Nguyen Minh

AllerCatPro - Prediction of protein allergenicity potential from the protein sequence

Published date : 18 Jan 2019

MOTIVATION:
Due to the risk of inducing an immediate type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens.

type
Journal Paper
journal
Bioinformatics. 2019 Jan 18. doi: 10.1093/bioinformatics/btz029
Impact Factor
5.481

Simulations of mutant p53 DNA binding domains reveal a novel druggable pocket

Published date : 15 Jan 2019

The DNA binding domain (DBD) of the tumor suppressor p53 is the site of several oncogenic mutations. A subset of these mutations lowers the unfolding temperature of the DBD. Unfolding leads to the exposure of a hydrophobic β-strand and nucleates aggregation which results in pathologies through loss of function and dominant negative/gain of function effects.

type
Journal Paper
journal
Nuclei Acids Research, 2019, doi: 10.1093/nar/gky1314
Impact Factor
11.561

The interfacial character of antibody paratopes: analysis of antibody-antigen structures

Published date : 16 Jun 2017

In this study, computational methods are applied to investigate the general properties of antigen engaging residues of a paratope from a non-redundant dataset of 403 antibody-antigen complexes to dissect the contribution of hydrogen bonds, hydrophobic, van der Waals contacts and ionic interactions, as well as role of water molecules in the antigen-antibody interface. Consistent with previous reports using smaller datasets, we found that Tyr, Trp, Ser, Asn, Asp, Thr, Arg, Gly, His contribute substantially to the interactions between antibody and antigen.

type
Journal Paper
journal
Bioinformatics, 2017, doi: 10.1093/bioinformatics/btx389
Impact Factor
7.307

Discovery of Rab1 binding sites using an ensemble of clustering methods

Published date : 25 Jan 2017

Targeting non-native-ligand binding sites for potential investigative and therapeutic applications is an attractive strategy in proteins that share common native ligands, as in Rab1 protein. Rab1 is a subfamily member of Rab proteins, which are members of Ras GTPase superfamily. All Ras GTPase superfamily members bind to native ligands GTP and GDP, that switch on and off the proteins, respectively. Rab1 is physiologically essential for autophagy and transport between endoplasmic reticulum and Golgi apparatus.

type
Journal Paper
journal
PROTEINS: Structure, Function, and Bioinformatics, doi: 10.1002/prot.25254
Impact Factor
2.499

Topology independent comparison of RNA 3D structures using the CLICK algorithm

Published date : 14 Sep 2016

RNA molecules are attractive therapeutic targets because non-coding RNA molecules have increasingly been found to play key regulatory roles in the cell. Comparing and classifying RNA 3D structures yields unique insights into RNA evolution and function. With the rapid increase in the number of atomic-resolution RNA structures, it is crucial to have effective tools to classify RNA structures and to investigate them for structural similarities at different resolutions.

type
Journal Paper
journal
Nuclei Acids Research 2016, doi: 10.1093/nar/gkw819
Impact Factor
6.03

The Multifaceted Roles of Molecular Dynamics Simulations in Drug Discovery

Published date : 01 Aug 2016

Discovery of new therapeutics is a very challenging, expensive and time-consuming process. With the number of approved drugs declining steadily, combined with increasing costs, a rational approach is needed to facilitate, expedite and streamline the drug discovery process. In silico methods are playing key roles in the discovery of a growing number of marketed drugs. The use of computational approaches, particularly molecular dynamics, in drug design is rapidly gaining momentum and acceptance as an essential part of the toolkit for modern drug discovery.

type
Journal Paper
journal
Current Pharmaceutical Design, Vol. 22, Issue 23, 2016, Pg. 3585-3600, doi: 10.2174/1381612822666160425120507
Impact Factor
3.052

Rclick: A web server for comparison of RNA 3D structures

Published date : 12 Nov 2014

Summary: RNA molecules play important roles in key biological processes in the cell and are becoming attractive for developing therapeutic applications. Since the function of RNA depends on its structure and dynamics, comparing and classifying the RNA 3D structures is of crucial importance to molecular biology. In this study, we have developed Rclick, a web server that is capable of superimposing RNA 3D structures by using clique matching and 3D least squares fitting. Our server Rclick has been benchmarked and compared to other popular servers and methods for RNA structural alignments.

type
Journal Paper
journal
Bioinformatics (2014) doi: 10.1093/bioinformatics/btu75