Chemical Language Model Linker: blending text and molecules with modular adapters

Authors: Deng, Yifan, Ericksen, Spencer S., Gitter, Anthony

Subject Terms: Computer Science - Machine Learning, Computer Science - Artificial Intelligence, Quantitative Biology - Quantitative Methods

Access URL: http://arxiv.org/abs/2410.20182

Bayes Optimal Informer Sets for Early-Stage Drug Discovery

Authors: Yu, Peng, Ericksen, Spencer S., Gitter, Anthony, Newton, Michael A.

Subject Terms: Statistics - Methodology

Access URL: http://arxiv.org/abs/2011.06122

Evaluating Scalable Supervised Learning for Synthesize-on-Demand Chemical Libraries

Authors: Alnammi, Moayad, Liu, Shengchao, Ericksen, Spencer S., Ananiev, Gene E., Voter, Andrew F., Guo, Song, Keck, James L., Hoffmann, F. Michael, Wildman, Scott A., Gitter, Anthony

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 63(17):5513-5528

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632592704&indx=1&recIds=ETOCRN632592704

Dereplication of Natural Product Antifungals via Liquid Chromatography–Tandem Mass Spectrometry and Chemical Genomics.

Authors: Brittin, Nathaniel J., Aceti, David J., Braun, Doug R., Anderson, Josephine M., Ericksen, Spencer S., Rajski, Scott R., Currie, Cameron R., Andes, David R., Bugni, Tim S.

Source: Molecules; Jan2025, Vol. 30 Issue 1, p77, 10p

Subject Terms: DRUG discovery, NATURAL products, MASS spectrometry, MYCOSES, CANDIDA albicans

Data mining of PubChem bioassay records reveals diverse OXPHOS inhibitory chemotypes as potential therapeutic agents against ovarian cancer.

Authors: Sharma, Sejal, Feng, Liping, Boonpattrawong, Nicha, Kapur, Arvinder, Barroilhet, Lisa, Patankar, Manish S., Ericksen, Spencer S.

Source: Journal of Cheminformatics; 10/7/2024, Vol. 16 Issue 1, p1-21, 21p

Subject Terms: HIGH throughput screening (Drug development), DATA libraries, DATA mining, REACTIVE oxygen species, OXIDATIVE phosphorylation, FUNCTIONAL groups

Practical Model Selection for Prospective Virtual Screening

Authors: Liu, Shengchao, Alnammi, Moayad, Ericksen, Spencer S., Voter, Andrew F., Ananiev, Gene E., Keck, James L., Hoffmann, F. Michael, Wildman, Scott A., Gitter, Anthony

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 59(1):282-293

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632680663&indx=1&recIds=ETOCRN632680663

Abiotic Small Molecule Inhibitors and Activators of the LasR Quorum Sensing Receptor in Pseudomonas aeruginosa with Potencies Comparable or Surpassing N‑Acyl Homoserine Lactones.

Authors: Manson, Daniel E., Ananiev, Gene E., Guo, Song, Ericksen, Spencer S., Santa, Emma E., Blackwell, Helen E.

Source: ACS Infectious Diseases; 4/12/2024, Vol. 10 Issue 4, p1212-1221, 10p

Machine Learning Consensus Scoring Improves Performance Across Targets in Structure-Based Virtual Screening

Authors: Ericksen, Spencer S., Wu, Haozhen, Zhang, Huikun, Michael, Lauren A., Newton, Michael A., Hoffmann, F. Michael, Wildman, Scott A.

Source: JOURNAL OF CHEMICAL INFORMATION AND MODELING. 57(7):1579-1590

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN632676154&indx=1&recIds=ETOCRN632676154

Preferred Binding Orientations of Phenacetin in CYP1A1 and CYP1A2 Are Associated with Isoform-Selective Metabolism

Authors: Huang, Qingbiao, Deshmukh, Rahul S., Ericksen, Spencer S., Tu, Youbin, Szklarz, Grazyna D. ^*

Source: In Drug Metabolism and Disposition December 2012 40(12):2324-2331

Ring Substituents on Substituted Benzamide Ligands Indirectly Mediate Interactions with Position 7.39 of Transmembrane Helix 7 of the D4 Dopamine Receptor

Authors: Ericksen, Spencer S. ¹, Cummings, David F. ², Teer, Michael E., Amdani, Shahnawaz, Schetz, John A. ^*

Source: In The Journal of Pharmacology and Experimental Therapeutics August 2012 342(2):472-485

Predicting kinase inhibitors using bioactivity matrix derived informer sets.

Authors: Zhang, Huikun¹, Ericksen, Spencer S.², Lee, Ching-pei³, Ananiev, Gene E.², Wlodarchak, Nathan⁴, Yu, Peng¹, Mitchell, Julie C.⁵, Gitter, Anthony^6,7, Wright, Stephen J.⁸, Hoffmann, F. Michael^2,9, Wildman, Scott A.², Newton, Michael A.^1,6 newton@stat.wisc.edu

Source: PLoS Computational Biology. 8/5/2019, Vol. 15 Issue 8, p1-29. 29p. 1 Diagram, 2 Charts, 3 Graphs.

