Analyzing functional similarity of protein sequences with discrete wavelet transform

This paper applies discrete wavelet transform (DWT) with various protein substitution models to find functional similarity of proteins with low identity. A new metric, 'S' function, based on the DWT is proposed to measure the pair-wise similarity. We also develop a segmentation technique, combined with DWT, to handle long protein sequences. The results are compared with those using the pair-wise alignment and PSI-BLAST.     

Pattern recognition methods for protein functional site prediction

Protein functional site prediction is closely related to drug design, hence to public health. In order to save the cost and the time spent on identifying the functional sites in sequenced proteins in biology laboratory, computer programs have been widely used for decades. Many of them are implemented using the state-of-the-art pattern recognition algorithms, including decision trees, neural networks and support vector machines. Although the success of this effort has been obvious, advanced and new algorithms are still under development for addressing some difficult issues. This review will go through the major stages in developing pattern recognition algorithms for protein functional site prediction and outline the future research directions in this important area.     

Monomer-scale design of functional protein polymers using consensus repeat sequences

Protein-based polymers possess chemically defined sequences that can encode diverse properties and functions into a new class of biopolymeric materials. However, sequence variation that emerges from evolution can obscure the sequence–function relationships of naturally derived polymers. One strategy to clarify these relationships is to identify common sequences between proteins with similar functions. These conserved sequences often emerge from repeat proteins, and “consensus repeat sequences” provide a convenient platform for systematic investigations of biopolymer sequence–property relationships. In this review, we highlight recent approaches to engineer tunable polymeric materials using monomer-scale design of consensus repeat proteins. We explore established and emerging protein-based materials with mechanical resilience, thermodynamic phase behavior, chemical responsiveness, biomolecular transport, and hierarchical structure. Overall, recent advances in the monomer-scale design of repetitive protein polymers present exciting fundamental and translational opportunities for polymer scientists and engineers.     

On the similarity of DNA primary sequences

We consider numerical characterization of graphical representations of DNA primary sequences. In particular we consider graphical representation of DNA of beta-globins of several species, including human, on the basis of the approach of A. Nandy in which nucleic bases are associated with a walk over integral points of a Cartesian x, y-coordinate system. With a so-generated graphical representation of DNA, we associate a distance/distance matrix, the elements of which are given by the quotient of the Euclidean and the graph theoretical distances, that is, through the space and through the bond distances for pairs of bases of graphical representation of DNA. We use eigenvalues of so-constructed matrices to characterize individual DNA sequences. The eigenvalues are used to construct numerical sequences, which are subsequently used for similarity/dissimilarity analysis. The results of such analysis have been compared and combined with similarity tables based on the frequency of occurrence of pairs of bases.     

Indexing scheme and similarity measures for macromolecular sequences

Nucleotide composition and distribution along a DNA sequence is known to play a vital role in the determination of gene functions. Protein coding regions, regulatory sequences, and other functional regions are determined generally by homology studies with comparable genes from other species or specific experimental verification. With the rapid and explosive increase in sequence information, new computational techniques for rapid determination of such information and comparative studies of different genes are becoming necessary which ideally should encompass not only DNA sequences but other macromolecular sequences as well.     

Quantum similarity study of atoms: a bridge between hardness and similarity indices

A hardness based similarity index for studying the quantum similarity for atoms is analyzed. The investigation of hardness and Fukui functions of atoms leads to the construction of a quantum similarity measure, which can be interpreted as a quantified comparison of chemical reactivity of atoms. Evaluation of the new measure reveals periodic tendencies throughout Mendeleev's table. Moreover on the diagonal the global hardness was recovered. Considering a corresponding quantum similarity index reveals that renormalization of the measure can mask periodic patterns. The hardness was calculated for atoms with nuclear charge 3相似文献   

Volatilities of codons and its application in similarity analysis of biological sequences

Volatilities of codons provide us a new way to characterize codons. In this article, we propose a new method measuring volatilities of codons base on the physics–chemical distances between amino acids and mutation frequencies between codons, then by which, we give a new graphical representation scheme for codon sequences. Finally, in order to show the effectiveness of our scheme, we analyze similarity among the coding codon sequences of exon 1 of beta-globin gene of human and those of other 10 species, find the result is consistent with those shown in the literature.     

The sieve ratio for characterization and similarity analysis of DNA sequences

A DNA sequence is a finite sequence of letters in the 4-letter DNA alphabet sigma = [A, C, G, T]. A set of condensed matrices was constructed to represent DNA sequences based on the sieve ratios of trinucleotide in sequence. Then, leading eigenvalues of these matrices were computed and considered as invariants for the DNA sequences. Similarity and dissimilarity analysis based on condensed matrices are given for eleven exon-1 genes of beta-globins of eleven species.     

铁硫蛋白活性中心铁硫簇的对称性破缺密度泛函 计算

应用密度泛函方法(DFT)计算了铁硫金属蛋白中的铁硫簇[Fe~2S~2(SCH~3)~4]^2^-,[Fe~3S~4(SCH~3)~3]^2^-以及[Fe~4S~4(SCH~3)~4]^2^-的几何参数和磁偶合性质。采用对称性破缺态(BS)来描述Fe－Fe自旋偶合。计算结果表明：采用高自旋态(HS)计算的Fe－Fe间距与实验值有较大偏差,而由BS方法所计算的Fe－Fe间距与晶体结构测定数据相吻合。根据HS态和BS态的能量,计算了体系的海森堡偶合参数J,计算结果也较为接近实验估算值。     

The adsorption of lysozymes: A model system

Hen egg white lysozyme was adsorbed onto clean borosilicate glass and n-pentyl silane-treated glass surfaces. Both modified (reductively methylated) and native lysozyme were studied. Variable angle X-ray photoelectron spectroscopy (VA-XPS) suggested differences in the nature of the adsorbed layer depending on substrate properties, as well as on degree of methylation of the protein. Adsorbed film thickness (as measured in the dehydrated state by XPS) ranged from 14 Å on hydrophilic glass to 25 Å on the hydrophobic surface. Degree of surface coverage ranged from 45% on the hydrophobic to 69% on the hydrophilic surface. The results suggest that lysozyme unfolds to a greater extent and covers more surface on the hydrophilic glass, possibly due to strong electrostatic interactions at the pH 7.4 conditions used in the study. An analysis of the surface structure of native hen lysozyme by molecular graphics has also been performed, suggesting that adsorption on hydrophobic surfaces should occur via the hydrophobic patch opposite the enzyme active site cleft. A comparison with human lysozyme has also been made using total internal reflection fluorescence (TIRF) spectroscopy to measure protein adsorption on model surfaces. The two proteins have significantly different interfacial properties.     

Numerical characterization and similarity analysis of DNA sequences based on 2-D graphical representation of the characteristic sequences

Based on the classifications of the four nucleic acid bases, He and Wang reduced a DNA sequence to three binary sequences, which are called the characteristic sequences (J. Chem. Inf. Comput. Sci. 42 (2002) 1080). In this paper, we associate each characteristic sequence with a (b)L / (b)L matrix by giving a 2-D 'two horizontal lines' graphical representation, and thus obtain a 3-component vector with entries being the sums of the maximal and minimal eigenvalues of the (b)L / (b)L matrices. The introduced vector results in more simple characterizations and comparisons among the coding sequences of exon 1 of beta-globin gene of eleven different species.     

Core trees and consensus fragment sequences for molecular representation and similarity analysis

A new type of molecular representation is introduced that is based on activity class characteristic substructures extracted from random fragment populations. Mapping of characteristic substructures is used to determine atom match rates in active molecules. Comparison of match rates of bonded atoms defines a hierarchical molecular fragmentation scheme. Active compounds are encoded as fragmentation pathways isolated from core trees. These paths are amenable to biological sequence alignment methods in combination with substructure-based scoring functions. From multiple core path alignments, consensus fragment sequences are derived that represent compound activity classes. Consensus fragment sequences weighted by increasing structural specificity can also be used to map molecules and search databases for active compounds.     

Polyhedral shapes of functional group distributions in biomolecules and related similarity measures

The distribution of the essential functional groups within biomolecules is described by a series of polyhedral models. As a function of a threshold of the electronic density of the biomolecule, the combinatorial types of these polyhedra are threshold-dependent within each series, resulting in a characteristic sequence of combinatorial types for each biomolecule. A comparison of combinatorial types is the basis for the introduction of new measures of shape similarity and shape complementarity between biomolecules. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 99–105, 1998