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Role of N-glycosylation in activation of proMMP-9. A molecular dynamics simulations study

. Opdenakker for encouraging conversation and his useful remarks to the text. Author Contributions Conceptualization: Sonu Kumar. Formal analysis: Sonu Kumar. Funding acquisition: Piotr Cieplak ... . Investigation: Sonu Kumar, Piotr Cieplak. Methodology: Sonu Kumar, Piotr Cieplak. Project administration: Piotr Cieplak. Supervision: Piotr Cieplak. Writing ± original draft: Sonu Kumar. Writing ± review

CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases

Background: A variety of neurodegenerative diseases (NDs) have been associated with deregulated caspase activation that leads to neuronal death. Caspases appear to be involved in the molecular pathology of NDs by directly cleaving important proteins. For instance, several proteins involved in Alzheimer’s disease, including β-amyloid precursor protein (APP) and presenilins, are...

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

CleavPredict ( is a Web server for substrate cleavage prediction for matrix metalloproteinases (MMPs). It is intended as a computational platform aiding the scientific community in reasoning about proteolytic events. CleavPredict offers in silico prediction of cleavage sites specific for 11 human MMPs. The prediction method employs the MMP...

Caspase Cleavage Sites in the Human Proteome: CaspDB, a Database of Predicted Substrates

Caspases are enzymes belonging to a conserved family of cysteine-dependent aspartic-specific proteases that are involved in vital cellular processes and play a prominent role in apoptosis and inflammation. Determining all relevant protein substrates of caspases remains a challenging task. Over 1500 caspase substrates have been discovered in the human proteome according to...

Understanding the Specificity of Human Galectin-8C Domain Interactions with Its Glycan Ligands Based on Molecular Dynamics Simulations

Human Galectin-8 (Gal-8) is a member of the galectin family which shares an affinity for β-galactosides. The tandem-repeat Gal-8 consists of a N- and a C-terminal carbohydrate recognition domain (N- and C-CRD) joined by a linker peptide of various length. Despite their structural similarity both CRDs recognize different oligosaccharides. While the molecular requirements of the N...

GlycoCD: a repository for carbohydrate-related CD antigens

Sonu Kumar 1 Thomas L utteke 0 Reinhard Schwartz-Albiez 1 Associate Editor: Janet Kelso 0 Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen , D-35392 Giessen

The G protein-coupled receptors in the pufferfish Takifugu rubripes

Anita Sarkar 0 Sonu Kumar 0 Durai Sundar 0 0 Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi , New Delhi , India Background: Guanine protein