Related papers: A geometrical framework for thinking about protein…
To better understand protein-solvent interaction we have analyzed a variety of physical and geometrical properties of the solvent-excluded surfaces (SESs) over a large set of soluble proteins with crystal structures. We discover that all…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
The purpose of this work is to demonstrate how an arbitrarily chosen background of the Universe can be made a solution of a simple geometric sigma model. Geometric sigma models are purely geometric theories in which spacetime coordinates…
Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose…
Learning meaningful protein representation is important for a variety of biological downstream tasks such as structure-based drug design. Having witnessed the success of protein sequence pretraining, pretraining for structural data which is…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Multimodal approaches that integrate protein structure and sequence have achieved remarkable success in protein-protein interface prediction. However, extending these methods to protein-peptide interactions remains challenging due to the…
Persistent homology is a powerful tool for characterizing the topology of a data set at various geometric scales. When applied to the description of molecular structures, persistent homology can capture the multiscale geometric features and…
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.
This paper investigates the foundations of deep learning through insight of geometry, algebra and differential calculus. At is core, artificial intelligence relies on assumption that data and its intrinsic structure can be embedded into…
Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…
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…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Recently described stochastic models of protein evolution have demonstrated that the inclusion of structural information in addition to amino acid sequences leads to a more reliable estimation of evolutionary parameters. We present a…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…
Inspired by protein folding, we explored the construction of three-dimensional structures and machines from one-dimensional chains of simple building blocks. This approach not only allows us to recreate the self-replication mechanism…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…