330 citations · 2.7k across the 74 of their papers we have counts for
21 papers · 1 filter
Generative structural elucidation from mass spectra as an iterative optimization problem
Mrunali Manjrekar, Runzhong Wang, Samuel Goldman +2
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical…
Optimal compound downselection to promote diversity and parallel chemistry
Jenna C. Fromer, Alexandra D. Volkova, Connor W. Coley
Early stage drug discovery and molecular design projects often follow iterative design-make-test cycles. The selection of which compounds to synthesize from all possible candidate…
An algorithmic framework for synthetic cost-aware decision making in molecular design
Jenna C. Fromer, Connor W. Coley
Small molecules exhibiting desirable property profiles are often discovered through an iterative process of designing, synthesizing, and testing sets of molecules. The selection of…
Pareto Optimization to Accelerate Multi-Objective Virtual Screening
Jenna C. Fromer, David E. Graff, Connor W. Coley
The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit…
MIST-CF: Chemical formula inference from tandem mass spectra
Samuel Goldman, Jiayi Xin, Joules Provenzano +1
Chemical formula annotation for tandem mass spectrometry (MS/MS) data is the first step toward structurally elucidating unknown metabolites. While great strides have been made towa…
Evaluating the roughness of structure-property relationships using pretrained molecular representations
David E. Graff, Edward O. Pyzer-Knapp, Kirk E. Jordan +2
Quantitative structure-property relationships (QSPRs) aid in understanding molecular properties as a function of molecular structure. When the correlation between structure and pro…
Generating Molecular Fragmentation Graphs with Autoregressive Neural Networks
Samuel Goldman, Janet Li, Connor W. Coley
The accurate prediction of tandem mass spectra from molecular structures has the potential to unlock new metabolomic discoveries by augmenting the community's libraries of experime…
Prefix-Tree Decoding for Predicting Mass Spectra from Molecules
Samuel Goldman, John Bradshaw, Jiayi Xin +1
Computational predictions of mass spectra from molecules have enabled the discovery of clinically relevant metabolites. However, such predictive tools are still limited as they occ…
Reinforced Genetic Algorithm for Structure-based Drug Design
Tianfan Fu, Wenhao Gao, Connor W. Coley +1
Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary ap…
De novo PROTAC design using graph-based deep generative models
Divya Nori, Connor W. Coley, Rocío Mercado
PROteolysis TArgeting Chimeras (PROTACs) are an emerging therapeutic modality for degrading a protein of interest (POI) by marking it for degradation by the proteasome. Recent deve…
Computer-Aided Multi-Objective Optimization in Small Molecule Discovery
Jenna C. Fromer, Connor W. Coley
Molecular discovery is a multi-objective optimization problem that requires identifying a molecule or set of molecules that balance multiple, often competing, properties. Multi-obj…
Roughness of molecular property landscapes and its impact on modellability
Matteo Aldeghi, David E. Graff, Nathan Frey +4
In molecular discovery and drug design, structure-property relationships and activity landscapes are often qualitatively or quantitatively analyzed to guide the navigation of chemi…
Self-focusing virtual screening with active design space pruning
David E. Graff, Matteo Aldeghi, Joseph A. Morrone +3
High-throughput virtual screening is an indispensable technique utilized in the discovery of small molecules. In cases where the library of molecules is exceedingly large, the cost…
pyscreener: A Python Wrapper for Computational Docking Software
David E. Graff, Connor W. Coley
pyscreener is a Python library that seeks to alleviate the challenges of large-scale structure-based design using computational docking. It provides a simple and uniform interface…
Machine learning on DNA-encoded library count data using an uncertainty-aware probabilistic loss function
Katherine S. Lim, Andrew G. Reidenbach, Bruce K. Hua +4
DNA-encoded library (DEL) screening and quantitative structure-activity relationship (QSAR) modeling are two techniques used in drug discovery to find small molecules that bind a p…
BioNavi-NP: Biosynthesis Navigator for Natural Products
Shuangjia Zheng, Tao Zeng, Chengtao Li +4
Nature, a synthetic master, creates more than 300,000 natural products (NPs) which are the major constituents of FDA-proved drugs owing to the vast chemical space of NPs. To date,…
Accelerating high-throughput virtual screening through molecular pool-based active learning
David E. Graff, Eugene I. Shakhnovich, Connor W. Coley
Structure-based virtual screening is an important tool in early stage drug discovery that scores the interactions between a target protein and candidate ligands. As virtual librari…
Message Passing Networks for Molecules with Tetrahedral Chirality
Lagnajit Pattanaik, Octavian-Eugen Ganea, Ian Coley +3
Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, m…
Autonomous discovery in the chemical sciences part II: Outlook
Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen
This two-part review examines how automation has contributed to different aspects of discovery in the chemical sciences. In this second part, we reflect on a selection of exemplary…
Autonomous discovery in the chemical sciences part I: Progress
Connor W. Coley, Natalie S. Eyke, Klavs F. Jensen
This two-part review examines how automation has contributed to different aspects of discovery in the chemical sciences. In this first part, we describe a classification for discov…
The Synthesizability of Molecules Proposed by Generative Models
Wenhao Gao, Connor W. Coley
The discovery of functional molecules is an expensive and time-consuming process, exemplified by the rising costs of small molecule therapeutic discovery. One class of techniques o…