Interactive Navigational Structures

Krzysztof Czaplewski,Zbigniew Wisniewski 한국항해항만학회 2006 한국항해항만학회 학술대회논문집 Vol.1 No.-

Satellite systems for objects positioning appeared indispensable for performing basic tasks of maritime navigation. Navigation, understood as safe and effective conducting a vehicle from one point to another, within a specific physical-geographical environment. [Kopacz, Urbanski, 1998]. However, the systems have not solved the problem of accessibility to reliable and highly accurate information about a position of an object, especially if surveyed toward on-shore navigational signs or in sea depth. And it's of considerable significance for many navigational tasks, carried out within the frameworks of special works performance and submarine navigation. In addition, positioning precisely the objects other than vessels, while executing hydrographical works, is not always possible with a use of any satellite system. Difficulties with GPS application show up also while positioning such off-lying dangers as wrecks, underwater and aquatic rocks also other natural and artificial obstacles. It is caused by impossibility of surveyors approaching directly any such object while its positioning. Moreover, determination of vessels positions mutually (mutual geometrical relations) by teams carrying out one common tasks at sea, demands applying the navigational techniques other than the satellite ones. Vessels' staying precisely on specified positions is of special importance in, among the others, the cases as follows: - surveying vessels while carrying out bathymetric works, wire dragging; - special tasks watercraft in course of carrying out scientific research, sea bottom exploration etc. The problems are essential for maritime economy and the Country defence readiness. Resolving them requires applying not only the satellite navigation methods, but also the terrestrial ones. The condition for implementation of the geo-navigation methods is at present the methods development both: in aspects of their techniques and technologies as well as survey data evaluation. Now, the classical geo-navigation comprises procedures, which meet out-of-date accuracy standards. To enable meeting the present-day requirements, the methods should refer to well-recognised and still developed methods of contemporary geodesy. Moreover, in a time of computerization and automation of calculating, it is feasible to create also such software, which could be applied in the integrated navigational systems, allowing carrying out navigation, provided with combinatory systems as well as with the new positioning methods. Whereas, as regards data evaluation, there should be applied the most advanced achievements in that subject; first of all the newest, although theoretically well-recognised estimation methods, including M -estimation [Hampel et al. 1986; Wisniewski 2005; Yang 1997; Yang et al. 1999]. Such approach to the problem consisting in positioning a vehicle in motion and solid objects under observation enables an opportunity of creating dynamic and interactive navigational structures . The main subject of the theoretical suggested in this paper is the Interactive Navigational Structure. In this paper, the Structure will stand for the existing navigational signs systems, any observed solid objects and also vehicles, carrying out navigation (submarines inclusive), which, owing to mutual dependencies, (geometrical and physical) allow to determine coordinates of this new Structure's elements and to correct the already known coordinates of other elements.

An efficient molecular docking using conformational space annealing

Lee, Kyoungrim,Czaplewski, Cezary,Kim, Seung-Yeon,Lee, Jooyoung John Wiley Sons, Inc. 2005 Journal of computational chemistry Vol.26 No.1

<P>Molecular docking falls into the general category of global optimization problems because its main purpose is to find the most stable complex consisting of a receptor and its ligand. Conformational space annealing (CSA), a powerful global optimization method, is incorporated with the Tinker molecular modeling package to perform molecular docking simulations of six receptor–ligand complexes (3PTB, 1ULB, 2CPP, 1STP, 3CPA, and 1PPH) from the Protein Data Bank. In parallel, Monte Carlo with the minimization (MCM) method is also incorporated into the Tinker package for comparison. The energy function, consisting of electrostatic interactions, van der Waals interactions, and torsional energy terms, is calculated using the AMBER94 all-atom empirical force field. Rigid docking simulations for all six complexes and flexible docking simulations for three complexes (1STP, 3CPA, and 1PPH) are carried out using the CSA and the MCM methods. The simulation results show that the docking procedures using the CSA method generally find the most stable complexes as well as the native-like complexes more efficiently and accurately than those using the MCM, demonstrating that CSA is a promising search method for molecular docking problems. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 78–87, 2005</P> <B>Graphic Abstract</B> <img src='wiley_img/01928651-2005-26-1-JCC20147-gra001.gif' alt='wiley_img/01928651-2005-26-1-JCC20147-gra001'>

