Current opinion in structural biology
Sep 14, 2021
Physics-based free energy simulations enable the rigorous calculation of properties, such as conformational equilibria, solvation or binding free energies. While historically most applications have occurred at the atomistic level of resolution, a ran...
Journal of chemical theory and computation
Sep 1, 2021
Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing mach...
This study was planned to in silico screening of ssDNA aptamer against Escherichia coli O157:H7 by combination of machine learning and the PseKNC approach. For this, firstly a total numbers of 47 validated ssDNA aptamers as well as 498 random DNA seq...
Rational protein design aims at the targeted modification of existing proteins. To reach this goal, software suites like Rosetta propose sequences to introduce the desired properties. Challenging design problems necessitate the representation of a pr...
Journal of chemical information and modeling
Aug 17, 2021
Accurate force fields are necessary for predictive molecular simulations. However, developing force fields that accurately reproduce experimental properties is challenging. Here, we present a machine learning directed, multiobjective optimization wor...
Journal of computer-aided molecular design
Jul 17, 2021
Accurate prediction of lipophilicity-logP-based on molecular structures is a well-established field. Predictions of logP are often used to drive forward drug discovery projects. Driven by the SAMPL7 challenge, in this manuscript we describe the steps...
Journal of chemical theory and computation
Jul 14, 2021
Computational capabilities are rapidly increasing, primarily because of the availability of GPU-based architectures. This creates unprecedented simulative possibilities for the systematic and robust computation of thermodynamic observables, including...
Langmuir : the ACS journal of surfaces and colloids
Jun 29, 2021
Soft low-Reynolds-number robotics hold the potential to significantly impact numerous fields including drug delivery, sensing, and diagnostics. Realizing this potential is predicated upon the ability to design soft robots tailored to their intended f...
Pyrolysis of agricultural biomass is a promising technique for producing renewable energy and effectively managing solid waste. In this study, groundnut shell (GNS) was processed at 500 °C in an inert gas atmosphere with a gas flow rate and a heating...
International journal of molecular sciences
May 28, 2021
The docking program PLANTS, which is based on ant colony optimization (ACO) algorithm, has many advanced features for molecular docking. Among them are multiple scoring functions, the possibility to model explicit displaceable water molecules, and th...