Related papers: Representing Rod-Shaped Protein 3D Structures in C…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
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…
Motivation: Proteins are known to undergo conformational changes in the course of their functions. The changes in conformation are often attributable to a small fraction of residues within the protein. Therefore identification of these…
The biological function of a protein stems from its 3-dimensional structure, which is thermodynamically determined by the energetics of interatomic forces between its amino acid building blocks (the order of amino acids, known as the…
Interactive molecular graphics applications facilitate analysis of three dimensional protein structures. Naturally, non-interactive 2-D snapshots of the protein structures do not convey the same level of geometric detail. Several 2-D…
Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work,…
Proteins are the basic building blocks of life. They usually perform functions by folding to a particular structure. Understanding the folding process could help the researchers to understand the functions of proteins and could also help to…
We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to…
The goal of Protein Structure Prediction (PSP) problem is to predict a protein's 3D structure (confirmation) from its amino acid sequence. The problem has been a 'holy grail' of science since the Noble prize-winning work of Anfinsen…
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic…
Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies and underlies the inverse protein folding problem. Herein, we outline our theories for fold-recognition in the "twilight-zone" of sequence…
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…
By using a mixture model for the density distribution of the three pseudobond angles formed by $C_\alpha$ atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural…
Proteins are fundamental biological entities that play a key role in life activities. The amino acid sequences of proteins can be folded into stable 3D structures in the real physicochemical world, forming a special kind of…
Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe…
Microproteins are a newly recognized and rapidly growing class of small proteins, typically encoded by fewer than 100 to 150 codons and translated from small open reading frames (smORFs). Although research has shown that smORFs and their…
Learning from 3D protein structures has gained wide interest in protein modeling and structural bioinformatics. Unfortunately, the number of available structures is orders of magnitude lower than the training data sizes commonly used in…