16 citations · 51 across the 38 of their papers we have counts for
11 papers · 1 filter
TALI: Protein Structure Alignment Using Backbone Torsion Angles
Xijiang Miao, Michael G. Bryson, Homayoun Valafar
This article introduces a novel protein structure alignment method (named TALI) based on the protein backbone torsion angle instead of the more traditional distance matrix. Because…
Identification of 1H-NMR Spectra of Xyloglucan Oligosaccharides: A Comparative Study of Artificial Neural Networks and Bayesian Classification Using Nonparametric Density Estimation
Faramarz Valafar, Homayoun Valafar, William S. York
Proton nuclear magnetic resonance (1H-NMR) is a widely used tool for chemical structural analysis. However, 1H-NMR spectra suffer from natural aberrations that render computer-assi…
A Preliminary Investigation in the Molecular Basis of Host Shutoff Mechanism in SARS-CoV
Niharika Pandala, Casey A. Cole, Devaun McFarland +2
Recent events leading to the worldwide pandemic of COVID-19 have demonstrated the effective use of genomic sequencing technologies to establish the genetic sequence of this virus.…
An Artificial Neural Network Based Approach for Identification of Native Protein Structures using an Extended ForceField
Timothy Matthew Fawcett, Stephanie Irausquin, Mikhail Simin +1
Current protein forcefields like the ones seen in CHARMM or Xplor-NIH have many terms that include bonded and non-bonded terms. Yet the forcefields do not take into account the use…
An Investigation of Minimum Data Requirement for Successful Structure Determination of Pf2048.1 with REDCRAFT
Casey A. Cole, Daniela Ishimaru, Mirko Hennig +1
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also know as nuclear Overhauser effects (NOEs). The use of NOEs as the p…
Improvements of the REDCRAFT Software Package
Casey A Cole, Caleb Parks, Julian Rachele +1
Traditional approaches to elucidation of protein structures by NMR spectroscopy rely on distance restraints also known as nuclear Overhauser effects (NOEs). The use of NOEs as the…
Aligning Multiple Protein Structures using Biochemical and Biophysical Properties
Paul Shealy, Homayoun Valafar
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships…
Using Residual Dipolar Couplings from Two Alignment Media to Detect Structural Homology
Ryan Yandle, Rishi Mukhopadhyay, Homayoun Valafar
The method of Probability Density Profile Analysis has been introduced previously as a tool to find the best match between a set of experimentally generated Residual Dipolar Coupli…
Minimum Data Requirements and Supplemental Angle Constraints for Protein Structure Prediction with REDCRAFT
E. Timko, P. Shealy, M. Bryson +1
One algorithm to predict protein structure is the residual dipolar coupling based residue assembly and filter tool (REDCRAFT). This algorithm exploits an exponential reduction of t…
Automated Assignment of Backbone Resonances Using Residual Dipolar Couplings Acquired from a Protein with Known Structure
P. Shealy, R. Mukhopadhyay, S. Smith +1
Resonance assignment is a critical first step in the investigation of protein structures using NMR spectroscopy. The development of assignment methods that require less experimenta…
Protein Fold Family Recognition From Unassigned Residual Dipolar Coupling Data
Rishi Mukhopadhyay, Paul Shealy, Homayoun Valafar
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are pr…