43 citations · 91 across the 10 of their papers we have counts for
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Estimation of Amino Acid Residue Substitution Rates at Local Spatial Regions and Application in Protein Function Inference: A Bayesian Monte Carlo Approach
Yan Y. Tseng, Jie Liang
The amino acid sequences of proteins provide rich information for inferring distant phylogenetic relationships and for predicting protein functions. Estimating the rate matrix of r…
Developing optimal nonlinear scoring function for protein design
Changyu Hu, Xiang Li, Jie Liang
Motivation. Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide t…
Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models
Jinfeng Zhang, Yu Chen, Rong Chen +1
In simple models side chains are often represented implicitly (e.g., by spin-states) or simplified as one atom. We study side chain effects using square lattice and tetrahedral lat…
Are residues in a protein folding nucleus evolutionarily conserved?
Yan Yuan Tseng, Jie Liang
It is important to understand how protein folding and evolution influences each other. Several studies based on entropy calculation correlating experimental measurement of residue…