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q-bio.MN2021
Dynamic network analysis improves protein 3D structural classification
Khalique Newaz, Jacob Piland, Patricia L. Clark +3
Protein structural classification (PSC) is a supervised problem of assigning proteins into pre-defined structural (e.g., CATH or SCOPe) classes based on the proteins' sequence or 3…
q-bio.MN2019
Network analysis of synonymous codon usage
Khalique Newaz, Gabriel Wright, Jacob Piland +4
Most amino acids are encoded by multiple synonymous codons. For an amino acid, some of its synonymous codons are used much more rarely than others. Analyses of positions of such ra…
q-bio.MN2016
Network approach integrates 3D structural and sequence data to improve protein structural comparison
Fazle E. Faisal, Julie L. Chaney, Khalique Newaz +4
Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approach…