the contact map and the buried/exposed pattern of residues. Then, a lattice Monte Carlo algorithm validates or dismisses the stability of the proposed fold. Examples of known structural similarities between proteins having weakly or unrelated sequences such as the globins and phycocyanins, the eight-member alpha/beta fold of triose phosphate isomerase and even a close structural equivalence between azurin and immunoglobulins are found.},
keywords = {globin-phycocyanin similarity, plastocyanin-azurin-immunoglobulin similarity, protein stability, protein structure prediction, TIM barrel similarity},
doi = {10.1016/0022-2836(92)90693-E},
url = {http://dx.doi.org/10.1016/0022-2836(92)90693-E},
author = {Adam Godzik and Jeffrey Skolnick and Andrzej Koli{\'n}ski}
}