Industrial biocatalysis is currently attracting much attention to rebuild or substitute traditional producing process of chemicals and drugs. One of key focuses in industrial biocatalysis is biocatalyst, which is usually one kind of microbial enzyme. In the recent, new technologies of bioinformatics have played and will continue to play more and more significant roles in researches of industrial biocatalysis in response to the waves of genomic revolution. One of the key applications of bioinformatics in biocatalysis is the discovery and identification of the new biocatalyst through advanced DNA and protein sequence search, comparison and analyses in Internet database using different algorithm and software. The unknown genes of microbial enzymes can also be simply harvested by primer design on the basis of bioinformatics analyses. The other key applications of bioinformatics in biocatalysis are the modification and improvement of existing industrial biocatalyst. In this aspect, bioinformatics is of great importance in both rational design and directed evolution of microbial enzymes. Based on the successful prediction of tertiary structures of enzymes using the tool of bioinformatics, the undermentioned experiments, i.e. site-directed mutagenesis, fusion protein construction, DNA family shuffling and saturation mutagenesis, etc, are usually of very high efficiency. On all accounts, bioinformatics will be an essential tool for either biologist or biological engineer in the future researches of industrial biocatalysis, due to its significant function in guiding and quickening the step of discovery and/or improvement of novel biocatalysts.
Biocatalysis ; Computational Biology ; trends ; Enzymes ; chemistry ; metabolism ; Industrial Microbiology

Internal environment of metabolism of traditional Chinese medicine (TCM) is a dynamic process, which is in line with the "holistic-dynamic-comprehensive-analytic" characteristics of metabonomics, therefore metabonomics have a unique advantage to reveal the metabolic pattern of TCM. The application of metabonomics in TCM has great practical significance in understanding the pharmacodynamic/toxic effect material basis, mechanisms and guiding for determination of dosage and treatment course; At the same time, the scientific compatibility of TCM prescription, the germplasm resources of TCM and the preclinical safety/toxicity can be widely researched. At present, metabolomics has become a leading technology in many industries and fields including the research and development of TCM. The core of metabolomics is analytical technology, because comprehensive metabolite profiles or accurate identification of known metabolites can be obtained from complex biological samples only by appropriate analytical techniques. At the same time, a series of bioinformatics/chemical informatics/stoichiometry methods are needed to process the data, so as to obtain the potential law and information in the mass data. In this paper, the concept of metabolomics, relevant analytical techniques, data processing methods and applications were explained and analyzed clearly. In addition, the core problems and countermeasures of metabolomics were summarized, and the future development of metabolomics was prospected as well.
Computational Biology ; Humans ; Medicine, Chinese Traditional ; Metabolomics ; Research ; trends

With the advanced development of information technology, there is a huge impact on various industries for the arrival of big data. In the biomedical field, innovative genome sequencing technology enables low-cost, high-throughput, and high-speed to become a reality, which leads to an explosive growth in data and also appeared in an urgent need to process those massive biological information. High performance computing (HPC) along with effective methods is one of the best ways to deal with the problem of big data in biomedical field which could serve the biomedical development best. We discussed the issues faced in biomedical big data processing and concluded that the bioinformatics is an indispensable component of biomedical technologies.
Biomedical Research ; trends ; Computational Biology ; Computing Methodologies ; Humans

Chinese medicinal formulae( CMF) were often used in the clinics of traditional Chinese medicine (TCM) which were critical for modernization of Chinese medicine to shed light on the interaction between CMF and biological organisms. In current studies, correlation between system and part, macroscopic actions and microcosmic mechanism, ADME process and pharmacologic actions were often neglected. Thus, we put forward integrative pharmacology, which could integrate the correlation between CMF and biological organisms from multi-levels and multi-dimensional views. Integrative pharmacology would reveal the molecular mechanism of CMF for ailments treatment and screen out effective material systematically, which would be the new paradigm of TCM research.
Absorption ; Computational Biology ; Medicine, Chinese Traditional ; methods ; trends ; Pharmacology ; methods ; trends ; Tissue Distribution

OBJECTIVES: Since the first human infection from avian influenza was reported in Hong Kong in 1997, many Asian countries have confirmed outbreaks of highly pathogenic H5N1 avian influenza viruses. In addition to Asian countries, the EU authorities also held an urgent meeting in February 2006 at which it was agreed that Europe could also become the next target for H5N1 avian influenza in the near future. In this paper, we provide the general and applicable information on the avian influenza in the bioinformatics field to assist future studies in preventive medicine. METHODS: We introduced some up-to-date analytical tools in bioinformatics research, and discussed the current trends of avian influenza outbreaks. Among the bioinformatics methods, we focused our interests on two topics: attern analysis using the secondary database of avian influenza, and structural analysis using the molecular dynamics simulations in vaccine design. RESULTS: Use of the public genome databases available in the bioinformatics field enabled intensive analysis of the genetic patterns. Moreover, molecular dynamic simulations have also undergone remarkable development on the basis of the high performance supercomputing infrastructure these days. CONCLUSIONS: The bioinformatics techniques we introduced in this study may be useful in preventive medicine, especially in vaccine and drug discovery.
Proteomics ; Preventive Medicine ; Korea ; *Influenza in Birds ; *Influenza A Virus, H5N1 Subtype ; Computational Biology/*trends ; Birds ; Animals

The research and development (R&D) process of Chinese medicine, with one notable feature, clinical application based, is significantly different from which of chemical and biological medicine, from laboratory research to clinics. Besides, compound prescription is another character. Therefore, according to different R&D theories between Chinese and Western medicine, we put forward a new strategy in drug design of Chinese medicine, which focuses on "combination-activity relationship (CAR)", taking prescription discovery, component identification and formula optimization as three key points to identify the drugs of high efficacy and low toxicity. The method of drug design of Chinese medicine includes: new prescription discovery based on clinical data and literature information, component identification based on computing and experimental research, as well as formula optimization based on system modeling. This paper puts forward the concept, research framework and techniques of drug design of Chinese medicine, which embodies the R&D model of Chinese medicine, hoping to support the drug design of Chinese medicine theoretically and technologically.
Algorithms ; Community Networks ; organization & administration ; Computational Biology ; methods ; Drug Design ; Drug Discovery ; methods ; Humans ; Medicine, Chinese Traditional ; methods ; trends ; Models, Biological ; Models, Theoretical ; Research Design