Steven A. Combs

Drugit: crowd-sourcing molecular design of non-peptidic VHL binders

Thomas Allan Scott, Christian Alan Paul Smethurst, Yvonne Westermaier, Moriz Mayer et autres

Building on the role of human intuition in small molecule drug design, we explored whether crowdsourcing could recruit citizen scientists to this task while in parallel building awareness for this scientific process. Here, we introduce Drugit ( https://drugit.org ), the small molecule …

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EGGNet, a Generalizable Geometric Deep Learning Framework for Protein Complex Pose Scoring

Zichen Wang, Ryan M. Brand, Jared Adolf‐Bryfogle, Jasleen Grewal et autres

Computational prediction of molecule-protein interactions has been key for developing new molecules to interact with a target protein for therapeutics development. Previous work includes two independent streams of approaches: (1) predicting protein-protein interactions (PPIs) between naturally occurring proteins and (2) predicting binding …

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Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders

Thomas Allan Scott, Christian Alan Paul Smethurst, Yvonne Westermaier, Moriz Mayer et autres

Given the role of human intuition in current drug design efforts, crowd-sourced 'citizen scientist' games have the potential to greatly expand the pool of potential drug designers. Here, we introduce ‘Drugit', the small molecule design mode of the online ‘citizen science’ game …

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EGGNet, a generalizable geometric deep learning framework for protein complex pose scoring

Zichen Wang, Ryan M. Brand, Jared Adolf‐Bryfogle, Jasleen Grewal et autres

Abstract Computational prediction of molecule-protein interactions has been key for developing new molecules to interact with a target protein for therapeutics development. Past work includes two independent streams of approaches: (1) predicting protein-protein interactions (PPI) between naturally occurring proteins and (2) predicting …

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LM-GVP: an extensible sequence and structure informed deep learning framework for protein property prediction

Zichen Wang, Steven A. Combs, Ryan M. Brand, Miguel Romero Calvo et autres

Proteins perform many essential functions in biological systems and can be successfully developed as bio-therapeutics. It is invaluable to be able to predict their properties based on a proposed sequence and structure. In this study, we developed a novel generalizable deep learning …

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LM-GVP: A Generalizable Deep Learning Framework for Protein Property Prediction from Sequence and Structure

Zichen Wang, Steven A. Combs, Ryan M. Brand, Miguel Romero Calvo et autres

Abstract Proteins perform many essential functions in biological systems and can be successfully developed as bio-therapeutics. It is invaluable to be able to predict their properties based on a proposed sequence and structure. In this study, we developed a novel generalizable deep …

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Exploring Tunable Hyperparameters for Deep Neural Networks with Industrial ADME Data Sets

Yadi Zhou, Suntara Cahya, Steven A. Combs, Christos A. Nicolaou et autres

Deep learning has drawn significant attention in different areas including drug discovery. It has been proposed that it could outperform other machine learning algorithms, especially with big data sets. In the field of pharmaceutical industry, machine learning models are built to understand …

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Holistic Approach to Partial Covalent Interactions in Protein Structure Prediction and Design with Rosetta

Steven A. Combs, Benjamin K. Mueller, Jens Meiler

Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identify and evaluate …

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A novel protocol for the design of artificial (β/α)8-barrel proteins

Cristina E. Martina, Maximiliano Figueroa Yévenes, Steven A. Combs, Rocco Moretti et autres

Designing de novo proteins of more than 100 amino acids is still challenging. The creation of artificial (β/α)8-barrel proteins had only one successful example in literature, thank to use of internal spatial symmetry. Here we present a protocol to design de novo …

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Northrop Grumman Operator Workstation

Khalid Alanazi, Steven A. Combs, Derrick Harney, J Coello De Portugal et autres

Computational design of protein-small molecule interfaces

Brittany Allison, Steven A. Combs, Samuel DeLuca, Gordon Lemmon et autres

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Small-molecule ligand docking into comparative models with Rosetta

Steven A. Combs, Samuel DeLuca, Stephanie H. DeLuca, Gordon Lemmon et autres

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