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(22) Balius, T. E.;* Chakrabarti, M; Tan, Y.S.; DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large-scale docking. J. Comput. Chem. 2024, 45 (1), 47-63, doi: 10.1002/jcc.27218, PMID: 37743732
Preprint: chemarxv
* corresponding author.
(23) Finci, L.I.; Chakrabarti, M; Gulten, G.; Finney, J.; Grose, C.; Fox, T.; Yang, R.; Nissley, D. V.; McCormick, F.; Esposito, D.; Balius, T. E.; Simanshu, D. K.; Structural dynamics of RAF1-HSP90-CDC37 and HSP90 complexes reveal asymmetric client interactions and key structural elements. 2024, 7(1), Article number: 260. Nature Communications biology. doi: 10.1038/s42003-024-05959-3, PMID: 38431713, PMCID: PMC10908828
(1. book chapter) Chakrabarti, M.; Tan,Y.S.; Balius, T.E.;* Considerations around Structure-Based Drug Discovery for KRAS using DOCK; Methods in Molecular Biology, Book Chapter 6. Book editors: Stephen, A. G.; Esposito, D.; Book Title: KRAS: Methods and Protocols; 2024, doi: 10.1007/978-1-0716-3822-4_6, PMID: 38570453,
(18) Stein, R. M.; Yang, Y.; Balius, T.E.; O'Meara, M. J.; Lyu, J.; Young, J.; Tang, K.; Shoichet, B. K.; Irwin, J. J. Property-unmatched decoys in docking benchmarks, JCIM, 2021, 61, 2, 699-714. doi: 10.1021/acs.jcim.0c00598, PMID: 33494610, PMCID: PMC7913603
(19) Van, Q. N.; Prakash, P.; Shrestha, R.; Balius, T. E.; Turbyville, T. J.; Stephen, A. G.; RAS nanoclusters: dynamic signaling platforms amenable to therapeutic intervention. Biomolecules, Review, 2021, 11, 377. doi: 10.3390/biom11030377,PMID: 33802474, PMCID: PMC8000715
(20) Kamenik, A. S.; Singh, I.; Lak, P.; Balius, T. E.;*, Liedl, K. R.;* Shoichet, B. K.;* Energy Penalties Enhance Flexible Receptor Docking in a Model Cavity, Proc. Natl. Acad. Sci. U. S. A., 2021, 118(36):e2106195118.doi: 10.1073/pnas.2106195118,PMID: 34475217
* corresponding author.
(21) Bender, B. J.; Gahbauer, S.; Luttens, A.; Lyu, J.; Webb, C. M.; Stein, R. M.; Fink, E. A.; Balius, T. E.; Carlsson, J.; Irwin, J. J.; Shoichet, B. K.; A Practical Guide to Large Scale Docking; Nature Methods, 2021, doi:10.1038/s41596-021-00597-z,PMID: 34561691
(16) Tran T. H.; Alexander, P.; Dharmaiah, S.; Agamasu, C.; McCormick, F.; Nissley, D. V.; Esposito, D.; Simanshu, D. K.; Stephen, A. G.; Balius, T. E.*; The small molecule BI-2852 induces a non-functional dimer of KRAS. Proc. Natl. Acad. Sci. U. S. A., 2020, 117 (7), 3363-3364. doi:10.1073/pnas.1918164117, PMID: 32047043, PMCID: PMC7035607. (Letter to the Editor in response to Kessler et al., 2019).
* corresponding author.
The Letter.
The Response by Kessler et al.
The Supplemental Information on FigShare.
Original paper by Kessler et al.
(17) Wan, X.; Yang, T.; Cuesta, A.; Pang, X.; Balius, T. E.; Irwin, J.; Shoichet, B. K.; Taunton, J. Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking. JACS, Communication, 2020, 142, 11, 4960-4964. doi: 10.1021/jacs.9b10377, PMID: 32105459, PMCID: PMC7136196.
(15) Lyu, J.*; Wang, S.*; Balius, T. E.*; Singh, I.*.; Levit, A.; Moroz, Y. S.; O'Meara, M. J.; Algaa, E.; Tolmachova K.; Tolmachev, A. A.; Shoichet, B. K.; Roth, B. L.; and Irwin, J. J.; Ultra-large library docking for discovering new chemotypes. Nature 2019, 566, 224-229. doi.org/10.1038/s41586-019-0917-9. PMID: 30728502, PMCID: PMC6383769
* these authors contributed equally to this work.
Nature Editorial.
Nature News & Views.
Highlighted in Science.
(14) Nnadi, C. I.; Jenkins, M. L.; Gentile, D. R.; Batemen, L. A.; Zaidman, D.; Balius, T. E.; Nomura, D. K.; Burke, J. E.; Shokat, K. M.; London, N.; Novel K-Ras G12C Switch-II covalent binders destabilize Ras and accelerate nucleotide exchange. J. Chem. Inf. Model. 2018, 58 (2), 464-471, doi:10.1021/acs.jcim.7b00399 , PMID: 29320178, PMCID: PMC6179444
(12) Balius, T. E.*; Fischer, M.*; Stein, R. M.; Adler, T. B.; Nguyen C. N.; Cruz A.;Gilsonc M. K.; Kurtzman, T.; Shoichet, B. K., Testing inhomogeneous solvation theory in structure-based ligand discovery. Proc. Natl. Acad. Sci. USA. 2017, 114 (33) E6839-E6846, doi:10.1073/pnas.1703287114. PMID: 28760952, PMCID: PMC5565424
* these authors contributed equally to this work.
(13) Allen, W. J.*; Fochtman, B.C.*; Balius, T. E.; Rizzo, R. C., Customizable de novo Design Strategies for DOCK: Application to HIVgp41 and Other Therapeutic Targets. J. Comput. Chem. 2017, 38, 2641-2663, doi: 10.1002/jcc.25052. PMID: 28940386, PMCID: PMC5659719
(9) Merski, M.*; Fischer, M.*; Balius, T. E.*; Eidam, O.; Shoichet, B. K., Homologous ligands accommodated by discrete conformations of a buried cavity. Proc. Natl. Acad. Sci. USA. 2015, 112 (16), 5039-5044, doi:10.1073/pnas.1500806112. PMID: 25847998, PMCID: PMC4413287
* these authors contributed equally to this work.
Highlighted in Science.

