Journal of computer-aided molecular design
Oct 28, 2021
The advent of computational drug discovery holds the promise of significantly reducing the effort of experimentalists, along with monetary cost. More generally, predicting the binding of small organic molecules to biological macromolecules has far-re...
The journal of physical chemistry letters
Sep 23, 2021
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential. The converg...
Engineering proteins to have desired properties by mutating amino acids at specific sites is commonplace. Such engineered proteins must be stable to function. Experimental methods used to determine stability at throughputs required to scan the protei...
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...
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