Alchemical free energy simulations without speed limits. A generic framework to calculate free energy differences independent of the underlying molecular dynamics program
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DOI: 10.1002/jcc.26877
Abstract: We describe the theory of the so‐called common‐core/serial‐atom‐insertion (CC/SAI) approach to compute alchemical free energy differences and its practical implementation in a Python package called Transformato. CC/SAI is not tied to a specific biomolecular simulation… read more here.
Keywords: alchemical free; molecular dynamics; energy; free energy ... See more keywords
An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
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DOI: 10.1021/acs.jcim.0c00520
Abstract: Alchemical free energy calculations typically rely on intermediate states to bridge between the relevant phase spaces of the two end states. These intermediate states are usually created by mixing the energies or parameters of the… read more here.
Keywords: intermediate states; energy calculations; energy; conventional intermediate ... See more keywords
Evolution of Alchemical Free Energy Methods in Drug Discovery
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DOI: 10.1021/acs.jcim.0c00547
Abstract: The goal of the present manuscript is to succinctly trace the key technological steps in the evolution of alchemical free energy methods (AFEMs) from a purely theoretical construct to a method that is now widely… read more here.
Keywords: energy methods; energy; alchemical free; drug ... See more keywords
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4
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DOI: 10.1021/acs.jcim.1c01229
Abstract: Accurate and rapid predictions of the binding affinity of a compound to a target are one of the ultimate goals of computer aided drug design. Alchemical approaches to free energy estimations follow the path from… read more here.
Keywords: methods applied; alchemical free; energy; free energy ... See more keywords
Alchemical Free Energy Calculations to Investigate Protein–Protein Interactions: the Case of the CDC42/PAK1 Complex
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DOI: 10.1021/acs.jcim.2c00348
Abstract: Here, we show that alchemical free energy calculations can quantitatively compute the effect of mutations at the protein–protein interface. As a test case, we have used the protein complex formed by the small Rho-GTPase CDC42… read more here.
Keywords: pak1; alchemical free; energy calculations; free energy ... See more keywords
Chemical Space Exploration with Active Learning and Alchemical Free Energies
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DOI: 10.1021/acs.jctc.2c00752
Abstract: Drug discovery can be thought of as a search for a needle in a haystack: searching through a large chemical space for the most active compounds. Computational techniques can narrow the search space for experimental… read more here.
Keywords: active learning; alchemical free; large chemical; space ... See more keywords
High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2
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DOI: 10.3390/biomedicines10112779
Abstract: The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. From the initial outbreak the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus.… read more here.
Keywords: receptor binding; alchemical free; energy calculations; energy ... See more keywords