PLIC: protein-ligand interaction clusters

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein-ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of similar to 68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC).

Uma Metodologia para Auxiliar no Processo de Conversão de Bases Cartográficas Utilizando o Padrão da Estrutura de Dados Geoespaciais Vetoriais.

Na década de 80, o surgimento de programas de computadores mais amigáveis para usuários e produtores de informação e a evolução tecnológica fizeram com que as instituições, públicas e privadas, se aperfeiçoassem em estudos sobre sistemas de produção cartográfica apoiados por computador, visando a implementação de Sistemas de Informação Geográfica (SIG). A pouca simultaneidade de forças entre órgãos interessados, resultou em uma grande quantidade de arquivos digitais com a necessidade de padronização. Em 2007, a Comissão Nacional de Cartografia (CONCAR) homologou a Estrutura de Dados Geoespaciais Vetoriais (EDGV) a fim de minimizar o problema da falta de padronização de bases cartográficas. A presente dissertação tem como foco elaborar uma metodologia de trabalho para o processo de conversão de bases cartográficas digitais existentes no padrão da Mapoteca Topográfica Digital (MTD), do Instituto Brasileiro de Geografia e Estatística (IBGE), para o padrão da EDGV, bem como suas potencialidades e limitações para integração e padronização de bases cartográficas digitais. Será feita uma aplicação da metodologia utilizando a carta topográfica de Saquarema, na escala de 1:50.000, vetorizada na Coordenação de Cartografia (CCAR) do IBGE e disponível na Internet. Como a EDGV foi elaborada segundo técnicas de modelagem orientada a objetos, foi necessário um mapeamento para banco de dados relacional, já que este ainda é utilizado pela maioria dos usuários e produtores de informação geográfica. Um dos objetivos específicos é elaborar um esquema de banco de dados, ou seja, um banco de dados vazio contendo todas as classes de objetos, atributos e seus respectivos domínios existentes na EDGV para que possa ser utilizado no processo de produção cartográfica do IBGE. Este esquema conterá todas as descrições dos objetos e de seus respectivos atributos, além de já permitir que o usuário selecione o domínio de um determinado atributo em uma lista pré definida, evitando que ocorra erro no preenchimento dados. Esta metodologia de trabalho será de grande importância para o processo de conversão das bases cartográficas existentes no IBGE e, com isso, gerar e disponibilizar bases cartográficas no padrão da EDGV.

Computer-based selection of joining processes

The assembly of any manufactured product involves joining. This paper describes ways of selecting processes for joining. The method allows discrimination of the joint geometry, joint loading, material, and other attributes of the joint itself, identifying the subset of available processes capable of meeting a given set of design constraints. A relational database containing data-tables for joining processes, materials to be joined, and joint geometry and mode of loading, allows the attributes of each of these to be stored in an appropriate format, and permits links to be created between those that are related. A search engine isolates the processes that meet design requirements on material, joint geometry and loading. The method is illustrated in Part 2 by case studies, utilising software that embodies the method.

关系数据库中多维数据分析及展现的研究

在对关系数据库业务模型分析的基础上通过建立多维模型定义使数据具有多维的概念,并在此基础上提供了一种B/S模式的多维数据查询和展现的方法,该方法充分利用了多种数据存储结构来优化数据的查询和显示。通过建立维度间的层次关系可实现多维数据的钻取、旋转、切片等操作,结合JFreeChart的图形功能提供了一种多维图形展现和分析的方法。

含空值关系数据库中关系代数的实现

本文从空值的完全语义出发,依据空值环境下信息等价和信息相容的含义,全面定义了空值环境下运算结果完备的关系代数运算,并对空值环境下关系代数运算的有效性和完备性进行了讨论。

基于5VL的含空值关系数据库的选择运算

本文首先介绍了文献［1］给出的基于空值完全语义的五值逻辑（5VL），定义了基于5VL的比较运算和逻辑运算的运算规则，并以此为基础结出了一般条件表达式下选择运算的处理策略和实现算法。

空值环境下含不确定及可能信息关系数据库的更新

本文在［１］扩展关系模型中引入属性级的不完全信息空值。为适应此环境下更新操作的需要，本文对［１］中的扩展关系模型进行了进一步的扩展，并以此模型为基础讨论了空值环境下含不确定及可能信息关系数据库的更新操作的策略，给出了相应的处理算法。

含有空值关系数据库的查询处理

本文在深刻理解空值语义的基础上，给出一种处理占位型空值的方法。讨论了空值环境下关系数据库的查询策略，定义了含三种查询操作的关系代数最小完备集中的关系代数运算，并对查询计算的有效性和完备性进行了分析。

空值环境下关系数据库的更新 Ⅰ：扩展关系模型及基本运算

本文从空值语义及更新操作的关系出发，提出了一种新的扩展关系模型，用以组织更新操作下的含有空值的关系数据库中的信息．同时，定义了这种模型下的基本关系代数运算．为实现空值环境下关系数据库的数据更新奠定了基础。

An intelligent assistant for design and material engineers in the submarine cable industry

This paper describes an industrial application of case-based reasoning in engineering. The application involves an integration of case-based reasoning (CBR) retrieval techniques with a relational database. The database is specially designed as a repository of experiential knowledge and with the CBR application in mind such as to include qualitative search indices. The application is for an intelligent assistant for design and material engineers in the submarine cable industry. The system consists of three components; a material classifier and a database of experiential knowledge and a CBR system is used to retrieve similar past cases based on component descriptions. Work has shown that an uncommon retrieval technique, hierarchical searching, well represents several search indices and that this techniques aids the implementation of advanced techniques such as context sensitive weights. The system is currently undergoing user testing at the Alcatel Submarine Cables site in Greenwich. Plans are for wider testing and deployment over several sites internationally.

Intelligent design assistant (IDA): a case base reasoning system for material and design

This paper describes the approach to the modelling of experiential knowledge in an industrial application of Case-Based Reasoning (CBR). The CBR involves retrieval techniques in conjunction with a relational database. The database is especially designed as a repository of experiential knowledge, and includes qualitative search indices. The system is intended to help design engineers and material engineers in the submarine cable industry. It consists of three parts: a materials database; a database of experiential knowledge; and a CBR system used to retrieve similar past designs based upon component and material qualitative descriptions. The system is currently undergoing user testing at the Alcatel Submarine Networks site in Greenwich.

A case based model to assist in the design process in the manufacture of furniture products

This paper describes progress on a project to utilise case based reasoning methods in the design and manufacture of furniture products. The novel feature of this research is that cases are represented as structures in a relational database of products, components and materials. The paper proposes a method for extending the usual "weighted sum" over attribute similarities for a ·single table to encompass relational structures over several tables. The capabilities of the system are discussed, particularly with respect to differing user objectives, such as cost estimation, CAD, cutting scheme re-use, and initial design. It is shown that specification of a target case as a relational structure combined with suitable weights can fulfil several user functions. However, it is also shown that some user functions cannot satisfactorily be specified via a single target case. For these functions it is proposed to allow the specification of a set of target cases. A derived similarity measure between individuals and sets of cases is proposed.

SOFT – generating highly flexible object code from XML specifications

Many code generation tools exist to aid developers in carrying out common mappings, such as from Object to XML or from Object to relational database. Such generated code tends to possess a high binding between the Object code and the target mapping, making integration into a broader application tedious or even impossible. In this paper we suggest XML technologies and the multiple inheritance capabilities of interface based languages such as Java, offer a means to unify such executable specifications, thus building complete, consistent and useful object models declaratively, without sacrificing component flexibility.

An analysis of human behaviour during the WTC disaster of 9/11 based on published survivor accounts

This paper presents an analysis of survivor experiences from the World Trade Centre (WTC) evacuation of 11 September 2001. The experiences were collected from published accounts appearing in the print and electronic mass media and are stored in a relational database specifically developed for this purpose.