A Maximum-Likelihood Approach to Force-Field Calibration

Zaborowski, Bartłomiej,Jagieła, Dawid,Czaplewski, Cezary,Hałabis, Anna,Lewandowska, Agnieszka,Ż,mudziń,ska, Wioletta,Ołdziej, Stanisław,Karczyń,ska, Agnieszka,Omieczynski, Christian American Chemical Society 2015 JOURNAL OF CHEMICAL INFORMATION AND MODELING Vol.55 No.9

<P>A new approach to the calibration of the force fields is proposed, in which the force-field parameters are obtained by maximum-likelihood fitting of the calculated conformational ensembles to the experimental ensembles of training system(s). The maximum-likelihood function is composed of logarithms of the Boltzmann probabilities of the experimental conformations, calculated with the current energy function. Because the theoretical distribution is given in the form of the simulated conformations only, the contributions from all of the simulated conformations, with Gaussian weights in the distances from a given experimental conformation, are added to give the contribution to the target function from this conformation. In contrast to earlier methods for force-field calibration, the approach does not suffer from the arbitrariness of dividing the decoy set into native-like and non-native structures; however, if such a division is made instead of using Gaussian weights, application of the maximum-likelihood method results in the well-known energy-gap maximization. The computational procedure consists of cycles of decoy generation and maximum-likelihood-function optimization, which are iterated until convergence is reached. The method was tested with Gaussian distributions and then applied to the physics-based coarse-grained UNRES force field for proteins. The NMR structures of the tryptophan cage, a small α-helical protein, determined at three temperatures (<I>T</I> = 280, 305, and 313 K) by Hałabis et al. (J. Phys. Chem. B<x> </x>2012<x>, </x>116<x>, </x>6898−<lpage>6907</lpage>), were used. Multiplexed replica-exchange molecular dynamics was used to generate the decoys. The iterative procedure exhibited steady convergence. Three variants of optimization were tried: optimization of the energy-term weights alone and use of the experimental ensemble of the folded protein only at <I>T</I> = 280 K (run 1); optimization of the energy-term weights and use of experimental ensembles at all three temperatures (run 2); and optimization of the energy-term weights and the coefficients of the torsional and multibody energy terms and use of experimental ensembles at all three temperatures (run 3). The force fields were subsequently tested with a set of 14 α-helical and two α + β proteins. Optimization run 1 resulted in better agreement with the experimental ensemble at <I>T</I> = 280 K compared with optimization run 2 and in comparable performance on the test set but poorer agreement of the calculated folding temperature with the experimental folding temperature. Optimization run 3 resulted in the best fit of the calculated ensembles to the experimental ones for the tryptophan cage but in much poorer performance on the training set, suggesting that use of a small α-helical protein for extensive force-field calibration resulted in overfitting of the data for this protein at the expense of transferability. The optimized force field resulting from run 2 was found to fold 13 of the 14 tested α-helical proteins and one small α + β protein with the correct topologies; the average structures of 10 of them were predicted with accuracies of about 5 Å C<SUP>α</SUP> root-mean-square deviation or better. Test simulations with an additional set of 12 α-helical proteins demonstrated that this force field performed better on α-helical proteins than the previous parametrizations of UNRES. The proposed approach is applicable to any problem of maximum-likelihood parameter estimation when the contributions to the maximum-likelihood function cannot be evaluated at the experimental points and the dimension of the configurational space is too high to construct histograms of the experimental distributions.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/2015/jcisd8.2015.55.issue-9/acs.jcim.5b00395/production/images/me