link to cover
(10) Allen, W. J.*; Balius, T. E.*; Mukherjee, S.; Brozell, S. R.; Moustakas, D. T.; Lang, P. T.; Case, D. A.; Kuntz, I. D.; Rizzo, R. C., DOCK 6: Impact of New Features and Current Docking Performance. J. Comput. Chem., 2015, 36 (15), 1132-1156, doi:10.1002/jcc.23905 . PMID: 25914306, PMCID: PMC4469538
* these authors contributed equally to this work.
(11) Teng, Y. G.; Berger, W. T.; Nesbitt, N. M.; Kumar, K.; Balius, T. E.; Rizzo, R. C.; Tonge, P.J.; Ojima, I.; Swaminathan, S., Computer-Aided Identification, Synthesis, and Biological Evaluation of Novel inhibitors for Botulinum Neurotoxin Serotype A. Bioorganic & Medicinal Chemistry, 2015, 23 (17), 5489-5495, doi:10.1016/j.bmc.2015.07.040. PMID: 26275678

link to cover
(8) Balius, T. E.*; Allen, W. J.*; Mukherjee, S.; Rizzo, R. C., Grid-Based Molecular Footprint Comparison Method for Docking and De Novo Design: Application to HIVgp41. J. Comput. Chem., 2013, 34 (14), 1226-1240, doi:10.1002/jcc.23245 . PMID: 23436713, PMCID: PMC4016043
* these authors contributed equally to this work.
(6) Brozell, S. R.; Mukherjee, S.; Balius, T. E.; Roe, D. R.; Case, D. A.; Rizzo, R. C. Evaluation of DOCK 6 as a Pose Generation and Database Enrichment Tool. J. Comput-Aided Mol Des, 2012, 26 (6), 749-773, doi:10.1007/s10822-012-9565-y . PMID: 22569593, PMCID: PMC3902891
(7) Berger, W. T.; Ralph, B. P.; Kaczocha, M.; Sun, J.; Balius, T. E.; Rizzo, R. C.; Haj- Dahmane, S.; Ojima, I.; Deutsch, D. G., Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters - A Novel Strategy for Development of Anti-Inflammatory and Anti-Nociceptive Drugs. PLOS One, 2012, 7 (12) e50968 doi:10.1371/journal.pone.0050968 . PMID: 23236415, PMCID: PMC3517626
(5) Balius, T.E.; Mukherjee S.; Rizzo, R. C. Implementation and Evaluation of a Docking-Rescoring Method using Molecular Footprint Comparisons. J. Comput. Chem., 2011, 32(10), 2273-2289, doi:10.1002/jcc.21814 PMID: 21541962, PMCID: PMC3181325
(2) Owonikoko T. K.; Ramalingam S. S.; Kanterewicz B.; Balius T. E.; Belani C. P.; Hershberger P. A. Vorinostat increases carboplatin and paclitaxel activity in non-small cell lung cancer cells. International Journal of Cancer 2010 126, 743-755, doi:10.1002/ijc.24759 . PMID: 19621389, PMCID: PMC2795066
(3) McGillick, B. E.*; Balius, T.E.*; Mukherjee, S.; Rizzo, R. C. Origins of Resistance to the HIVgp41 Viral Entry Inhibitor T20. Biochemistry, 2010, 49 (17), 3575-3592, doi:10.1021/bi901915g . PMID: 20230061, PMCID: PMC2867330
* these authors contributed equally to this work.
(4) Mukherjee S.; Balius, T.E.; Rizzo, R. C. Docking Validation Resources: Protein Family and Ligand Flexibility Experiments. J. Chem. Inf. Model., 2010, 50 (11), 1986-2000, doi:10.1021/ci1001982 . PMID: 21033739, PMCID: PMC3058392
(1) Balius, T.E.; Rizzo, R. C. Quantitative Prediction of Fold Resistance for Inhibitors of EGFR. Biochemistry, 2009, 48 (35), 8435-8448, doi:10.1021/bi900729a . PMID: 19627157, PMCID: PMC2741091
(0) Balius, T.E. Application and Development of Computational Tools in Drug Discovery, Ph.D Dissertation, Stony Brook University, 2012. PDF, proquest link

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modified: 2024/04/08