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Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized,…

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…

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…

The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…

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…

Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…

Recent years have seen tremendous developments in the use of machine learning models to link amino acid sequence, structure and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and…

We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is…

A model to describe the mechanism of conformational dynamics in protein based on matter interactions using lagrangian approach and imposing certain symmetry breaking is proposed. Both conformation changes of proteins and the injected…

We show that the folding rates (k_F) of RNA are determined by N, the number of nucleotides. By assuming that the distribution of free energy barriers separating the folded and the unfolded states is Gaussian, which follows from central…

For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…

Proteins are macromolecules responsible for essential functions in almost all living organisms. Designing reasonable proteins with desired functions is crucial. A protein's sequence and structure are strongly correlated and they together…

The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins.…

Many types of peripheral and transmembrane proteins can sense and generate membrane curvature. Laterally isotropic proteins and crescent proteins with twofold rotational symmetry, such as Bin/Amphiphysin/Rvs superfamily proteins, have been…

Theory of multi-dimensional representation of free energy surface of protein folding is developed by adopting structural order parameters of multiple regions in protein as multiple coordinates. Various scenarios of folding are classified in…

We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…

We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…

A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into…

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…

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…