Related papers: Geometric and physical considerations for realisti…
Changes in the extent of local concavity along with changes in surface roughness of binding sites of proteins have long been considered as useful markers to identify functional sites of proteins. However, an algorithm that describes the…
A simple lattice model for proteins that allows for distinct sizes of the amino acids is presented. The model is found to lead to a significant number of conformations that are the unique ground state of one or more sequences or encodable.…
The idea of this project is to study the protein structure and sequence relationship using the hidden markov model and artificial neural network. In this context we have assumed two hidden markov models. In first model we have taken protein…
The primary building block of the body is collagen, which is found in the extracellular matrix and in many stress-bearing tissues such as tendon and cartilage. It provides elasticity and support to cells and tissues while influencing…
The Automated Protein Structure Analysis (APSA) method, which describes the protein backbone as a smooth line in 3-dimensional space and characterizes it by curvature kappa and torsion tau as a function of arc length s, was applied on 77…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
The ability to consistently distinguish real protein structures from computationally generated model decoys is not yet a solved problem. One route to distinguish real protein structures from decoys is to delineate the important physical…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
This chapter gives a graceful introduction to problem of protein three- dimensional structure prediction, and focuses on how to make structural sense out of a single input sequence with unknown structure, the 'query' or 'target' sequence.…
Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…
The folding of a polypeptide is an example of the cooperative effects of the amino-acid residues. Of recent interest is how a secondary structure, such as a helix, spontaneously forms during the collapse of a peptide from an initial…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…
Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…
Tissue engineering aims to grow artificial tissues \emph{in vitro} to replace those in the body that have been damaged through age, trauma or disease. A recent approach to engineer artificial cartilage involves seeding cells within a…
We have studied the competition between helix formation and aggregation for a simple polymer model. We present simulation results for a system of two such polymers, examining the potential of mean force, the balance between inter and…
In the standard approach to lattice proteins the models based on nearest neighbor interaction are used. In this kind of models it is difficult to explain the existence of secondary structures --- special preferred conformations of protein…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…