96 citations · 441 across the 21 of their papers we have counts for
5 papers · 1 filter
Interstrand pairing patterns in -barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction
Ronald Jackups, Jie Liang
-barrel membrane proteins are found in the outer membrane of gram-negative bacteria, mitochondria, and chloroplasts. We have developed probabilistic models to quantify propensit…
Knowledge-based energy functions for computational studies of proteins
Xiang Li, Jie Liang
This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction,…
Computation of protein geometry and its applications: Packing and function prediction
Jie Liang
This chapter discusses geometric models of biomolecules and geometric constructs, including the union of ball model, the weigthed Voronoi diagram, the weighted Delaunay triangulati…
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…
Protein folding dynamics via quantification of kinematic energy landscape
Sëma Kachalo, Hsiao-Mei Lu, Jie Liang
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master…