Protein topology and stability define the space of allowed sequences
We describe a new approach to explore and quantify the sequence space associated with a
given protein structure. A set of sequences are optimized for a given target structure, using …
given protein structure. A set of sequences are optimized for a given target structure, using …
Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations
J Higo, N Ito, M Kuroda, S Ono, N Nakajima… - Protein …, 2001 - Wiley Online Library
The energy landscape of a peptide [Ace‐Lys‐Gln‐Cys‐Arg‐Glu‐Arg‐Ala‐Nme] in explicit
water was studied with a multicanonical molecular dynamics simulation, and the AMBER …
water was studied with a multicanonical molecular dynamics simulation, and the AMBER …
Geometry selects highly designable structures
V Shahrezaei, MR Ejtehadi - The Journal of Chemical Physics, 2000 - pubs.aip.org
By enumerating all sequences of length 20, we study the designability of structures in a two-
dimensional hydrophobic-polar HP lattice model in a wide range of intermonomer …
dimensional hydrophobic-polar HP lattice model in a wide range of intermonomer …
Correlations between designability and various structural characteristics of protein lattice models
Using six kinds of lattice types ( 4× 4, 5× 5, and 6× 6 square lattices; 3× 3× 3 cubic
lattice; and 2+ 3+ 4+ 3+ 2 and 4+ 5+ 6+ 5+ 4 triangular lattices), three different size …
lattice; and 2+ 3+ 4+ 3+ 2 and 4+ 5+ 6+ 5+ 4 triangular lattices), three different size …
Secondary-structure-favored hydrophobic-polar lattice model of protein folding
H Chen, X Zhou, ZC Ou-Yang - Physical Review E, 2001 - APS
Protein folding is studied using a two-dimensional lattice model with the Hamiltonian
including both hydrophobic interactions and main chain hydrogen bond interactions of …
including both hydrophobic interactions and main chain hydrogen bond interactions of …