Related papers: Quantum Proteomics
Due to the highly complex chemical structure of biomolecules, the extensive understanding of the electronic information for proteomics can be challenging. Here, we constructed a charge transfer database at residue level derived from…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
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…
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…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
A class of analog computers built from large numbers of microscopic probabilistic machines is discussed. It is postulated that such computers are implemented in biological systems as ensembles of protein molecules. The formalism is based on…
A comparative classification scheme provides a good basis for several approaches to understand proteins, including prediction of relations between their structure and biological function. But it remains a challenge to combine a…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when…
High-throughput approximations of quantum mechanics calculations and combinatorial experiments have been traditionally used to reduce the search space of possible molecules, drugs and materials. However, the interplay of structural and…
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…
Binding energy is a fundamental thermodynamic property that governs molecular interactions, playing a crucial role in fields such as healthcare and the natural sciences. It is particularly relevant in drug development, vaccine design, and…
Theoretical studies in attosecond physics and chemistry require a full-fledged quantum physical framework including light-field-controlled pulses; this is one hypothesis lying behind the present work. At laboratory level electromagnetic…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
We propose a novel physical realization of a quantum computer. The qubits are electric dipole moments of ultracold diatomic molecules, oriented along or against an external electric field. Individual molecules are held in a 1-D trap array,…
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…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
The dielectric properties of proteins, particularly in their hydrated state, have been extensively studied. Numerous theoretical and experimental investigations have reported values of both the permittivity and the intrinsic dipole moments…
We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…