生物大分子
All human diseases involve proteins, yet our current tools to characterize and quantify them are limited. To better elucidate proteins across space, time, and molecular composition, we provide provocative projections for technologies to…
In several previous works, I presented the mirror symmetry in the set of protein amino acids, expressed through the number of atoms. Here, however, the same thing is shown but over the number of nucleons and molecules mass. Compared to the…
Antibiotic resistance is a topical problem for both humans and animals and has been the subject of special monitoring for two decades. Several recent studies, including ours, have shown that this phenomenon is accentuated by the transfer of…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
Boltzmann machines (BM) are widely used as generative models. For example, pairwise Potts models (PM), which are instances of the BM class, provide accurate statistical models of families of evolutionarily related protein sequences. Their…
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…
Novel diagnostic and therapeutic radiopharmaceuticals are increasingly becoming a central part of personalized medicine. Continued innovation in the development of new radiopharmaceuticals is key to sustained growth and advancement of…
We investigate melting transition of DNA sequences embedded in a Langevin fluctuation-dissipation thermal bath. Torsional effects are considered by a twist angle $\varphi$ between neighboring base pairs stacked along the molecule backbone.…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Single-molecule F\"{o}rster resonance energy transfer (smFRET) has become a mainstream technique for probing biomolecular structural dynamics. The rapid and wide adoption of the technique by an ever-increasing number of groups has generated…
It is challenging to parameterize the force field for calcium ions (Ca2+) in calcium-binding proteins because of their unique coordination chemistry that involves the surrounding atoms required for stability. In this work, we observed wide…
Furin is a serine protease that takes part in the processing and activation of the host cell pre-proteins. The enzyme also plays an important role in the activation of several viruses like the newly emerging SARS-CoV-2 virus that causes…
A challenge in developing machine learning regression models is that it is difficult to know whether maximal performance has been reached on a particular dataset, or whether further model improvement is possible. In biology this problem is…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
Heparin has been found to have antiviral activity against SARS-CoV-2. Here, by means of sliding window docking, molecular dynamics simulations and biochemical assays, we investigate the binding mode of heparin to the virus spike…
We present a data set from a first-principles study of amino-methylated and acetylated (capped) dipeptides of the 20 proteinogenic amino acids - including alternative possible side chain protonation states and their interactions with…
The outcome of an epidemic is closely related to the network of interactions between the individuals. Likewise, protein functions depend on the 3D arrangement of their residues and on the underlying energetic interaction network. Borrowing…
Spike proteins, 1200 amino acids, are divided into two nearly equal parts, S1 and S2. We review here phase transition theory, implemented quantitatively by thermodynamic scaling. The theory explains the evolution of Coronavirus extremely…
Progress in real-time, simultaneous in vivo detection of multiple neurotransmitters will help accelerate advances in neuroscience research. The need for development of probes capable of stable electrochemical detection of rapid…
The native state structures of globular proteins are stable and well-packed indicating that self-interactions are favored over protein-solvent interactions under folding conditions. We use this as a guiding principle to derive the geometry…