Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces

Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To empirically quantify the importance of β contacts, we design βACV, an SVM classifier with β contacts as input, to classify homodimers from crystal packing. We found that our βACV is able to achieve the state-of-the-art classification performance superior to SVM classifiers with distance-based contacts as input. Our βACV also outperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performance suggests that β contacts can truly identify critical specific contacts in protein binding interfaces. β contacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-based contacts

P2PDocTagger: Content management through automated P2P collaborative tagging

As the amount of user generated content grows, personal information management has become a challenging problem. Several information management approaches, such as desktop search, document organization and (collaborative) document tagging have been proposed to address this, however they are either inappropriate or inefficient. Automated collaborative document tagging approaches mitigate the problems of manual tagging, but they are usually based on centralized settings which are plagued by problems such as scalability, privacy, etc. To resolve these issues, we present P2PDocTagger, an automated and distributed document tagging system based on classification in P2P networks. P2P-DocTagger minimizes the efforts of individual peers and reduces computation and communication cost while providing high tagging accuracy, and eases of document organization/retrieval. In addition, we provide a realistic and flexible simulation toolkit -- P2PDMT, to facilitate the development and testing of P2P data mining algorithms.</jats:p

Classification in P2P Networks with Cascade Support Vendor Machines

Classification in Peer-to-Peer (P2P) networks is important to many real applications, such as distributed intrusion detection, distributed recommendation systems, and distributed antispam detection. However, it is very challenging to perform classification in P2P networks due to many practical issues, such as scalability, peer dynamism, and asynchronism. This article investigates the practical techniques of constructing Support Vector Machine (SVM) classifiers in the P2P networks. In particular, we demonstrate how to efficiently cascade SVM in a P2P network with the use of reduced SVM. In addition, we propose to fuse the concept of cascade SVM with bootstrap aggregation to effectively balance the trade-off between classification accuracy, model construction, and prediction cost. We provide theoretical insights for the proposed solutions and conduct an extensive set of empirical studies on a number of large-scale datasets. Encouraging results validate the efficacy of the proposed approach.</jats:p

Organisational Resilience in Acquisition Integration—Organisational Antecedents and Contingency Effects of Flexibility and Redundancy

Resilience has received increasing attention in organisational research; however, it has remained understudied in the context of acquisitions. This is surprising given acquisitions involve challenging events that would benefit from a consideration of organisational resilience. We outline how flexibility and redundancy, as dimensions of organisational resilience, influence acquisition outcomes. We find flexibility can lower negative impacts of competitor retaliation and employee resistance during acquisition integration, but this depends on a decentralised approach to managing integration. Additionally, it appears developing organisational resilience depends on acquisition experience