PeSA: A software tool for peptide specificity analysis.

The discovery and characterization of molecular interactions is crucial towards a better understanding of complex biological processes. Particularly protein-protein interactions (i.e., PPIs), which are responsible for a variety of cellular functions from intracellular signaling to enzyme-substrate specificity, have been studied broadly over the past decades. Position-specific scoring matrices (PSSM) in particular are used extensively to help determine interaction specificity or candidate interaction motifs at the residue level. However, not all studies successfully report their results as a candidate interaction motif. In many cases, this may be due to a lack of suitable tools for simple analysis and motif generation. Peptide Specificity Analyst (PeSA) was developed with the goal of filling this information gap and providing an easy to use software to aid peptide array analysis and motif generation. PeSA utilizes two models of motif creation: (1) frequency-based using a user-defined peptide list, and (2) weight-based using experimental binding results. The ability to produce motifs effortlessly will make studying, interpreting and disseminating peptide specificity results in an effortless and straightforward process.

Recent advances in histone modification and histone modifying enzyme assays.

Introduction: Histone modifying enzymes (HMEs)-catalyzed histone modifications are important epigenetic markers that play critical roles in the regulation of a variety of cellular functions, especially the regulation of gene expression. The aberrant histone modifying enzyme activity and the abnormal histone modification level are closely associated with various human diseases including cancers, making them become the promising and attractive disease biomarkers. Consequently, the development of efficient assays for accurate and sensitive detection of histone modifications and HMEs are crucial for disease diagnosis. Areas covered: In this review, we summarize the advances in histone modifications and HMEs assays in recent 5 years (2013-2018), including the development of various methods based on fluorescent, bioluminescent, colorimetric, electrochemical, surface-enhanced Raman scattering, and mass spectrometry strategies. Their principles and applications for in vitro and in vivo assays are reviewed, and the future directions are discussed as well. Expert commentary: In comparison with the conventional radioactive and Western blot assays, the newly developed histone modifications and HMEs assays exhibit distinct advantages. Especially, the introduction of novel nanomaterials and advanced analytical techniques in recent years has greatly improved the assay performances, promoting their further applications in biomedical research and clinical diagnosis.