Linear motifs (LMs), used by a subset of all protein-protein interactions (PPIs), bind to globular receptors or domains and play an important role in signaling networks. LMPID (Linear Motif mediated Protein Interaction Database) is a manually curated database which provides comprehensive experimentally validated information about the LMs mediating PPIs from all organisms on a single platform. A...

Protein-protein interactions (PPIs) play key roles in life processes, such as signal transduction, transcription regulations, and immune response, etc. Identification of PPIs enables better understanding of the functional networks within a cell. Common experimental methods for identifying PPIs are time consuming and expensive. However, recent developments in computational approaches for inferri...

Proteins in living organisms express various important functions by interacting with other proteins and molecules. Therefore, many efforts have been made to investigate and predict protein-protein interactions (PPIs). Analysis of strengths of PPIs is also important because such strengths are involved in functionality of proteins. In this paper, we propose several feature space mappings from pro...

Understanding the cell as a system has become one of the foremost challenges in the post-genomic era. As a result of advances in high-throughput (HTP) methodologies, we have seen a rapid growth in new types of data at the whole-genome scale. Over the last decade, HTP experimental techniques such as yeast two-hybrid assays and co-affinity purification couple with mass spectrometry have generated...

Modification of protein-protein interactions (PPIs) holds promise for novel rational drug design. Disrupting or modifying protein interactions offers new challenges in terms of chemical compound libraries and techniques for compound validation. As proteins interact with several partners in different allosteric conformation in a pathological and tissue-specific fashion, it is difficult to predic...

Inhibition of protein-protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection method...

Protein-protein interactions (PPIs) intimately govern various biological processes and disease states therefore have been identified as attractive therapeutic targets for small-molecule drug discovery. However, the development of highly potent inhibitors PPIs has proven to be extremely challenging with limited clinical success stories. Herein, we report irreversible human double minute 2 (HDM2)...

Protein-protein interactions (PPI) are vital processes in molecular biology. However, the current understanding of PPIs is far from satisfactory. Improved methods of predicting PPIs are very much needed. Since experimental methods are labour and time consuming and lack accuracy, the improvement is expected to come from the area of computational methods. We designed and implemented a new algorit...

Protein-protein interactions (PPIs) play a critical role in many cellular functions. A number of experimental techniques have been applied to discover PPIs; however, these techniques are expensive in terms of time, money, and expertise. There are also large discrepancies between the PPI data collected by the same or different techniques in the same organism. We therefore turn to computational t...

Protein-protein interactions (PPIs) have been widely studied to understand the biological processes or molecular functions associated with different disease systems like cancer. While focused studies on individual cancers have generated valuable information, global and comparative analysis of datasets from different cancer types has not been done. In this work, we carried out bioinformatic anal...