An Alternative Strategy for Count and Storage of Kekulé and Longer Range Resonance Valence Bond Structures

Cai, Fei; Shao, Heqing; Liu, Chungen; Jiang, Yuansheng

doi:10.1021/ci049770a

Cited by 5 publications

(6 citation statements)

References 57 publications

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“…28-32 therein. Accordingly,t he jackknifet est has been widely recognized and increasingly used by investigators to examine the quality of various predictors (see, e.g., [56,57,84,[108][109][110][111][112][113].I nv iew of this, the jackknife test method has also been used in the current study.…”

Section: Jackknife Testmentioning

confidence: 99%

iPhos‐PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory

Qiu

Sun

Xiao

et al. 2016

Molecular Informatics

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Protein phosphorylation plays a critical role in human body by altering the structural conformation of a protein, causing it to become activated/deactivated, or functional modification. Given an uncharacterized protein sequence, can we predict whether it may be phosphorylated or may not? This is no doubt a very meaningful problem for both basic research and drug development. Unfortunately, to our best knowledge, so far no high throughput bioinformatics tool whatsoever has been developed to address such a very basic but important problem due to its extremely complexity and lacking sufficient training data. Here we proposed a predictor called iPhos-PseEvo by (1) incorporating the protein sequence evolutionary information into the general pseudo amino acid composition (PseAAC) via the grey system theory, (2) balancing out the skewed training datasets by the asymmetric bootstrap approach, and (3) constructing an ensemble predictor by fusing an array of individual random forest classifiers thru a voting system. Rigorous jackknife tests have indicated that very promising success rates have been achieved by iPhos-PseEvo even for such a difficult problem. A user-friendly web-server for iPhos-PseEvo has been established at http://www.jci-bioinfo.cn/iPhos-PseEvo, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved. It has not escaped our notice that the formulation and approach presented here can be used to analyze many other problems in protein science as well.

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Section: Jackknife Testmentioning

confidence: 99%

iPhos‐PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory

Qiu

Sun

Xiao

et al. 2016

Molecular Informatics

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“…Based on the reduced graph of a molecule, Dzonova-Jerman-Blazic and Trinajstić 12 discussed an elegant algorithm for the enumeration and display of Kekulé valence structures for benzenoids. Cai et al 13 proposed a method for generating Kekulé valence structures and longer range resonance valence structures (Dewar structures) using the adjacency matrix and adjacency bonding array. The adjacency matrix A is defined as a square The adjacency matrix is related to the well-known Hückel's Hamiltonian matrix.…”

Section: Introductionmentioning

confidence: 99%

“…For any kind of system we record the number of all unique (single) bonds and their positions and we call this representation "list of nonredundant bonds". The idea is similar to that described by Cai et al 13 but in terms of adjacency matrix, we use only the upper triangle (or the transpose of the lower triangle) of this matrix. Our method is very economical in memory and very efficient in computing time.…”

Section: Introductionmentioning

confidence: 99%

Generation of Kekulé valence structures and the corresponding valence bond wave function

Rashid¹,

Lenthe²

2010

J Comput Chem

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A new scheme, called "list of nonredundant bonds", is presented to record the number of bonds and their positions for the atoms involved in Kekulé valence structures of (poly)cyclic conjugated systems. Based on this scheme, a recursive algorithm for generating Kekulé valence structures has been developed and implemented. The method is general and applicable for all kinds of (poly)cyclic conjugated systems including fullerenes. The application of the algorithm in generating Valence Bond (VB) wave functions, in terms of Kekulé valence structures, is discussed and illustrated in actual VB calculations. Two types of VBSCF calculations, one involving Kekulé valence structures only and the second one involving all covalent VB structures, were performed for benzene, pentalene, benzocyclobutadiene, and naphthalene. Both strictly local and delocalised p-orbitals were used in these calculations. Our results show that, when the orbitals are restricted to their own atoms, other VB structures (Dewar structures) also have a significant contribution in the VB wave function. When removing this restriction, the other VB structures (Dewar and also the ionic structures) are accommodated in the Kekulé valence structures, automatically. Therefore, at VBSCF delocal level, the ground states of these systems can be described almost quantitatively by considering Kekulé valence structures only at a considerable saving of time.

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“…Thus, each member in the bond list is coded by (i, j, [A] ij ), with i and j referring Since the skeleton adjacency array is the same for all the Kekule´and higher resonance VB structures in one molecule, it is only needed to save a onedimensional array K[N] for each structure. Based on the adjacency bonding arrays, Cai et al 188 developed very efficient algorithms for the systematic search for K, S 3 and D 3,3 structures. These authors listed in their paper K, K þ S 3 and K þ S 3 þ D 3,3 numbers for 72 selected conjugated molecules.…”

Section: Buckminsterfullerene Vukicˇevic´and Randic´1 74 Examined Thmentioning

confidence: 99%

“…In Table 6, we present the K, K þ S 3 and K þ S 3 þ D 3,3 numbers of several conjugated molecules taken from Table 3 from the paper by Cai et al 188 2.3 Walks. -The definitions of walks and random walks are given in a number of mathematical texts, e.g.…”

Section: Buckminsterfullerene Vukicˇevic´and Randic´1 74 Examined Thmentioning

confidence: 99%

Combinatorial enumeration in chemistry

Babic¹,

Klein²,

Knop³

et al.

Chemical Modelling

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An Alternative Strategy for Count and Storage of Kekulé and Longer Range Resonance Valence Bond Structures

Cited by 5 publications

References 57 publications

iPhos‐PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory

iPhos‐PseEvo: Identifying Human Phosphorylated Proteins by Incorporating Evolutionary Information into General PseAAC via Grey System Theory

Generation of Kekulé valence structures and the corresponding valence bond wave function

Combinatorial enumeration in chemistry

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