Subject Terms: *CHEMICAL inhibitors, *KINASE inhibitors

Transmembrane Segment Five Serines of the D4 Dopamine Receptor Uniquely Influence the Interactions of Dopamine, Norepinephrine, and Ro10-4548

Authors: Cummings, David F., Ericksen, Spencer S., Goetz, Angela, Schetz, John A. ^*

Source: In The Journal of Pharmacology and Experimental Therapeutics June 2010 333(3):682-695

Ligand Selectivity of D2 Dopamine Receptors Is Modulated by Changes in Local Dynamics Produced by Sodium Binding

Authors: Ericksen, Spencer S., Cummings, David F., Weinstein, Harel, Schetz, John A. ^*

Source: In The Journal of Pharmacology and Experimental Therapeutics January 2009 328(1):40-54

Multivariate chemogenomic screening prioritizes new macrofilaricidal leads.

Authors: Wheeler, Nicolas J., Ryan, Kaetlyn T., Gallo, Kendra J., Henthorn, Clair R., Ericksen, Spencer S., Chan, John D., Zamanian, Mostafa

Source: Communications Biology; 1/13/2023, Vol. 6 Issue 1, p1-15, 15p

Subject Terms: DEEP learning, PARASITE life cycles, DRUG development, BIOLOGICAL fitness, PROTEIN structure, CHEMICAL potential

Oxidative stress via inhibition of the mitochondrial electron transport and Nrf-2-mediated anti-oxidative response regulate the cytotoxic activity of plumbagin

Authors: Kapur, Arvinder, Beres, Thomas, Rathi, Kavya, Nayak, Amruta P., Czarnecki, Austin, Felder, Mildred, Gillette, Amani, Ericksen, Spencer S., Sampene, Emmanuel, Skala, Melissa C., Barroilhet, Lisa, Patankar, Manish S.

Source: Scientific reports. 8(1)

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100131381584.0x000001&indx=1&recIds=ETOCvdc_100131381584.0x000001

Structural Determinants for High-Affinity Zolpidem Binding to GABA-A receptors

Authors: Sancar, Feyza, Ericksen, Spencer S., Kucken, Amy M., Teissére, Jeremy A., Czajkowski, Cynthia ^*

Source: In Molecular Pharmacology January 2007 71(1):38-46

Atovaquone: An Inhibitor of Oxidative Phosphorylation as Studied in Gynecologic Cancers.

Authors: Kapur, Arvinder, Mehta, Pooja, Simmons, Aaron D, Ericksen, Spencer S., Mehta, Geeta, Palecek, Sean P., Felder, Mildred, Stenerson, Zach, Nayak, Amruta, Dominguez, Jose Maria Ayuso, Patankar, Manish, Barroilhet, Lisa M.

Source: Cancers; May2022, Vol. 14 Issue 9, pN.PAG-N.PAG, 17p

Subject Terms: ATOVAQUONE, ENERGY metabolism, IN vitro studies, FLOW cytometry, OVARIAN tumors, IN vivo studies, ANIMAL experimentation, OXYGEN consumption, METABOLOMICS, MITOCHONDRIA, CELL survival, CELL proliferation, CELL lines, FEMALE reproductive organ tumors, MICE

In Silico Modeling and Scoring of PROTAC-Mediated Ternary Complex Poses.

Authors: Liao, Junzhuo, Nie, Xueqing, Unarta, Ilona Christy, Ericksen, Spencer S., Tang, Weiping

Source: Journal of Medicinal Chemistry; 4/28/2022, Vol. 65 Issue 8, p6116-6132, 17p

Correction to "Abiotic Small Molecule Inhibitors and Activators of the LasR Quorum Sensing Receptor in Pseudomonas aeruginosa with Potencies Comparable or Surpassing N‑Acyl Homoserine Lactones".

Authors: Manson, Daniel E., Ananiev, Gene E., Guo, Song, Ericksen, Spencer S., Santa, Emma E., Blackwell, Helen E.

Source: ACS Infectious Diseases; 6/14/2024, Vol. 10 Issue 6, p2333-2334, 2p

Arachidonic and eicosapentaenoic acid metabolism by human CYP1A1: highly stereoselective formation of 17( R),18( S)-epoxyeicosatetraenoic acid

Authors: Schwarz, Dieter, Kisselev, Pyotr, Ericksen, Spencer S, Szklarz, Grazyna D, Chernogolov, Alexey, Honeck, Horst, Schunck, Wolf-Hagen, Roots, Ivar

Source: In Biochemical Pharmacology 2004 67(8):1445-1457