Biomedical subjects

Hai-Xu Tang

Publications and source records attributed to Hai-Xu Tang.

7 recordsLinked to original sources

PubMed2004

Predicting polymerase II core promoters by cooperating transcription factor binding sites in eukaryotic genes.

Several discriminate functions for predicting core promoters that based on the potential cooperation between transcription factor binding sites (TFBSs) are discussed. It is demonstrated that the promoter predicting accuracy is improved when the cooperation among TFBSs is taken into consideration. The core promoter region of a newly discovered gene CKLFSF1 is predicted to locate more than 1.5 kb far away from the 5' end of the transcript and in the last intron of its upstream gene, which is experimentally confirmed later. The core promoters of 3402 human RefSeq sequences, obtained by extending the mRNAs in human genome sequences, are predicted by our algorithm, and there are about 60% of the predicted core promoters locating within the +/- 500 bp region relative to the annotated transcription start site.

Algorithms↗

PubMed2003

[A novel approach for peptide identification by tandem mass spectrometry].

High throughput scoring algorithms that are used to find the match of a tandem mass spectrum to a predicted mass spectrum of a peptide within a database have been applied in shotgun proteomics. However, these algorithms could produce a significant number of incorrect peptide identifications. Here a novel approach was developed to scoring tandem mass spectra against a peptide database, in which fragment ion probabilities, number of enzymatic termini of candidate peptides, matching quality and match pattern between experimental and theoretical spectrum were considered. Benchmarking the novel scorer on a large set of experimental MS/MS spectra, it is demonstrated that PepSearch performs significantly better than the widely used software SEQUEST. The PepSearch software is available at http://compbio.sibsnet.org/projects/pepsearch.

Databases, Protein↗

PubMed1999

Engineering Novel Functional Proteins Grafting Active Sites into Natural Scaffolds.

Engineering novel small functional proteins by grafting active sites into small but stable proteins is an efficient protein design method. Combining heterogeneous self-consistent ensemble optimization (hetero-SCEO) with 3D-motif search tool, we developed a system to accomplish such method. It is tested by transferring zinc-binding site of carbonic anhydrase form B to charybdotoxin and its efficiency is demonstrated.

Journal Article↗

PubMed1998

Flexible Docking of Proteins and "Drug-like" Ligands.

By using "tabu search" algorithm and Gehlhaar potential function, a new approach is presented for flexible docking of protein and its "drug-like" ligand has been developed. Computational test for this method with a set of 100 complexes has been performed, which indicated that the deviation of 89% of the predicted complex conformation was less than 0.25 nm. Compared with GOLD, a program of genetic algorithm, our method has high accuracy, low limit and short computation time.

Journal Article↗

PubMed1998

Design of Protein Cores by Screening Combinatorial Sequence Library.

We have developed a new method, heterogeneous self-consistent ensemble optimization (hetero-SCEO), to select appropriate hydrophobic cores of proteins. It has been tested with five kinds of proteins: lambda-repressor, phage 434 CRO protein, interleukin-4, thioredoxin and ubiquitin. The results show that the method can be used for the de novo desigh of the hydrophobic cores of proteins.

Journal Article↗

PubMed1998

Predicting Binding Free Energy for Protein Complexes.

A novel empirical free energy function and a computationally more effect algorithm are applied to 21 protein complexes to predict the free energies of binding. Compared with the other works what have done in literature, better agreement between the predicted and measured binding free energies is obtained. The predicted values, are typically within 1.0 kcal/mol of the measured, while keeping a high correlation coefficient of 96 %. Predicting the binding free energy of a typical protease-inhibitor complex takes about 2 min on SGI-IMPACT R10000 Workstation. What is more, the results reconfirm that the interactions between the hydrophilic atoms may play a more favorable role in binding than in folding.

Journal Article↗

PubMed1996

Large-scale Homologous Analysis of Genome Sequence.

We described a new method for the large-scale homologous analysis of genome sequences, which used hashing technique combined with sparse dynamic programming to get a sequence alignment. Three examples, the plant chloroplast genomes, the mammalian T-cell receptors C(alpha)/C(delta) gene loci and the mammalian gamma-crystallin gene clusters were analysed. The results showed that the method was more rapid to obtain accurate enough data and might be useful in genome analysis.

Journal Article↗