Journal of chemical theory and computation
Nov 18, 2021
An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen-major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we appl...
Journal of chemical information and modeling
Nov 9, 2021
In recent years, the use of deep learning (neural network) potential energy surface (NNPES) in molecular dynamics simulation has experienced explosive growth as it can be as accurate as quantum chemistry methods while being as efficient as classical ...
While the construction of a dependable force field for performing classical molecular dynamics (MD) simulation is crucial for elucidating the structure and function of biomolecular systems, the attempts to do this for glycans are relatively sparse co...
The journal of physical chemistry letters
Oct 27, 2021
The utilization of artificial neural networks (ANNs) provides strategies for accelerating molecular simulations. Herein, ANNs are implemented as propagators of the time-dependent Schrödinger equation to simulate the quantum dynamics of systems with t...
The main protease of SARS-CoV-2 is a critical target for the design and development of antiviral drugs. 2.5 M compounds were used in this study to train an LSTM generative network via transfer learning in order to identify the four best candidates ca...
Blocking the main replicating enzyme, 3 Chymotrypsin-like protease (3CL) is the most promising drug development strategy against the SARS-CoV-2 virus, responsible for the current COVID-19 pandemic. In the present work, 9101 drugs obtained from the dr...
Despite their rich information content, electronic structure data amassed at high volumes in ab initio molecular dynamics simulations are generally under-utilized. We introduce a transferable high-fidelity neural network representation of such data i...
Small (Weinheim an der Bergstrasse, Germany)
Sep 15, 2021
Multiprincipal element alloys (MPEAs) have gained surging interest due to their exceptional properties unprecedented in traditional alloys. However, identifying an MPEA with desired properties from a huge compositional space via a cost-effective desi...
The current pandemic outbreak clearly indicated the urgent need for tools allowing fast predictions of bioactivity of a large number of compounds, either available or at least synthesizable. In the computational chemistry toolbox, several such tools ...
Finding optimal parameters for force fields used in molecular simulation is a challenging and time-consuming task, partly due to the difficulty of tuning multiple parameters at once. Automatic differentiation presents a general solution: run a simula...