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The PentUnFOLD algorithm as a tool to distinguish the dark and the light sides of the structural instability of proteins

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AMINO ACIDS 2022年第8期54卷 1155-1171页

作者： Poboinev, Victor Vitoldovich Khrustalev, Vladislav Victorovich Khrustaleva, Tatyana Aleksandrovna Kasko, Tihon Evgenyevich Popkov, Vadim Dmitrievich Belarusian State Med Univ Dept Gen Chem Dzerzinskogo 83 Minsk BELARUS Natl Acad Sci Belarus Biochem Grp Inst Physiol Multidisciplinary Diagnost Lab Minsk BELARUS

Intrinsically disordered proteins are frequently involved in important regulatory processes in the cell thanks to their ability to bind several different targets performing sometimes even opposite functions. The PentUnFOLD algorithm is a physicochemical method that is based on new propensity scales for disordered, nonstable and stable elements of secondary structure and on the counting of stabilizing and destabilizing intraprotein contacts. Unlike other methods, it works with a PDB file, and it can determine not only those fragments of alpha helices, beta strands, and random coils that can turn into disordered state (the "dark" side of the disorder), but also nonstable regions of alpha helices and beta strands which are able to turn into random coils (the "light" side), and vice versa (H <-> C, E <-> C). The scales have been obtained from structural data on disordered regions from the middle parts of amino acid sequences only, and not on their expectedly disordered N- and C-termini. Among other tendencies we have found that regions of both alpha helices and beta strands that can turn into the disordered state are relatively enriched in residues of Ala, Met, Asp, and Lys, while regions of both alpha helices and beta strands that can turn into random coil are relatively enriched in hydrophilic residues, and Cys, Pro, and Gly. Moreover, PentUnFOLD has the option to determine the effect of secondary structure transitions on the stability of a given region of a protein.

关键词： Intrinsically disordered proteins Structural shifts computer algorithm Amino acid substitution Human prion protein

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Importance of standardized assessment of late gadolinium enhancement for quantification of infarct size by cardiac magnetic resonance: implications for comparison with electrocardiogram

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JOURNAL OF ELECTROCARDIOLOGY 2011年第5期44卷 538-543页

作者： Welinder, Annika Hakacova, Nina Martin, Thomas Engblom, Henrik Lund Univ Dept Clin Physiol SE-22185 Lund Sweden Lund Univ Dept Pediat Cardiol SE-22185 Lund Sweden Skane Univ Hosp SE-22185 Lund Sweden Ninewells Hosp Dept Cardiol Dundee DD1 9SY Scotland

Background: Cardiac magnetic resonance (CMR) is currently considered the reference standard for in vivo assessment of myocardial infarction (MI). There is, however, no international consensus on how MI quantification from CMR should be performed. The aim of this study was to test how previously published manual quantification of MI using CMR images compares with MI quantification using a semiautomated, validated method and how this impacts the relationship with MI size estimated by 12-lead electrocardiogram (ECG). Methods: Twenty-five patients, from a previously published cohort, were included in the study. All patients had presented with clinical signs of acute coronary syndrome 6 to 12 months before undergoing a CMR examination. The patients had a standard 12-lead ECG recorded at the time of the CMR examination. The previously reported manually quantified MI size was compared with MI size determined using a semiautomated method validated by computer phantom data, experimental in vivo and ex vivo data, and patient data. The MI sizes from the 2 CMR approaches were then compared with the ECG-estimated MI size. Results: There was a strong correlation between MI size determined with the 2 CMR methods (r(2) = 0.94, P < .001). There was, however, a systematic overestimation of MI size of approximately 50% by the previously published manually quantified MI size compared with the semiautomated method. This affected the comparison with estimated MI size by ECG, which showed a significant underestimation of MI size compared with manual CMR measurements, but no bias compared with the semiautomated CMR method. Conclusions: Manual quantification of MI size by CMR can differ significantly from semiautomated, validated methods taking partial volume effects into account and can lead to erroneous conclusions when compared with ECG. (C) 2011 Elsevier Inc. All rights reserved.

关键词： Myocardial infarction Cardiac magnetic resonance Selvester QRS scoring computer algorithm

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ST/HR hysteresis - Exercise and recovery phase ST depression/heart rate analysis of the exercise ECG

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JOURNAL OF ELECTROCARDIOLOGY 1999年 32卷 198-204页

作者： Lehtinen, R Tampere Univ Technol Ragnar Granit Inst FIN-33101 Tampere Finland Acad Finland Helsinki Finland

