Matthew Holcomb
Overview
Explore the profile of Matthew Holcomb including associated specialties, affiliations and a list of published articles.
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Articles
26
Citations
97
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Recent Articles
1.
Wang S, Woods E, Jo J, Zhu J, Hansel-Harris A, Holcomb M, et al.
J Am Chem Soc
. 2025 Feb;
147(10):8312-8325.
PMID: 40013487
() is an opportunistic human pathogen that causes over one million deaths around the world each year. We recently identified a family of serine hydrolases termed fluorophosphonate binding hydrolases (Fphs)...
2.
Hansel-Harris A, Tillack A, Santos-Martins D, Holcomb M, Forli S
Protein Sci
. 2025 Feb;
34(3):e70082.
PMID: 39998966
Recent advances in structural biology have led to the publication of a wealth of high-resolution x-ray crystallography (XRC) and cryo-EM macromolecule structures, including many complexes with small molecules of interest...
3.
Garza C, Holcomb M, Santos-Martins D, Torbett B, Forli S
Biophys J
. 2024 Dec;
124(2):417-427.
PMID: 39690744
The HIV-1 capsid is an irregularly shaped protein complex containing the viral genome and several proteins needed for integration into the host cell genome. Small molecules, such as the drug-like...
4.
Wang S, Woods E, Jo J, Zhu J, Hansel-Harris A, Holcomb M, et al.
bioRxiv
. 2024 Nov;
PMID: 39574702
Staphylococcus aureus () is an opportunistic human pathogen that causes over one million deaths around the world each year. We recently identified a family of serine hydrolases termed fluorophosphonate binding...
5.
Bruciaferri N, Eberhardt J, Llanos M, Loeffler J, Holcomb M, Fernandez-Quintero M, et al.
J Chem Inf Model
. 2024 Oct;
64(21):8227-8235.
PMID: 39436011
Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including...
6.
7.
Garza C, Holcomb M, Santos-Martins D, Torbett B, Forli S
bioRxiv
. 2024 Apr;
PMID: 38559213
The HIV-1 capsid is an irregularly shaped complex of about 1200 protein chains containing the viral genome and several viral proteins. Together, these components are the key to unlocking passage...
8.
Huynh H, Le K, Vu L, Nguyen T, Holcomb M, Forli S, et al.
J Comput Chem
. 2024 Mar;
45(18):1552-1561.
PMID: 38500409
Investigation of Lewis acid-base interactions has been conducted by ab initio calculations and machine learning (ML) models. This study aims to resolve two critical tasks that have not been quantitatively...
9.
Bianco G, Holcomb M, Santos-Martins D, Tillack A, Hansel-Harris A, Forli S
J Chem Inf Model
. 2023 Aug;
63(17):5631-5640.
PMID: 37639635
We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in...
10.
Holcomb M, Santos-Martins D, Tillack A, Forli S
QRB Discov
. 2023 Aug;
3:e18.
PMID: 37529284
Macrocycles represent an important class of ligands, both in natural products and designed drugs. In drug design, macrocyclizations can impart specific ligand conformations and contribute to passive permeation by encouraging...