REFERENCES
- ToofannyRD, DaggettV. Understanding protein unfolding from molecular simulations. Wiley Interdiscip Rev. Comput. Mol. Sci. 2012;2:405–423.
- SakaeY, OkamotoY. Folding simulations of three proteins having all alpha-helix, all beta-strand and alpha/beta-structures. Mol. Simul. 2010;36:302–310.
- MeierK, van GunsterenWF. Cyclic beta-helical/beta-hairpin d,l-alpha-peptide: study of its folding properties and structure refinement using molecular dynamics. J. Phys. Chem. A. 2010;114:1852–1859.
- FreddolinoPL, HarrisonCB, LiuYX, SchultenK. Challenges in protein-folding simulations. Nat. Phys. 2010;6:751–758.
- SudolM, RecinosCC, AbraczinskasJ, HumbertJ, FarooqA. WW or WoW: the WW domains in a union of bliss. IUBMB Life. 2005;57:773–778.
- IlsleyJL, SudolM, WinderSJ. The WW domain: linking cell signalling to the membrane cytoskeleton. Cell Signal. 2002;14:183–189.
- CieplakM, HoangTX. Coarse grained description of protein folding. Phys. Rev. E. 1998;58:3589–3596.
- TianXH, ZhengYH, JiaoX, LiuCX, ChangS. Computational model for protein unfolding simulation. Phys. Rev. E. 2011;83:061910.
- ChangS, JiaoX, HuJP, ChenY, TianXH. Stability and folding behavior analysis of zinc-finger using simple models. Int. J. Mol. Sci. 2010;11:4014–4034.
- ClementiC. Coarse-grained models of protein folding: toy models or predictive tools?Curr. Opin. Struct. Biol. 2008;18:10–15.
- ChenWW, TayDKS, LeongSSJ, KwakSK. Three-dimensional structure of human beta-defensin 28 via homology modelling and molecular dynamics. Mol. Simul. 2012;38:90–101.
- ZhangJ, LiWF, WangJ, QinM, WuL, YanZQ, XuWX, ZuoGH, WangW. Protein folding simulations: from coarse-grained model to all-atom model. IUBMB Life. 2009;61:627–643.
- WangDQ, JaunB, van GunsterenWF. Folding and unfolding of two mixed alpha/beta peptides. Chembiochem. 2009;10:2032–2041.
- ChenC, XiaoY. Observation of multiple folding pathways of beta-hairpin trpzip2 from independent continuous folding trajectories. Bioinformatics. 2008;24:659–665.
- MaciasMJ, GervaisV, CiveraC, OschkinatH. Structural analysis of WW domains and design of a WW prototype. Nat. Struct. Mol. Biol. 2000;7:375–379.
- KimE, JangS, LimM, PakY. Free energy landscape of the FBP28 WW domain by all-atom direct folding simulation. J. Phys. Chem. B. 2010;114:7686–7691.
- KaranicolasJ, BrooksCL. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc. Natl. Acad. Sci. U S A. 2004;101:3432–3437.
- KaranicolasJ, BrooksCL. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design. Proc. Natl. Acad. Sci. U S A. 2003;100:3954–3959.
- MuY, NordenskioldL, TamJP. Folding, misfolding, and amyloid protofibril formation of WW domain FBP28. Biophys. J. 2006;90:3983–3992.
- XuJ, HuangL, ShakhnovichEI. The ensemble folding kinetics of the FBP28 WW domain revealed by an all-atom Monte Carlo simulation in a knowledge-based potential. Proteins. 2011;79:1704–1714.
- JuraszekJ, BolhuisPG. (Un)Folding mechanisms of the FBP28 WW domain in explicit solvent revealed by multiple rare event simulation methods. Biophys. J. 2010;98:646–656.
- LuoZ, DingJ, ZhouY. Temperature-dependent folding pathways of Pin1 WW domain: an all-atom molecular dynamics simulation of a GM model. Biophys. J. 2007;93:2152–2161.
- LuoZ, DingJ, ZhouY. Folding mechanisms of individual beta-hairpins in a Go model of Pin1 WW domain by all-atom molecular dynamics simulations. J. Chem. Phys. 2008;128:225103.
- SocolichM, LocklessSW, RussWP, LeeH, GardnerKH, RanganathanR. Evolutionary information for specifying a protein fold. Nature. 2005;437:512–518.
- SugitaY, OkamotoY. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999;314:141–151.
- LiWF, ZhangJ, WangW. Understanding the folding and stability of a zinc finger-based full sequence design protein with replica exchange molecular dynamics simulations. Proteins. 2007;67:338–349.
- ZhangJ, QinM, WangW. Folding mechanism of β-hairpins studied by replica exchange molecular simulations. Proteins. 2006;62:672–685.
- KawashimaY, SasakiYC, SugitaY, YodaT, OkamotoY. Replica-exchange molecular dynamics simulation of diffracted X-ray tracking. Mol. Simul. 2007;33:97–102.
- YodaT, SugitaY, OkamotoY. Cooperative folding mechanism of a beta-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation. Proteins. 2007;66:846–859.
- PhillipsJC, BraunR, WangW, GumbartJ, TajkhorshidE, VillaE, ChipotC, SkeelRD, KaleL, SchultenK. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005;26:1781–1802.
- VanommeslaegheK, HatcherE, AcharyaC, KunduS, ZhongS, ShimJ, DarianE, GuvenchO, LopesP, VorobyovI, MacKerellAD. CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 2010;31:671–690.
- DardenT, YorkD, PedersenL. Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993;98:10089–10092.
- RyckaertJ-P, CiccottiG, BerendsenHJC. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977;23:327–341.
- FerrenbergAM, SwendsenRH. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 1989;63:1195–1198.
- ZhangJ, LiWF, WangJ, QinM, WangW. All-atom replica exchange molecular simulation of protein BBL. Proteins. 2008;72:1038–1047.
- WeiZ, ChunW, YongD. Convergence of replica exchange molecular dynamics. J. Chem. Phys. 2005;123:154105.
- SeibertMM, PatrikssonA, HessB, van der SpoelD. Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 2005;354:173–183.