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-

Liwo, Adam,Sieradzan, Adam K.,Lipska, Agnieszka G.,Czaplewski, Cezary,Joung, InSuk,Ż,mudziń,ska, Wioletta,Hałabis, Anna,Ołdziej, Stanisław American Institute of Physics 2019 The Journal of chemical physics Vol.150 No.15

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field

Krupa, Paweł,Mozolewska, Magdalena A.,Joo, Keehyoung,Lee, Jooyoung,Czaplewski, Cezary,Liwo, Adam American Chemical Society 2015 Journal of chemical information and modeling Vol.55 No.6

<P>A new approach to the prediction of protein structures that uses distance and backbone virtual-bond dihedral angle restraints derived from template-based models and simulations with the united residue (UNRES) force field is proposed. The approach combines the accuracy and reliability of template-based methods for the segments of the target sequence with high similarity to those having known structures with the ability of UNRES to pack the domains correctly. Multiplexed replica-exchange molecular dynamics with restraints derived from template-based models of a given target, in which each restraint is weighted according to the accuracy of the prediction of the corresponding section of the molecule, is used to search the conformational space, and the weighted histogram analysis method and cluster analysis are applied to determine the families of the most probable conformations, from which candidate predictions are selected. To test the capability of the method to recover template-based models from restraints, five single-domain proteins with structures that have been well-predicted by template-based methods were used; it was found that the resulting structures were of the same quality as the best of the original models. To assess whether the new approach can improve template-based predictions with incorrectly predicted domain packing, four such targets were selected from the CASP10 targets; for three of them the new approach resulted in significantly better predictions compared with the original template-based models. The new approach can be used to predict the structures of proteins for which good templates can be found for sections of the sequence or an overall good template can be found for the entire sequence but the prediction quality is remarkably weaker in putative domain-linker regions.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jcisd8/2015/jcisd8.2015.55.issue-6/acs.jcim.5b00117/production/images/medium/ci-2015-00117f_0010.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ci5b00117'>ACS Electronic Supporting Info</A></P>

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field

Mozolewska, Magdalena A.,Krupa, Paweł,Zaborowski, Bartłomiej,Liwo, Adam,Lee, Jooyoung,Joo, Keehyoung,Czaplewski, Cezary American Chemical Society 2016 JOURNAL OF CHEMICAL INFORMATION AND MODELING Vol.56 No.11

<P>Recently, we developed a new approach to protein-structure prediction, which combines template-based modeling with the physics-based coarse-grained UNited RESidue (UNRES) force field. In this approach, restrained multiplexed replica exchange molecular dynamics simulations with UNRES, with the C-alpha-distance and virtual-bond-dihedral angle restraints derived from knowledge-based models are carried out. In this work, we report a test of this approach in the 11th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP11), in which we used the template-based models from early-stage predictions by the LEE group CASP11 server (group 038, called 'nns'), and further improvement of the method. The quality of the models obtained in CASP11 was better than that resulting from unrestrained UNRES simulations; however, the obtained models were generally worse than the final nns models. Calculations with the final nns models, performed after CASP11, resulted in substantial improvement, especially for multi-domain proteins. Based on these results, we modified the procedure by deriving restraints from models from multiple servers, in this study the four top-performing servers in CASP11 (nns, BAKER-ROSETTASERVER, Zhang-server, and QUARK), and implementing either all restraints or only the restraints on the fragments that appear similar in the majority of models (the consensus fragments), outlier models discarded. Tests with 29 CASP11 human-prediction targets with length less than 400 amino-acid residues demonstrated that the consensus-fragment approach gave better results, i.e., lower a-carbon root-mean-square deviation from the experimental structures, higher template modeling score, and global distance test total score values than the best of the parent server models. Apart from global improvement (repacking and improving the orientation of domains and other substructures), improvement was also reached for template-based modeling targets, indicating that the approach has refinement capacity. Therefore, the consensus-fragment analysis is able to remove lower-quality models and poor-quality parts of the models without knowing the experimental structure.</P>