Solvatochromism occurs in both homogeneous solvents and more complex biological environments, such as proteins. While in both cases the solvatochromic effects report on the surroundings of the chromophore, their interpretation in proteins becomes mor...
Electrostatic calculations are generally used in studying the thermodynamics and kinetics of biomolecules in solvent. Generally, this is performed by solving the Poisson-Boltzmann equation on a large grid system, a process known to be time consuming....
Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecule...
Drosophila Ncd proteins are motor proteins that play important roles in spindle organization. Ncd and the tubulin dimer are highly charged. Thus, it is crucial to investigate Ncd-tubulin dimer interactions in the presence of ions, especially ions tha...
Chemistry (Weinheim an der Bergstrasse, Germany)
Sep 28, 2023
In the context of drug discovery, computational methods were able to accelerate the challenging process of designing and optimizing a new drug candidate. Amongst the possible atomistic simulation approaches, metadynamics (metaD) has proven very power...
Journal of chemical information and modeling
Aug 21, 2023
Many challenges persist in developing accurate computational models for predicting solvation free energy (Δ). Despite recent developments in Machine Learning (ML) methodologies that outperformed traditional quantum mechanical models, several issues r...
Robots typically interact with their environments via feedback loops consisting of electronic sensors, microcontrollers, and actuators, which can be bulky and complex. Researchers have sought new strategies for achieving autonomous sensing and contro...
CO sorption in physical solvents is one of the promising approaches for carbon capture from highly concentrated CO streams at high pressures. Identifying an efficient solvent and evaluating its solubility data at different operating conditions are hi...
FSATOOL is an integrated molecular simulation and data analysis program. Its old molecular dynamics engine only supports simulations in vacuum or implicit solvent. In this work, we implement the well-known smooth particle mesh Ewald method for simula...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 3, 2023
Protein secondary structure, solvent accessibility and torsion angle predictions are preliminary steps to predict 3D structure of a protein. Deep learning approaches have achieved significant improvements in predicting various features of protein str...
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