Related papers: Introducing Protein Folding Using Simple Models
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We use a free energy functional theory to elucidate general properties of heterogeneously ordering, fast folding proteins, and we test our conclusions with lattice simulations. We find that both structural and energetic heterogeneity can…
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
A small fraction of all protein structures characterized so far are entangled. The challenge of understanding the properties of these knotted proteins, and the why and the how of their natural folding process, has been taken up in the past…
Theoretical studies of protein folding on lattice models relie on the assumption that water close to amino-acids is always in thermal equilibrium all along the folding pathway. Within this framework, it has always been considered that…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We review some of our recent results obtained within the scope of simple lattice models and Monte Carlo simulations that illustrate the role of native geometry in the folding kinetics of two state folders.
The principles underlying protein folding remains one of Nature's puzzles with important practical consequences for Life. An approach that has gathered momentum since the late 1990's, looks at protein hetero-polymers and their folding…
Natural protein sequences somehow encode the structural forms that these molecules adopt. Recent developments in structure-prediction are agnostic to the mechanisms by which proteins fold and represent them as static objects. However, the…
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…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…