Dynamic formation and breaking of disulfide bonds in molecular dynamics simulations with the UNRES force field
M Chinchio, C Czaplewski, A Liwo… - Journal of chemical …, 2007 - ACS Publications
Many proteins contain disulfide bonds that are usually essential for maintaining function and
a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds …
a stable structure. Several algorithms attempt to predict the arrangement of disulfide bonds …
Replica exchange and multicanonical algorithms with the coarse-grained united-residue (UNRES) force field
M Nanias, C Czaplewski… - Journal of chemical theory …, 2006 - ACS Publications
Three algorithms, namely, a replica exchange method (REM), a replica exchange
multicanonical method (REMUCA), and a replica exchange multicanonical method with …
multicanonical method (REMUCA), and a replica exchange multicanonical method with …
Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 2. Off-lattice tests of the method with single proteins
S Ołdziej, A Liwo, C Czaplewski, J Pillardy… - The Journal of …, 2004 - ACS Publications
We describe the application of our recently proposed method of hierarchical optimization of
the protein energy landscape to optimize our off-lattice united-residue (UNRES) force field …
the protein energy landscape to optimize our off-lattice united-residue (UNRES) force field …
PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics
A key regulator of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptor
traffic, PICK1 is known to interact with over 40 other proteins, including receptors …
traffic, PICK1 is known to interact with over 40 other proteins, including receptors …
Implementations of Nosé–Hoover and Nosé–Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain
DS Kleinerman, C Czaplewski, A Liwo… - The Journal of chemical …, 2008 - pubs.aip.org
Molecular dynamics (MD) simulations generate a canonical ensemble only when integration
of the equations of motion is coupled to a thermostat. Three extended phase space …
of the equations of motion is coupled to a thermostat. Three extended phase space …
Molecular dynamics with the united-residue force field: Ab initio folding simulations of multichain proteins
The implementation of molecular dynamics with the united-residue (UNRES) force field is
extended to treat multichain proteins. Constant temperature was maintained in the …
extended to treat multichain proteins. Constant temperature was maintained in the …
A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
D Alemani, F Collu, M Cascella… - Journal of chemical …, 2010 - ACS Publications
We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of
proteins. This term mimics the backbone dipole− dipole interactions and accounts for the …
proteins. This term mimics the backbone dipole− dipole interactions and accounts for the …
Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization
We report the application of the hierarchical optimization method of protein potential-energy
landscapes described in the accompanying papers (Liwo, A.; Arłukowicz, P.; Ołdziej, S.; …
landscapes described in the accompanying papers (Liwo, A.; Arłukowicz, P.; Ołdziej, S.; …
[HTML][HTML] Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach
Coarse-grained models are useful tools to investigate the structural and thermodynamic
properties of biomolecules. They are obtained by merging several atoms into one interaction …
properties of biomolecules. They are obtained by merging several atoms into one interaction …
Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems: Toward millisecond-scale …
We report the implementation of our united-residue UNRES force field for simulations of
protein structure and dynamics with massively parallel architectures. In addition to coarse …
protein structure and dynamics with massively parallel architectures. In addition to coarse …