Influence of protein structure databases on the predictive power of statistical pair potentials

A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139–149, 1998. © 1998 Wiley-Liss, Inc.     

Structural classification of αββ and ββα supersecondary structure units in proteins

We present a fully automatic structural classification of supersecondary structure units, consisting of two hydrogen-bonded β strands, preceded or followed by an α helix. The classification is performed on the spatial arrangement of the secondary structure elements, irrespective of the length and conformation of the intervening loops. The similarity of the arrangements is estimated by a structure alignment procedure that uses as similarity measure the root mean square deviation of superimposed backbone atoms. Applied to a set of 141 well-resolved nonhomologous protein structures, the classification yields 11 families of recurrent arrangements. In addition, fragments that are structurally intermediate between the families are found; they reveal the continuity of the classification. The analysis of the families shows that the α helix and β hairpin axes can adopt virtually all relative orientations, with, however, some preferable orientations; moreover, according to the orientation, preferences in the left/right handedness of the α–β connection are observed. These preferences can be explained by favorable side by side packing of the α helix and the β hairpin, local interactions in the region of the α–β connection or stabilizing environments in the parent protein. Furthermore, fold recognition procedures and structure prediction algorithms coupled to database-derived potentials suggest that the preferable nature of these arrangements does not imply their intrinsic stability. They usually accommodate a large number of sequences, of which only a subset is predicted to stabilize the motif. The motifs predicted as stable could correspond to nuclei formed at the very beginning of the folding process. Proteins 30:193–212, 1998. © 1998 Wiley-Liss, Inc.     

生物信息学在食用菌研究中的应用

食用菌因其富含多种氨基酸及微量元素等物质,具有较高的营养价值和药用价值,越来越受到人们的关注和喜爱。我国作为最重要的食用菌生产国,食用菌生产规模不断扩大,产量也在逐年提高。为了更好地发展食用菌产业,迫切需要在传统的食用菌产业链,如优良品种选育及栽培生产中融入新技术。生物信息学作为一门研究分析生物生命结构的技术门类,通过运用数学、计算机科学等工具揭示了数据所蕴含的生物学意义,极大地促进了生命科学研究的发展,也为食用菌更深入的研究与应用提供了技术保障。本文从食用菌育种及种质资源调查、病虫害防治、基因组学、食用菌安全等几方面阐述了生物信息学在食用菌领域的具体应用,对生物信息学在食用菌及农业领域的发展进行了展望,以期为促进食用菌研究和生产发展提供参考。     

A database of mutants and effects of site-directed mutagenesis experiments on G protein-coupled receptors

A database system and computer programs for storage and retrieval of information about guanine nucleotide-binding protein (G protein) -coupled receptor mutants and associated biological effects have been developed. Mutation data on the receptors were collected from the literature and a database of mutants and effects of mutations was developed. The G protein-coupled receptor, family A, point mutation database (GRAP) provides detailed information on ligand-binding and signal transduction properties of more than 2130 receptor mutants. The amino acid sequences of receptors for which mutation experiments have been reported were aligned, and from this alignment mutation data may be retrieved. Alternatively, a search form allowing detailed specification of which mutants to retrieve may be used, for example, to search for specific amino acid substitutions, substitutions in specific protein domains or reported biological effects. Furthermore, ligand and bibliographic oriented queries may be performed. GRAP is available on the Internet (URL: http://www-grap.fagmed.uit.no/GRAP/homepage.html ) using the World-Wide Web system. © 1996 Wiley-Liss, Inc.     

Quo vadis G protein-coupled receptor ligands? A tool for analysis of the emergence of new groups of compounds over time

Exponential growth in the number of compounds with experimentally verified activity towards particular target has led to the emergence of various databases gathering data on biological activity. In this study, the ligands of family A of the G Protein-Coupled Receptors that are collected in the ChEMBL database were examined, and special attention was given to serotonin receptors. Sets of compounds were examined in terms of their appearance over time, they were mapped to the chemical space of drugs deposited in DrugBank, and the emergence of structurally new clusters of compounds was indicated. In addition, a tool for detailed analysis of the obtained visualizations was prepared and made available online at http://chem.gmum.net/vischem, which enables the investigation of chemical structures while referring to particular data points depicted in the figures and changes in compounds datasets over time.     

海洋污损生物数据管理系统的设计与构建

固着或栖息在船舶和人工设施水下部位的海洋污损生物, 会对人们的涉海活动产生不利影响, 其群落的形成和发展过程与温度、盐度、深度、季节、海域、浸海时间、离岸距离和附着基类型等多种因素密切相关。为便于系统分析和综合处理各海区污损生物资料, 理清各要素之间的内在关系, 需要一个能将上述因子与生物群落参数有机地结合起来的数据平台, 将分散、零星的资料予以归纳整合并通过网络共享, 以更好地为生产实践和科学研究服务。本研究采用Internet技术, 应用ASP.NET框架和MySQL数据库, 使用MS Visual Studio 2013设计并开发了服务端部署在Windows 7或Windows Server 2008 R2 (推荐)操作系统上的海洋污损生物数据管理系统, 实现了基于网络的海洋污损生物数据集成、储存与管理, 可完成来源不同、时相变化和海区多样的污损生物数据资料的集成与储存, 能通过单一或多种组合条件进行查询和检索, 并可根据用户的需要导出多种格式的检索结果报表。该系统具备操作简便、方便网络共享、易于升级更新和开拓新功能等特点, 能有效满足科研、生产和管理部门的需要。     

长链非编码RNA数据库资源

长链非编码RNA（long non coding RNA, lncRNA)在多个水平参与调节机体的各项基础生物进程,其功能紊乱常伴随疾病的发生。鉴定lncRNA的生物学功能已成为近年来的研究热点。然而,目前从各种真核生物高通量测序中鉴定的几十万个lncRNA中,只有极少数的功能已被实验验证,这对于该领域的深入研究是个巨大的挑战。因此,许多科研机构都建立了lncRNA数据库,并且持续周期性更新,这为研究者共享、注释和分析lncRNA功能提供了十分有效的工具。本文从lncRNA原始资源整合、筛选、鉴定及功能分析和lncRNA与人类疾病等4个方面介绍各lncRNA数据库资源的最新特征和应用范围。这为研究者在选择不同数据库资源进行lncRNA鉴定和分析时提供参考。     

基于Oracle数据库的水稻病虫综合防治专家系统

应用数据库、计算机网络和空间信息技术,研制出基于Oracle数据库的“水稻病虫综合防治专家系统RIPMES Ⅱ”。系统包括数据采集、数据维护专家决策和GIS应用等子系统,能解决实时数据采集、海量数据存贮与分析、病虫害防治辅助决策、虫害空间分布特征分析等问题,是水稻病虫害综合防治的一个有效工具,同时也可为类似的专家系统的研究提供参考。