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The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to the standard Monte Carlo dynamics. In accord with previous theoretical predictions we find that the folding time grows… (More)

Finite size effects on the calorimetric cooperatity of the folding-unfolding transition in two-state proteins are considered using the Go lattice models with and without side chains. We show that for models without side chains a dimensionless measure of calorimetric cooperativity κ2 defined as the ratio of the van't Hoff to calorimetric enthalpy does not… (More)

We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that ∆T /T F ∼ N −1 , where T F is the folding transition temperature and ∆T is the transition width computed using the temperature dependence of the order parameter that distinguishes… (More)

Scaling of folding properties of proteins is studied in a toy system – the lattice Go model with various two-and three-dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with the system size. The corresponding exponents are not universal. Scaling of the thermodynamic stability also indicates… (More)

- N. S. Lam, M. Kouza, H. Zung, M. S. Li, Ulrich H. E. Hansmann, Jan H. Meinke +7 others
- 2008

Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above.… (More)

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omegac, scales as Nzeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta=1+gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk.… (More)

An accurate estimation of binding free energy of a ligand to receptor ΔG(bind) is one of the most important problems in drug design. The success of solution of this problem is expected to depend on force fields used for modeling a ligand-receptor complex. In this paper, we consider the impact of four main force fields, AMBER99SB, CHARMM27, GROMOS96 43a1,… (More)

Since March 2009, the rapid spread of infection during the recent A/H1N1 swine flu pandemic has raised concerns of a far more dangerous outcome should this virus become resistant to current drug therapies. Currently oseltamivir (tamiflu) is intensively used for the treatment of influenza and is reported effective for 2009 A/H1N1 virus. However, as this… (More)

Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature (T) and the number of chains (M). While these models are, at best, caricatures of peptides, we show that a number of generic features thought to govern fibril assembly are captured by the toy model. The monomer,… (More)

Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales (τ f ib) for their formation depend on a balance between hydrophobic and coulomb interactions. The extent of population… (More)