@article {Milik1997,
title = {Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinates},
journal = {Journal of Computational Chemistry},
volume = {18},
number = {1},
year = {1997},
month = {jan},
pages = {80{\textendash}85},
abstract = {A method for generating a full backbone protein structure from the coordinates of α-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the basic advantage of the presented method is its simplicity and speed. In a test run, the present program is shown to be much faster than existing database searching algorithms, and reconstructs about 8000 residues per second. Thus, it may be included as an independent procedure in protein folding algorithms to rapidly generate approximate coordinates of backbone atoms.},
issn = {0192-8651},
doi = {10.1002/(SICI)1096-987X(19970115)18:1<80::AID-JCC8>3.0.CO;2-W},
url = {http://doi.wiley.com/10.1002/(SICI)1096-987X(19970115)18:1<80::AID-JCC8>3.0.CO;2-W},
author = {Mariusz Milik and Andrzej Koli{\'n}ski and Jeffrey Skolnick}
}
@article {Milik1995,
title = {Neural network system for the evaluation of side-chain packing in protein structures},
journal = {Protein Engineering},
volume = {8},
number = {3},
year = {1995},
pages = {225{\textendash}236},
abstract = {An artificial neural network system is used for pattern recognition in protein side-chain-side-chain contact maps. A back-propagation network was trained on a set of patterns which are popular in side-chain contact maps of protein structures. Several neural network architectures and different training parameters were tested to decide on the best combination for the neural network. The resulting network can distinguish between original (from protein structures) and randomized patterns with an accuracy of 84.5\% and a Matthews{\textquoteright} coefficient of 0.72 for the testing set. Applications of this system for protein structure evaluation and refinement are also proposed. Examples include structures obtained after the application of molecular dynamics to crystal structures, structures obtained from X-ray crystallography at various stages of refinement, structures obtained from a de novo folding algorithm and deliberately misfolded structures.},
url = {http://peds.oxfordjournals.org/content/8/3/225.short},
author = {Mariusz Milik and Andrzej Koli{\'n}ski and Jeffrey Skolnick}
}
@article {Kolinski1995a,
title = {A reduced model of short range interactions in polypeptide chains},
journal = {Journal of Chemical Physics},
volume = {103},
number = {September},
year = {1995},
pages = {4312{\textendash}4323},
abstract = {A simple model of short range interactions is proposed for a reduced lattice representation of polypeptide conformation. The potential is derived on the basis of statistical regularities seen in the known crystal structures of globular proteins. This potential accounts for the generic stiffness of polypeptides, the correlation between peptide bond plates, and the sequence dependent correlations between consecutive segments of the Ca-trace. This model is used for simulation of the equilibrium and dynamic properties of polypeptides in the denatured state. It is shown that the proposed factorization of the local conformational propensities reproduces secondary structure tendencies encoded in the protein sequence. Possible applications for modeling of protein folding are briefly discussed. {\textcopyright} 1995 American Institute of Physics.},
url = {http://smartech.gatech.edu/handle/1853/27082},
author = {Andrzej Koli{\'n}ski and Mariusz Milik and Jakub Rycombel and Jeffrey Skolnick}
}
@article {Milik1992,
title = {Monte Carlo studies of an idealized model of a lipid-water system},
journal = {The Journal of Physical Chemistry},
volume = {96},
number = {10},
year = {1992},
month = {may},
pages = {4015{\textendash}4022},
abstract = {Employing Monte Carlo dynamics, the equilibrium and dynamic properties of lipid-water systems are studied in the context of a diamond lattice realization. The model faithfully describes the lipid molecule geometry and reproduces the essential physical properties of real membranes. These include the phase transitions from quasi-crystalline phase - liquid bilayer nonbilayer, quasi-hexagonal phase - dissolved liquid solution. Furthermore, the structure, ordering, and dynamics of the model liquid bilayer are in good accord with experiment, and the values of segmental ordering parameters are close to those obtained from NMR data. Due to the diamond lattice representation and a very efficient simulation algorithm, the intermediate distance scale dynamic features of the water-lipid system could be examined; these include lateral diffusion in the bilayer, the formation of a nonbilayer phase, the transbilayer diffusion of the lipid molecule, and the diffusion of a lipid molecule in the water phase. The present model can be also used to generate initial configurations for more detailed molecular (or Brownian) dynamics studies of lipid-water systems.},
issn = {0022-3654},
doi = {10.1021/j100189a020},
url = {http://pubs.acs.org/doi/abs/10.1021/j100189a020},
author = {Mariusz Milik and Jeffrey Skolnick and Andrzej Koli{\'n}ski}
}
@article {Kolinski1991,
title = {Static and dynamic properties of a new lattice model of polypeptide chains},
journal = {The Journal of Chemical Physics},
volume = {94},
number = {5},
year = {1991},
pages = {3978},
abstract = {The equilibrium and dynamic properties of a new lattice model of proteins are explored in the athermal limit. In this model, consecutive α-carbons of the model polypeptide are connected by vectors of the type ({\textpm}2,{\textpm}1,0). In all cases, the chains have a finite backbone thickness which is close to that present in real proteins. Three different polypeptides are examined: polyglycine, polyalanine, and polyleucine. In the latter two cases, the side chains (whose conformations are extracted from known protein crystal structures) are included. For the equilibrium chain dimensions, with increasing side chain bulkiness, the effective chain length is smaller. The calculations suggest that these model polypeptides are in the same universality class as other polymer models. One surprising result is that although polyalanine and polyleucine have chiral sidechains, they do not induce a corresponding handedness of the main chain. For both polyleucine and polyalanine, the scaling of the self-diffusion constant and the terminal relaxation time are consistent with Rouse dynamics of excluded volume chains. Polyglycine exhibits a slightly stronger chain length dependence for these properties. This results from a finite length effect due to moderately long lived, local self-entanglements arising from the thin effective cross section of the chain backbone.},
keywords = {Alanines, Chains, Glycine, Lattice Dynamics, Polypeptides, Proteins, Relaxation Time, Self-Diffusion},
issn = {00219606},
doi = {10.1063/1.460675},
url = {http://link.aip.org/link/JCPSA6/v94/i5/p3978/s1\&Agg=doi},
author = {Andrzej Koli{\'n}ski and Mariusz Milik and Jeffrey Skolnick}
}
@article {Milik1990,
title = {Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model},
journal = {The Journal of Chemical Physics},
volume = {93},
number = {6},
year = {1990},
pages = {4440{\textendash}4446},
abstract = {The static and dynamic properties of a dense system of flexible lattice chain molecules, one of whose ends is constrained to lie near an impenetrable interface, have been studied by means of the dynamic Monte Carlo method. It is found that increasing the surface density of the chains in the layer increases the orientational order. The value of the order parameter of the chain segments decreases with increasing distance from the interace. The short time dynamics of the model chains are similar to those observed in polymer melts. Then, there is a time regime of strongly hindered collective motion at intermediate distance scales. Finally, for distances greater than the chain dimensions, free lateral diffusion of the chains is recovered. It is shown that the model exhibits many features of the real systems such as detergents on a surface and lipid bilayers.},
keywords = {Bilayers, Chains, Constraints, Density, Interface Phenomena, Lipids, Liquid Structure, Membranes, Monte Carlo Method, Order Parameters, Orientation},
url = {http://link.aip.org/link/JCPSA6/v93/i6/p4440/s1},
author = {Mariusz Milik and Andrzej Koli{\'n}ski and Jeffrey Skolnick}
}