AIMC Topic: Substrate Specificity
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A novel aspartic protease from Rhizomucor miehei expressed in Pichia pastoris and its application on meat tenderization and preparation of turtle peptides.
Food chemistry
Oct 23, 2017
A novel aspartic protease gene (RmproA) was cloned from the thermophilic fungus Rhizomucor miehei CAU432 and expressed in Pichia pastoris. The RmproA was successfully expressed in P. pastoris as an active extracellular protease. High protease activit...
FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity.
Journal of chemical information and modeling
Aug 7, 2017
UNLABELLED: We report on the further development of FAst MEtabolizer (FAME; J. Chem. Inf.
Knowledge-transfer learning for prediction of matrix metalloprotease substrate-cleavage sites.
Scientific reports
Jul 18, 2017
Matrix Metalloproteases (MMPs) are an important family of proteases that play crucial roles in key cellular and disease processes. Therefore, MMPs constitute important targets for drug design, development and delivery. Advanced proteomic technologies...
Systematic Prediction of the Impacts of Mutations in MicroRNA Seed Sequences.
Journal of integrative bioinformatics
May 18, 2017
MicroRNAs are a class of small non-coding RNAs that are involved in many important biological processes and the dysfunction of microRNA has been associated with many diseases. The seed region of a microRNA is of crucial importance to its target recog...
Machine Learning of Global Phosphoproteomic Profiles Enables Discrimination of Direct versus Indirect Kinase Substrates.
Molecular & cellular proteomics : MCP
Mar 6, 2017
Mass spectrometry allows quantification of tens of thousands of phosphorylation sites from minute amounts of cellular material. Despite this wealth of information, our understanding of phosphorylation-based signaling is limited, in part because it is...
Unveiling antimicrobial peptide-generating human proteases using PROTEASIX.
Journal of proteomics
Feb 27, 2017
UNLABELLED: Extracting information from peptidomics data is a major current challenge, as endogenous peptides can result from the activity of multiple enzymes. Proteolytic enzymes can display overlapping or complementary specificity. The activity spe...
Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features.
BMC bioinformatics
Dec 23, 2016
BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) aspartic protease is an important enzyme owing to its imperative part in viral development and a causative agent of deadliest disease known as acquired immune deficiency syndrome (AIDS). Dev...
Molecular Properties of Drugs Interacting with SLC22 Transporters OAT1, OAT3, OCT1, and OCT2: A Machine-Learning Approach.
The Journal of pharmacology and experimental therapeutics
Aug 3, 2016
Statistical analysis was performed on physicochemical descriptors of ∼250 drugs known to interact with one or more SLC22 "drug" transporters (i.e., SLC22A6 or OAT1, SLC22A8 or OAT3, SLC22A1 or OCT1, and SLC22A2 or OCT2), followed by application of ma...
Membrane Transport Proteins
Protein Conformation
Substrate Specificity
Organic Cation Transporter 1
Organic Anion Transport Protein 1
Models, Molecular
Organic Anion Transporters, Sodium-Independent
Pharmaceutical Preparations
Hydrogen-Ion Concentration
Machine Learning
Protein Binding
Computational Biology
Protease Inhibitors in View of Peptide Substrate Databases.
Journal of chemical information and modeling
Jun 9, 2016
Protease substrate profiling has nowadays almost become a routine task for experimentalists, and the knowledge on protease peptide substrates is easily accessible via the MEROPS database. We present a shape-based virtual screening workflow using vROC...
Development of a Support Vector Machine-Based System to Predict Whether a Compound Is a Substrate of a Given Drug Transporter Using Its Chemical Structure.
Journal of pharmaceutical sciences
Jun 1, 2016
The aim of this study was to develop an in silico prediction system to assess which of 7 categories of drug transporters (organic anion transporting polypeptide [OATP] 1B1/1B3, multidrug resistance-associated protein [MRP] 2/3/4, organic anion transp...
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