ST segment depression/heart rate (ST/HR) hysteresis is a recently introduced novel computer method for integrating the exercise and recovery phase ST/HR analysis for improved detection of coronary artery disease (CAD). It is a continuous diagnostic variable that extracts the prevailing direction and average magnitude of the hysteresis in ST depression against HR during the first 3 consecutive minutes of postexercise recovery. This article reviews the development and evaluation of this new method in a clinical population of 347 patients referred for a routine bicycle exercise electrocardiographic (ECG) test at Tampere University Hospital, Finland. Of these patients, 127 had angiographically proven CAD, whereas 13 had no CAD according to angiography, 18 had no perfusion defect according to Tc-99m-sestamibi myocardial imaging and single photon emission computed tomography, and 189 were clinically normal with respect to cardiac diseases. For each patient, the values for ST/HR hysteresis, ST/HR index, end-exercise ST depression, and recovery ST depression were determined for each lead of the Mason-Likar modification of the standard 12-lead exercise ECG and maximum value from the lead system (aVL, aVR, and V-1 excluded). The area under the receiver operating characteristics curve (ie, the discriminative capacity) of the ST/HR hysteresis was 89%, which was significantly larger than that of the end-exercise ST depression (76%, P < .0001), recovery ST depression (84%, P = .0063) or ST/HR index (83%, P = .0023), indicating the best diagnostic performance of the ST/HR hysteresis ill detection of CAD regardless of the partition value selection. Furthermore, the superior diagnostic performance of the method was relatively insensitive to the ST segment measurement point or to the ECG lead selection. These results suggest that the ST/HR hysteresis improves the clinical utility of the exercise ECG test in detection of CAD.

关键词： ST/HR analysis computer algorithm exercise ECG coronary artery disease

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A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays

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PROTEINS-STRUCTURE FUNCTION AND GENETICS 2000年第3期38卷 273-287页

作者： Glick, M Goldblum, A Hebrew Univ Jerusalem Sch Pharm Dept Pharmaceut Chem IL-91120 Jerusalem Israel

A novel automated method for the optimal placement of polar hydrogens in a protein structure is presented. The algorithm adds initially, to a protein data bank file of the protein, nonrotatable hydrogens such as peptide backbone hydrogens according to geometric considerations, Then, water protons and polar side chain protons of lysine, serine, threonine, tyrosine, aspartic acid, glutamic acid, and the C and N termini of a protein are added according to energy considerations. A unique stochastic approach has been developed to overcome a combinatorial explosion in the search for the lowest energy structure. First, the system is divided into ensembles. Each ensemble is treated separately: N conformations are sampled at random, their energies computed, whereas common components of high-energy combinations are gathered on one hand, and low-energy combinations on the other. Components that yield only high-energy conformations and do not contribute to any low energies are excluded, This is reiterated while the total amount of combinations is decreased along the iterative process. When the total number of combinations is lower than a user defined threshold, all remaining combinations are evaluated by exhaustive search. Energy evaluations use nonbonding energy expressions alone. The program was tested on five high-resolution crystal structures: bovine pancreatic trypsin inhibitor (Brookhaven Protein Data Bank file 5PTI), RNase-A (5RSA), trypsin (1NTP), and carbon monoxymyoglobin (2MB5), for which neutron diffraction structures are available, as well as phosphate binding protein (1IXH) for which very high resolution X-ray crystallography was used. The low RMS values prove the efficiency of this algorithm as a tool for positioning protons in proteins. It may be used for other biological structures. (C) 2000 Wiley-Liss, Inc.

关键词： polar hydrogens hydrogen bond computer algorithm combinatorial explosion minimization crystal structure

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algorithmS TO SEARCH FOR OPTIMAL ROW-AND-COLUMN DESIGNS

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JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY 1979年第2期41卷 210-216页

作者： JONES, B University of Kent at Canterbury

An algorithm is described that searches for the row and column components to form an optimal row-and-column design. It is based on one given previously (Jones, 1976) for block designs. A second algorithm is described for combining the components to form a row-and-column design. Both algorithms are suitable for use on a computer. The optimality criterion used allows treatment contrasts to be weighted. Examples of the use of the algorithms are given and their performance is discussed.

关键词： column component computer algorithm efficiency optimal design optimality criterion row component row-and-column design trace minimization weighted covariance matrix of treatment contrasts

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An Iterative computer Procedure for Mixed-Up Values in Experiments

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Journal of the Royal Statistical Society: Series C (Applied Statistics) 1974年第1期23卷 73-74页

作者： D. A. Preece J. C. Gower University of Kent at Canterbury Rothamsted Experimental Station Harpenden Hertfordshire

Healy and Westmacott (1956) gave an iterative computer procedure for dealing with missing values in experiments. Pearce (1965) and others discussed an improved version of the procedure. This improved version is now ex... 详细信息

关键词： computer algorithm iterative procedure missing values mixed-up values

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Some Identities related to Restricted Lattice Paths 9

Some Identities related to Restricted Lattice Paths

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9th International Symposium on Computational Intelligence and Design (ISCID)

作者： Lv, Lun Liu, Zhihong Hebei Univ Sci & Technol Sch Sci Shijiazhuang 050018 Peoples R China

Notations and techniques from discrete mathematics play an important role in computer science. In this paper, by applying the concatenation of some restricted lattice paths, we derive the combinatorial interpretations... 详细信息

ISBN: (纸本)9781509035588

关键词： computer algorithm Catalan numbers restricted lattice paths

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On Coxeter type classification of loop-free edge-bipartite graphs and matrix morsifications

On Coxeter type classification of loop-free edge-bipartite g...

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15th International Symposium on Symbolic and Numeric algorithms for Scientific Computing (SYNASC)

作者： Bocian, Rafal Felisiak, Mariusz Simson, Daniel Nicolaus Copernicus Univ Fac Math & Comp Sci Torun Poland

ISBN: (纸本)9781479930357

We continue and complete a Coxeter spectral study (presented in our talk given in SYNASC11 and SYNASC12) of the root systems in the sense of Bourbaki, the mesh geometries Gamma(R-Delta, Phi(A)) of roots of Delta in the sense of [J. Pure Appl. Algebra, 215 (2010), 13-34], and matrix morsifications A is an element of Mor(Delta), for simply laced Dynkin diagrams Delta is an element of {A(n), D-n, E-6, E-7, E-8}. Here we report on algorithmic and morsification technique for the Coxeter spectral analysis of connected loop-free edge-bipartite graphs Delta with n >= 2 vertices by means of the Coxeter matrix Cox(Delta) is an element of M-n(Z), the Coxeter spectrum specc(Delta), and an inflation algorithm associating to any connected loop-free positive bigraph Delta a simply laced Dynkin diagram D Delta, and defining a Z-congruence of the symmetric Gram matrices G(Delta) and G(D Delta). We also present a computer aided technique that allows us to construct a Z-congruence of the non-symmetric Gram matrices G(Delta) and. G Delta', if the Coxeter spectra specc(Delta) and specc(Delta)' coincide. A complete Coxeter spectral classification of positive edge-bipartite graphs Delta of Coxeter-Dynkin types D Delta is an element of {A(n), D-n, E-6, E-7}, with n <= 7, is obtained by a reduction to computer calculation of Gl(n, Z)(D Delta)-orbits in the set Mor(D Delta), where Gl(n, Z)(D Delta) is the isotropy group of the Dynkin diagram D Delta.

关键词： computer algorithm Coxeter polynomial Coxeter spectrum Dynkin diagram Edge-bipartite graph Matrix morsification Mesh geometry of roots Bipartite graph loop-free matrices Root systems type classification Speaking

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Preprocessing Large Data Sets by the Use of Quick Sort algorithm 8th

Preprocessing Large Data Sets by the Use of Quick Sort Algor...

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8th International Conference on Knowledge, Information, and Creativity Support Systems (KICSS)

作者： Wozniak, Marcin Marszalek, Zbigniew Gabryel, Marcin Nowicki, Robert K. Silesian Tech Univ Inst Math Ul Kaszubska 23 PL-44100 Gliwice Poland Czestochowa Tech Univ Inst Computat Intelligence Al Armii Krajowej 36 PL-42200 Czestochowa Poland

ISBN: (纸本)9783319190907;9783319190891

Sorting algorithms help to organize large amounts of data. However, sometimes it is not easy to determine the correct order in large data sets, especially if there are special poses on the input. It often complicates sorting, results in time prolongation or even unable sorting. In such situations, the most common method is to perform sorting process to reshuffled input data or change the algorithm. In this paper, the authors examined quick sort algorithm in two versions for large data sets. The algorithms have been examined in performance tests and the results helped to compare them.

关键词： computer algorithm Data sorting Data mining Analysis of computer algorithms

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computer Simulations in solid-state NMR.: II.: Implementations for static and rotating samples

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CONCEPTS IN MAGNETIC RESONANCE PART A 2003年第1期18A卷 1-23页

作者： Edén, M Stockholm Univ Arrhenius Lab Div Phys Chem SE-10691 Stockholm Sweden

In the first article in this series (Concepts Magn Reson Part A 17A: 117-154, 2003), we outlined a theoretical framework for calculating solid-state NMR time-domain signals and frequency-domain spectra. This article explains how the theory may be implemented on a computer for simulating NMR signals from a single crystal in a static and rotating sample. The general building blocks of a computer program for numerically calculating NMR signals are discussed. computer algorithms for carrying out the simulations are presented as flowcharts and implemented in C/C++ code. (C) 2003 Wiley Periodicals, Inc.

关键词： solid-state NMR numerical simulation computer algorithm static solids magic-angle-spinning dynamically inhomogeneous Hamiltonian spherical tensor

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