Use of fuzzy clustering technique and matrices to classify amino acids and its impact to Chou's pseudo amino acid composition

DN Georgiou, TE Karakasidis, JJ Nieto… - Journal of theoretical …, 2009 - Elsevier
In this paper we present a study of classification of the 20 amino acids via a fuzzy clustering
technique. In order to calculate distances among the various elements we employ two …

Evaluating polymer representations via quantifying structure–property relationships

R Ma, Z Liu, Q Zhang, Z Liu, T Luo - Journal of chemical …, 2019 - ACS Publications
Machine learning techniques are being applied in quantifying structure–property
relationships for a wide variety of materials, where the properly represented materials play …

Graph theory-based sequence descriptors as remote homology predictors

G Agüero-Chapin, D Galpert, R Molina-Ruiz… - Biomolecules, 2019 - mdpi.com
Alignment-free (AF) methodologies have increased in popularity in the last decades as
alternative tools to alignment-based (AB) algorithms for performing comparative sequence …

New descriptors of amino acids and their application to peptide QSAR study

Z Lin, H Long, Z Bo, Y Wang, Y Wu - Peptides, 2008 - Elsevier
A new set of descriptors was derived from a matrix of three structural variables of the natural
amino acid, including van der Waal's volume, net charge index and hydrophobic parameter …

HP-Lattice QSAR for dynein proteins: experimental proteomics (2D-electrophoresis, mass spectrometry) and theoretic study of a Leishmania infantum sequence

MA Dea-Ayuela, Y Pérez-Castillo… - Bioorganic & Medicinal …, 2008 - Elsevier
The toxicity and inefficacy of actual organic drugs against Leishmaniosis justify research
projects to find new molecular targets in Leishmania species including Leishmania infantum …

Using entropy of drug and protein graphs to predict FDA drug-target network: theoretic-experimental study of MAO inhibitors and hemoglobin peptides from Fasciola …

F Prado-Prado, X García-Mera, P Abeijón… - European journal of …, 2011 - Elsevier
There are many drugs described with very different affinity to a large number of receptors. In
this work, we selected Drug-Target pairs (DTPs/nDTPs) of drugs with high affinity/non-affinity …

Alignment-Free Prediction of Polygalacturonases with Pseudofolding Topological Indices: Experimental Isolation from Coffea arabica and Prediction of a New …

G Agüero-Chapin, J Varona-Santos… - Journal of proteome …, 2009 - ACS Publications
Polygalacturonases (PGs) have called the attention of microbiology scientists and
biotechnology or pharmaceutical industry because they are protein enzymes relevant to …

3D entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in Leishmania parasites

R Concu, MA Dea-Ayuela, LG Perez-Montoto… - … et Biophysica Acta (BBA …, 2009 - Elsevier
The number of protein 3D structures without function annotation in Protein Data Bank (PDB)
has been steadily increased. This fact has led in turn to an increment of demand for …

Quantitative sequence-activity model (QSAM): applying QSAR strategy to model and predict bioactivity and function of peptides, proteins and nucleic acids

P Zhou, F Tian, Y Wu, Z Li… - Current Computer-Aided …, 2008 - ingentaconnect.com
Traditional quantitative structure-activity relationship (QSAR) is a term describing a variety of
approaches that are of substantial interest for chemistry. Quantitative sequence-activity …