Protein and Peptide Letters - Volume 15, Issue 5, 2008

We are very pleased to offer this special issue to the readers of Protein and Peptide Letters by selecting the candidate papers from the 2007 International Conference on Intelligent Computing (ICIC), held in Qingdao, Shandong Province, China, 21-24 August 2007. Twelve papers (representing less than one half of one percent of all eligible papers accepted at the 2007 ICIC) were selected for inclusion in this special Read More

We present two efficient network propagation algorithms that operate on a binary tree, i.e., a sparse-edged substitute of an entire similarity network. TreeProp-N is based on passing increments between nodes while TreeProp-E employs propagation to the edges of the tree. Both algorithms improve protein classification efficiency.

This paper applies and studies the behavior of three learning algorithms, i.e. the Support Vector machine (SVM), the Radial Basis Function Network (the RBF network), and k-Nearest Neighbor (k-NN) for predicting HIV-1 drug resistance from genotype data. In addition, a new algorithm for classifier combination is proposed. The results of comparing the predictive performance of three learning algorithms show that, SVM yie Read More

A new approach based on the implementation of support vector machine (SVM) with the error correcting output codes (ECOC) is presented for recognition of multi-class protein folds. The experimental show that the proposed method can improve prediction accuracy by 4%-10% on two datasets containing 27 SCOP folds.

In this work, in order to reveal protein surface patterns in a systems biology framework, we analyze the similarity among the surface cavities by investigating the features of the pocket similarity network such as the community structure, the small-world property, the scale-free characteristic, and the hubs.

This paper presents a framework for annotating protein domains with predicted domain-domain interaction networks. Specially, domain annotation is formalized as a multi-class classification problem in this work. The numerical experiments on InterPro domains show promising results, which proves the efficiency of our proposed methods.

This paper explores the use of support vector machine (SVM) for protein function prediction. Studies are conducted on several groups of proteins with different functions including DNA-binding proteins, RNA-binding proteins, Gprotein coupled receptors, drug absorption proteins, drug metabolizing enzymes, drug distribution and excretion proteins. The computed accuracy for the prediction of these proteins is found to Read More

This paper proposes a flexible ant colony (FAC) algorithm for solving protein folding problems based on the hydrophobic-polar square lattice model. Collaborations of novel pheromone and heuristic strategies in the proposed algorithm make it more effective in predicting structures of proteins compared with other state-of-the-art algorithms.

In this paper, we adopted the bounded support vector machine to locate the key long-range interaction sites by the use of predicted local lowest B-factors. As a result, the key long-range interaction residues can be located based on information of local lowest B-factor sites.

A novel artificial immune network based algorithm for the diagnosis of diabetes is presented. The algorithm's implementation includes: (1) creating the initial immune antibody network; (2) the network is evolved with the learning from foreign antigens; (3) diagnosis process is accomplished by majority vote of the k nearest neighbor antibodies.

This paper proposes an efficient ensemble system to tackle the protein secondary structure prediction problem with neural networks as base classifiers. The experimental results show that the multi-layer system can lead to better results. When deploying more accurate classifiers, the higher accuracy of the ensemble system can be obtained.

From the extensive analysis, we identified three highly conserved sequence segments in HCV NS5A proteins and one binding motif in human proteins. The binding motif of human proteins often forms a full helix or an extended strand-loop structure, and is in good agreement with the experimental findings of previous studies.

Tre-2/Bub2/Cdc16 domain-containing proteins (TBC proteins) participate in wide range cellular processes. With computational approaches, 137 non-redundant TBC proteins from five model organisms were identified and classified into 13 subfamilies base on molecular evolutionary tree. This phylogenetic analysis provides useful functional annotation of newly-identified TBC proteins and guides for further experimentation.

We have examined the structure of two Humanin (HN) analog peptides, HNG and AGA-(C8R)HNG17, in the presence of sodium dodecylsulfate (SDS) and trifluoroethanol (TFE) using CD and sedimentation velocity. Both HNG and AGA-(C8R)HNG17 underwent complex conformational changes with increasing concentrations of SDS and TFE, in contrast to general trend of increasing α-helix with their concentration. To our surprise, bot Read More

Measurements of [θ]222 of E. coli phosphatase on heating from 20° to 90° and subsequent cooling to 20° shows a gradual increase in [θ]222 on heating, while cooling shows a symmetric transition centered at 45°. Reheating and cooling shows the same phenomenon. Enzyme heated and cooled once is fully active. The activity of the enzyme depends on its storage conditions (buffer and pH for example), but such changes Read More

Conformational and structural changes of lentil seedlings amine oxidase (LSAO) were studied in the presence of trifluoroethanol (TFE) by spectroscopic and analytical techniques. At TFE concentrations up to 5%, the induction of a structural transition from β-sheet to α-helix and up to 10% TFE a structural transition from α-helix to β-sheet as well as inactivation of the enzyme are observed. At TFE concentrations betwe Read More

In the present study, carbonic anhydrase (CA) enzyme was purified from rainbow trout (RT) liver with a specific activity of 4318 EUxmg-1 and a yield of 38% using Sepharose-4B-L tyrosine-sulfanilamide affinity gel chromatography. The overall purification was approximately 2260-fold. To check the purity and determine subunit molecular weight of enzyme, SDS-polyacrylamide gel electrophoresis was performed, which sho Read More

Antimicrobial peptides (AMPs) are generally produced as precursor peptides containing a signal sequence, a pro-region and the mature peptide. A computational analysis of β-defensin precursors predicts cleavage solely by signal peptidase to release the mature peptide, with no pro-region. This supports the extensive transcriptional control of β- defensin expression compared with other AMP genes.

The N-acetylglutamate kinase from Streptococcus mutans was expressed in Escherichia coli in soluble form and purified to homogeneity. Crystals suitable for X-ray diffraction were obtained by hanging-drop vapor diffusion method and diffracted to 2.06 Å. The crystal belonged to space group P21212, with unit cell parameters a = 57.19 Å, b =94.76 Å, c =47.58 Å. The gel filtration and initial phasing results showed that the enzy Read More