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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

Film Review: Concerning Violence - Nine Scenes From the Anti-imperialistic Self-Defense (2014)

-Defense Director: Göran Olsson Sweden, Finland, Denmark, USA, 2014 Reviewed by Piotr Cieplak Brunel University London Göran Olsson’s Concerning Violence - Nine Scenes From the Anti-Imperialistic Self

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...

Letter to the Editor: Caspase cleavage sites in the human proteome: CaspDB, a database of predicted substrates

Piotr Cieplak 0 Dear Editor 0 0 P. Cieplak (&) Sanford Burnham Medical Research Institute , 10901 North Torrey Pines Road, La Jolla, CA 92037 , USA Caspases are enzymes belonging to a conserved

CleavPredict: A Platform for Reasoning about Matrix Metalloproteinases Proteolytic Events

CleavPredict (http://cleavpredict.sanfordburnham.org) 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

Bram J. van Raam 0 Guy S. Salvesen 0 Piotr Cieplak 0 Shawn B. Bratton, The University of Texas MD Anderson Cancer Center, United States of America 0 Sanford Burnham Medical Research Institute , La Jolla

High-Resolution Analysis and Functional Mapping of Cleavage Sites and Substrate Proteins of Furin in the Human Proteome

Background There is a growing appreciation of the role of proteolytic processes in human health and disease, but tools for analysis of such processes on a proteome-wide scale are limited. Furin is a ubiquitous proprotein convertase that cleaves after basic residues and transforms secretory proproteins into biologically active proteins. Despite this important role, many furin...

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

R.E.D. Server is a unique, open web service, designed to derive non-polarizable RESP and ESP charges and to build force field libraries for new molecules/molecular fragments. It provides to computational biologists the means to derive rigorously molecular electrostatic potential-based charges embedded in force field libraries that are ready to be used in force field development...

New Details of HCV NS3/4A Proteinase Functionality Revealed by a High-Throughput Cleavage Assay

Background The hepatitis C virus (HCV) genome encodes a long polyprotein, which is processed by host cell and viral proteases to the individual structural and non-structural (NS) proteins. HCV NS3/4A serine proteinase (NS3/4A) is a non-covalent heterodimer of the N-terminal, ∼180-residue portion of the 631-residue NS3 protein with the NS4A co-factor. NS3/4A cleaves the...

R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries

The web-based RESP ESP charge DataBase (R.E.DD.B., http://q4md-forcefieldtools.org/REDDB) is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation...

Matrix Metalloproteinase Proteolysis of the Myelin Basic Protein Isoforms Is a Source of Immunogenic Peptides in Autoimmune Multiple Sclerosis

Background Matrix metalloproteinases (MMPs) play a significant role in the fragmentation of myelin basic protein (MBP) and demyelination leading to autoimmune multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). The classic MBP isoforms are predominantly expressed in the oligodendrocytes of the CNS. The splice variants of the single MBP gene (Golli-MBP...

PMAP: databases for analyzing proteolytic events and pathways

The Proteolysis MAP (PMAP, http://www.proteolysis.org) is a user-friendly website intended to aid the scientific community in reasoning about proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. The foundation databases, ProteaseDB and SubstrateDB, are driven by an automated annotation pipeline that generates dynamic...

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS...