Perspective: Coarse-grained models for biomolecular systems
WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …
grained (CG) models provide significant computational and conceptual advantages with …
Three-dimensional protein structure prediction: Methods and computational strategies
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …
D) structure of a protein when only a sequence of amino acid residues is given. Many …
Statistical potential for assessment and prediction of protein structures
Protein structures in the Protein Data Bank provide a wealth of data about the interactions
that determine the native states of proteins. Using the probability theory, we derive an atomic …
that determine the native states of proteins. Using the probability theory, we derive an atomic …
Residue–residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
S Miyazawa, RL Jernigan - Journal of molecular biology, 1996 - Elsevier
Attractive inter-residue contact energies for proteins have been re-evaluated with the same
assumptions and approximations used originally by us in 1985, but with a significantly larger …
assumptions and approximations used originally by us in 1985, but with a significantly larger …
Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment
A wealth of protein and DNA sequence data is being generated by genome projects and
other sequencing efforts. A crucial barrier to deciphering these sequences and …
other sequencing efforts. A crucial barrier to deciphering these sequences and …
Implicit solvent models
B Roux, T Simonson - Biophysical chemistry, 1999 - Elsevier
Implicit solvent models for biomolecular simulations are reviewed and their underlying
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …
statistical mechanical basis is discussed. The fundamental quantity that implicit models seek …
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
The distance‐dependent structure‐derived potentials developed so far all employed a
reference state that can be characterized as a residue (atom)‐averaged state. Here, we …
reference state that can be characterized as a residue (atom)‐averaged state. Here, we …
Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V
A Antonellis, RE Ellsworth, N Sambuughin… - The American Journal of …, 2003 - cell.com
Charcot-Marie-Tooth disease type 2D (CMT2D) and distal spinal muscular atrophy type V
(dSMA-V) are axonal peripheral neuropathies inherited in an autosomal dominant fashion …
(dSMA-V) are axonal peripheral neuropathies inherited in an autosomal dominant fashion …
Conservation and prediction of solvent accessibility in protein families
Currently, the prediction of three‐dimensional (3D) protein structure from sequence alone is
an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued …
an exceedingly difficult task. As an intermediate step, a much simpler task has been pursued …
From genes to protein structure and function: novel applications of computational approaches in the genomic era
J Skolnick, JS Fetrow - Trends in biotechnology, 2000 - cell.com
The genome-sequencing projects are providing a detailed 'parts list'of life. A key to
comprehending this list is understanding the function of each gene and each protein at …
comprehending this list is understanding the function of each gene and each protein at …