700 research outputs found
TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions
Although deep learning approaches have had tremendous success in image, video
and audio processing, computer vision, and speech recognition, their
applications to three-dimensional (3D) biomolecular structural data sets have
been hindered by the entangled geometric complexity and biological complexity.
We introduce topology, i.e., element specific persistent homology (ESPH), to
untangle geometric complexity and biological complexity. ESPH represents 3D
complex geometry by one-dimensional (1D) topological invariants and retains
crucial biological information via a multichannel image representation. It is
able to reveal hidden structure-function relationships in biomolecules. We
further integrate ESPH and convolutional neural networks to construct a
multichannel topological neural network (TopologyNet) for the predictions of
protein-ligand binding affinities and protein stability changes upon mutation.
To overcome the limitations to deep learning arising from small and noisy
training sets, we present a multitask topological convolutional neural network
(MT-TCNN). We demonstrate that the present TopologyNet architectures outperform
other state-of-the-art methods in the predictions of protein-ligand binding
affinities, globular protein mutation impacts, and membrane protein mutation
impacts.Comment: 20 pages, 8 figures, 5 table
Improved prediction of ligand-protein binding affinities by meta-modeling
The accurate screening of candidate drug ligands against target proteins
through computational approaches is of prime interest to drug development
efforts, as filtering potential candidates would save time and expenses for
finding drugs. Such virtual screening depends in part on methods to predict the
binding affinity between ligands and proteins. Given many computational models
for binding affinity prediction with varying results across targets, we herein
develop a meta-modeling framework by integrating published empirical
structure-based docking and sequence-based deep learning models. In building
this framework, we evaluate many combinations of individual models, training
databases, and linear and nonlinear meta-modeling approaches. We show that many
of our meta-models significantly improve affinity predictions over individual
base models. Our best meta-models achieve comparable performance to
state-of-the-art exclusively structure-based deep learning tools. Overall, we
demonstrate that diverse modeling approaches can be ensembled together to gain
substantial improvement in binding affinity prediction while allowing control
over input features such as physicochemical properties or molecular
descriptors.Comment: 61 pages, 3 main tables, 6 main figures, 6 supplementary figures, and
supporting information. For 8 supplementary tables and code, see
https://github.com/Lee1701/Lee2023
Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
Structure-based virtual screening (VS) is a widely used approach that employs the knowledge of the three-dimensional structure of the target of interest in the design of new lead compounds from large-scale molecular docking experiments. Through the prediction of the binding mode and affinity of a small molecule within the binding site of the target of interest, it is possible to understand important properties related to the binding process. Empirical scoring functions are widely used for pose and affinity prediction. Although pose prediction is performed with satisfactory accuracy, the correct prediction of binding affinity is still a challenging task and crucial for the success of structure-based VS experiments. There are several efforts in distinct fronts to develop even more sophisticated and accurate models for filtering and ranking large libraries of compounds. This paper will cover some recent successful applications and methodological advances, including strategies to explore the ligand entropy and solvent effects, training with sophisticated machine-learning techniques, and the use of quantum mechanics. Particular emphasis will be given to the discussion of critical aspects and further directions for the development of more accurate empirical scoring functions
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