API Development Increases Access to Shared Computing Resources at Boston University

Jones, George; Wakefield, Amanda; Triplett, Jeff; Idrissa, Kojo; Goebel, James R.; Kozakov, Dima; Vajda, Sándor

doi:10.4236/jsea.2022.156011

Cited by 3 publications

(2 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For additional assistance with submitting jobs and analyzing results, the “Help” page can be viewed for more detailed instructions. We note that an E-FTMap calculation submitted using the web server will typically complete in 0.5–2 h, depending on the availability of computational resources on Boston University’s Shared Computing Cluster …”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites

Khan,

Jones,

Lazou

et al. 2024

J. Chem. Inf. Model.

Self Cite

View full text Add to dashboard Cite

The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment−lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein−ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.

show abstract

Section: Methodsmentioning

confidence: 99%

“…We note that an E-FTMap calculation submitted using the web server will typically complete in 0.5−2 h, depending on the availability of computational resources on Boston University's Shared Computing Cluster. 92…”

Section: Journal Of Chemicalmentioning

confidence: 99%