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Ranking the binding of small molecules to protein receptors through physics-based computation remains challenging. Though inroads have been made using free energy methods, these fail when the underlying classical mechanical force fields are insufficient. In principle, a more accurate approach is provided by quantum mechanical density functional theory (DFT) scoring, but even with approximations, this has yet to become practical on drug discovery-relevant timescales and resources. Here, we describe how to overcome this barrier using algorithms for DFT calculations that scale on widely available cloud architectures, enabling full density functional theory, without approximations, to be applied to protein-ligand complexes with approximately 2500 atoms in tens of minutes. Applying this to a realistic example of 22 ligands binding to MCL1 reveals that density functional scoring outperforms classical free energy perturbation theory for this system. This raises the possibility of broadly applying fully quantum mechanical scoring to real-world drug discovery pipelines.
We predict the enhanced light harvesting of a protein-pigment complex when assembled to a quantum dot (QD) antenna. Our prototypical nanoassembly setup is composed of a Fenna-Mattews-Olson system hosting 8 Bacteriochlorophyll (BChl) a dyes, and a nea
We describe the development of a scientific cloud computing (SCC) platform that offers high performance computation capability. The platform consists of a scientific virtual machine prototype containing a UNIX operating system and several materials s
Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in general. The accu
The conventional technique for solving the equations of quantum chemistry (of solid state) is extended unconventionally to the structures possessing certain symmetries. This proposal concerns changing the way for selection of occupied orbitals, allow
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented