Nurul Hashimah Ahamed Hassain Malim

Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

BackgroundData fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This paper tests the correctness of this assumption.ResultsSets of 25 searches using either the same reference structure and 25 different similarity measures (similarity fusion) or 25 different reference structures and the same similarity measure (group fusion) show that large numbers of unique molecules are retrieved by just a single search, but that the numbers of unique molecules decrease very rapidly as more searches are considered. This rapid decrease is accompanied by a rapid increase in the fraction of those retrieved molecules that are active. There is an approximately log-log relationship between the numbers of different molecules retrieved and the number of searches carried out, and a rationale for this power-law behaviour is provided.ConclusionsUsing multiple searches provides a simple way of increasing the precision of a similarity search, and thus provides a justification for the use of data fusion methods in virtual screening.

Enhancing the Effectiveness of Fingerprint-Based Virtual Screening: Use of Turbo Similarity Searching and of Fragment Frequencies of Occurrence

Binary fingerprints encoding the presence of 2D fragment substructures in molecules are extensively used for similarity-based virtual screening in the agrochemical and pharmaceutical industries. This paper describes two techniques for enhancing the effectiveness of screening: the use of a second-level search based on the nearest neighbours of the initial reference structure; and the use of weighted fingerprints encoding the frequency of occurrence, rather than just the mere presence, of substructures. Experiments using several databases for which both structural and bioactivity data are available demonstrate the effectiveness of these two approaches.

Advanced Persistent Threat Mitigation Using Multi Level Security --- Access Control Framework

Bring Your Own Device BYOD concept has become popular amongst organization. However, due to its portability and information available through social network, BYOD has become susceptible to information stealing attacks such as Advanced Persistent Threat APT attack. APT attack uses tricky methods in getting access into the targets machine and mostly motives and stand as a threat to politics, corporate, academic and even military. Various mitigation techniques have been proposed in tackling this attack but, most of them are relying on available information of the attacks and does not provide data protection. Hence, it is challenging in providing protection against APT attack. In this paper, we will investigate on the available mitigation techniques and its problems in tackling APT attack by looking on the root cause of the attack inside BYOD environment. Lastly, based on the information obtained we will propose a new framework in reducing APT attack.

New strategy for Turbo Similarity Searching: Implementation and testing

Virtual screening is one of the most vital methods applied in Chemoinformatics, the field that contributes to drug discovery process. Turbo Similarity Searching (TSS) and data fusion are two of the latest chemical similarity searching strategies, which has evolved from the conventional similarity searching (SS) that apply the concept of multi-target searching instead of just an individual target search. The indirect relationship exists in TSS, with the inclusion of Nearest Neighbours (NN) has been proven to have better performance than the direct relationship (i.e. between query structure and database structures) that exists in similarity searching process. In this paper, we will focus on the implementation and improvement of the existing TSS. By adding in another layer of indirect relationship between the reference compound and the database compounds, along with an additional fusion layer, the performance of the new TSS strategy can be observed. The initial results indicated that there is an obvious increment in the recall value when applying the new strategy. The results are also evaluated with the significance test to show that the result produced by the new strategy is true and does not occurred by chance. Further work on different activity classes and different descriptors on the new strategy are expected to generate a better performance than the existing TSS.

Comparison of Similarity Coefficients for Chemical Database Retrieval

Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.

Smart university: reservation system with contactless technology

This paper introduces a reservation system for sport facilities which consist of a web application and an Android-based mobile application. The system simplifies the reservation process for users to book available sport facilities within a university to be more efficient. The proposed system is utilized together with a contactless technology where a brief introduction of the contactless technology is provided in the paper. We selected the Near Field Communication (NFC) as the contactless technology for our proposed system. The efficiency of the proposed system is explored within this paper as well.

Leisure Technology for the Elderly: A Survey, User Acceptance Testing and Conceptual Design

The Alzheimer’s disease damages neuronal and synaptic system due to the high level of amyloid beta in the brain. It is the common cause of dementia which is more common to afflict the elderly where they will gradually loss their memory and communication skills as well as deterioration of thinking and reasoning ability. Hence, it is crucial for elderly people to monitor their cognitive performance consistently and continuously to detect the Alzheimer’s symptoms, such as dementia or Mild Cognitive Impairment. There are many technologies that have been established in healthcare for its detection; however, such technologies, mostly medical treatments could not be self-catered by elderly on daily basis and in fact the use of this technology incurs cost each time. Therefore, this study looks at an alternative technology called leisure technology that allows access to the elderly every day at home in an enjoyable and relaxing manner. The aim of this study is to study applications of leisure activities that could stimulate brain cognitive function to be turned to a leisure technology application. Prior to proposing the conceptual design of this application, a user acceptance study of leisure technology among elderly people has been conducted. This study involves interviews and survey through distribution of questionnaires. The survey results shows that 90% of the participants stated that there was an improvement in cognitive abilities after using leisure technology and 98.4% of the participants stated that they could adapt to leisure technology. On the other hand, the outcomes from the interview show that they agreed that different types of leisure technology provide heterogeneous benefits, which can improve their cognitive abilities. Finally, this study proposes a conceptual design for leisure technology application that elderly people can adapt to.

N-LibSys: Library System Using NFC Technology

This paper examines the weaknesses of an existing library system which is the Online Public Access Catalog (OPAC) and proposes an enhanced platform that overcomes the weaknesses of the previous system. The existing OPAC platform acts as a search engine for reading materials in the library is commonly complicated and not user friendly. The Near Field Communication (NFC) technology is introduced in this project as part of a mobile application. NFC is a set of protocols on portable devices which perform wireless and contactless short range, two-way communication between compatible devices. Transmission of data between devices is completed over radio waves and magnetic induction with passive NFC devices. As mobile devices, especially smartphones are more commonly utilized by users all around the world including university students, the proposed system would be able to enhance the performance of a library to be more convenient, secure, and more user friendly. Indirectly, the development of this mobile application can improve the visitation rates of students to the library by simplifying the searching, tracking reading materials and borrowing activities.

GPU implementation of Turbo Similarity Searching using binary and fragment occurrence descriptors

Turbo Similarity Search (TSS) has been proved as one of the best simplest method for virtual screening. A lot of researches have been done to investigate the performance of TSS in different environment e.g. using MDDR database on Graphic Processing Unit GPU. However, TSS has not been tested with larger database such as ChEMBL database on similar platform. This has become the main motivation for this study to investigating the effect of different representation of chemical structures, binary and fragment occurrence descriptors towards the speed and adaptability in the architecture of GPU using TSS algorithm inside MDDR and ChEMBL database. At the end, this study gained that both parallel version of TSS using binary and fragment occurrence descriptors are scalable on the ChEMBL database. However, fragment occurrence descriptors performed better compared to binary descriptors. Therefore, this study could conclude that the complexity of the descriptors gives a bigger impact on the TSSs execution performance.

Children and social media usage: Malaysian initial perspective

The rapid growth of the Web has given birth to a heavily emphasized user-generated content platform such as Facebook. As a result, more and more users are utilizing such platforms to share their ideas and opinions to a wider audience. Young children who represents the new generation are also relying on this platform for many of their needs. Our research which was conducted among Malaysian children has found that such reliance is quite evident as well. As this need increases, the exposure to issues such as cyberbullying also increases. A survey was conducted among children from 9 to 12 years old in order to identify such reliance. The objective of this study is to identify the existing level of social media usages among Malaysian children. From the initial results, media sharing and social networking has become the most popular sites among the children. This indicates that further exploration into the usage trends among children as social media platforms becomes more utilized by the younger generation.