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Helix-helix packing and interfacial pairwise interactions of residues in membrane proteins.
Helix-helix packing plays a critical role in maintaining the tertiary structures of helical membrane proteins. By examining the overall distribution of voids and pockets in the transmembrane (TM)… Expand
Are proteins well-packed?
The average packing density inside proteins is as high as in crystalline solids. Does this mean proteins are well-packed? We go beyond average densities, and look at the full distribution functions… Expand
Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction.
beta-Barrel membrane proteins are found in the outer membrane of Gram-negative bacteria, mitochondria, and chloroplasts. Little is known about how residues in membrane beta-barrels interact… Expand
Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape
- J. Liang, H. Edelsbrunner, P. Fu, P. Sudhakar, S. Subramaniam
- Computer Science, Medicine
- 1 October 1998
The size and shape of macromolecules such as proteins and nucleic acids play an important role in their functions. Prior efforts to quantify these properties have been based on various discretization… Expand
Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
- X. Li, O. Keskin, B. Ma, R. Nussinov, J. Liang
- Chemistry, Medicine
- Journal of molecular biology
- 26 November 2004
Energetic hot spots account for a significant portion of the total binding free energy and correlate with structurally conserved interface residues. Here, we map experimentally determined hot spots… Expand
Computation of molecular electrostatics with boundary element methods.
In continuum approaches to molecular electrostatics, the boundary element method (BEM) can provide accurate solutions to the Poisson-Boltzmann equation. However, the numerical aspects of this method… Expand
Structural location of disease-associated single-nucleotide polymorphisms.
- N. Stitziel, Y. Y. Tseng, Dimitri Pervouchine, D. Goddeau, S. Kasif, J. Liang
- Biology, Medicine
- Journal of molecular biology
- 11 April 2003
Non-synonymous single-nucleotide polymorphism (nsSNP) of genes introduces amino acid changes to proteins, and plays an important role in providing genetic functional diversity. To understand the… Expand
Facile synthesis of alumina-decorated multi-walled carbon nanotubes for simultaneous adsorption of cadmium ion and trichloroethylene
Abstract An adsorbent was prepared by decorating alumina onto the surface of multi-wall carbon nanotubes (MWCNTs) for simultaneous removal of cadmium ion (Cd(II) ion) and trichloroethylene (TCE) from… Expand
Combinatorial interpretations of congruences for the spt-function
Let spt(n) denote the total number of appearances of the smallest parts in all the partitions of n. In 1988, the second author gave new combinatorial interpretations of Ramanujan’s partition… Expand
Inferring functional relationships of proteins from local sequence and spatial surface patterns.
We describe a novel approach for inferring functional relationship of proteins by detecting sequence and spatial patterns of protein surfaces. Well-formed concave surface regions in the form of… Expand