References

Please refer to https://silcsbio.com/category/publications/ for a full list of publications featuring SilcsBio technology.

1

Wenbo Yu, Sunhwan Jo, Sirish Kaushik Lakkaraju, David J Weber, and Alexander D MacKerell Jr. Exploring protein-protein interactions using the Site-Identification by Ligand Competitive Saturation methodology. Proteins, 87(4):289–301, April 2019. doi: 10.1002/prot.25650.

2

Sunhwan Jo, Amy Xu, Joseph E Curtis, Sandeep Somani, and Alexander D MacKerell Jr. Computational characterization of antibody-excipient interactions for rational excipient selection using the site identification by ligand competitive saturation-biologics approach. Mol. Pharm., 17(11):4323–4333, November 2020. doi: 10.1021/acs.molpharmaceut.0c00775.

3

K Vanommeslaeghe, E Hatcher, C Acharya, S Kundu, S Zhong, J Shim, E Darian, O Guvench, P Lopes, I Vorobyov, and Alexander D MacKerell Jr. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem., 31(4):671–690, March 2010. doi: 10.1002/jcc.21367.

4

Kenno Vanommeslaeghe and Alexander D MacKerell Jr. Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing. J. Chem. Inf. Model., 52(12):3144–3154, December 2012. doi: 10.1021/ci300363c.

5

Anastasia Croitoru, Sang-Jun Park, Anmol Kumar, Jumin Lee, Wonpil Im, Alexander D MacKerell Jr, and Alexey Aleksandrov. Additive CHARMM36 force field for nonstandard amino acids. J. Chem. Theory Comput., 17(6):3554–3570, June 2021. doi: 10.1021/acs.jctc.1c00254.

6

Samo Lesnik, Milan Hodoscek, Urban Bren, Christoph Stein, and Ana-Nicoleta Bondar. Potential energy function for fentanyl-based opiod pain killers. J. Chem. Inf. Model, 60(7):3566–3576, July 2020. doi: 10.1021/acs.jcim.0c00185.

7

Oskar Klaja, James A Frank, and Ana-Nicoleta Bondar. Potential energy function for a photo-switchable lipid molecule. J. Comput. Chem., 41(27):2336–2351, October 2020. doi: 10.1002/jcc.26387.

8

You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D MacKerell Jr, and Lennart Nilsson. Additive CHARMM force field for naturally occurring modified ribonucleotides. J. Comput. Chem., 37(10):896–912, April 2016. doi: 10.1002/jcc.24307.

9

Alexander D MacKerell Jr, Sunhwan Jo, Sirish Kaushik Lakkaraju, Christoffer Lind, and Wenbo Yu. Identification and characterization of fragment binding sites for allosteric ligand design using the Site Identification by Ligand Competitive Saturation Hotspots approach (SILCS-Hotspots). Biochim. Biophys. Acta. Gen. Subj., 1864(4):129519–129519, April 2020. doi: 10.1016/j.bbagen.2020.129519.

10

Olgun Guvench and Alexander D MacKerell Jr. Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation. PLoS Comput. Biol., 5(7):e1000435–12, July 2009. doi: 10.1371/journal.pcbi.1000435.

11

Abhishek A Kognole, Anthony Hazel, and Alexander D MacKerell Jr. SILCS-RNA: Towards a structure-based drug design approach for targeting RNAs with small molecules. J. Chem. Theory Comput., 18(9):5672–5691, July 2022. 10.1021/acs.jctc.2c00381.

12

E Prabhu Raman, Wenbo Yu, Olgun Guvench, and Alexander D MacKerell Jr. Reproducing crystal binding modes of ligand functional groups using Site Identification by Ligand Competitive Saturation (SILCS) simulations. J. Chem. Inf. Model., 51(4):877–896, April 2011. 10.1021/ci100462t.

13

Sirish Kaushik Lakkaraju, E Prabhu Raman, Wenbo Yu, and Alexander D MacKerell Jr. Sampling of organic solutes in aqueous and heterogeneous environments using oscillating excess chemical potentials in grand canonical-like Monte Carlo-molecular dynamics simulations. J. Chem. Theory Comput., 10(6):2281–2290, June 2014. doi: 10.1021/ct500201y.

14

Vincent D Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, and Alexander D MacKerell Jr. Optimization and evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a tool for target-based ligand optimization. J. Chem. Inf. Model., 59(6):3018–3035, April 2019. doi: 10.1021/acs.jcim.9b00210.

15

Himanshu Goel, Anthony Hazel, Vincent D Ustach, Sunhwan Jo, Wenbo Yu, and Alexander D MacKerell Jr. Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation. Chem. Sci., 12(25):8844–8858, May 2021. doi: 10.1039/d1sc01781k.

16

Yang Zhang and Jeffrey Skolnick. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem., 25(6):865–871, April 2004. doi: 10.1002/jcc.20011.

17

Richard D Taylor, Malcolm MacCoss, and Alastair D G Lawson. Rings in drugs. J. Med. Chem., 57(14):5845–5859, July 2014. doi: 10.1021/jm4017625.

18

Marc O’Reilly, Anne Cleasby, Thomas G Davies, Richard J Hall, R Frederick Ludlow, Christopher W Murray, Dominic Tisi, and Harren Jhoti. Crystallographic screening using ultra-low-molecular-weight ligands to guide drug design. Drug Discov. Today, 24(5):1081–1086, May 2019. doi: 10.1016/j.drudis.2019.03.009.

19

E Prabhu Raman, Wenbo Yu, Sirish K Lakkaraju, and Alexander D MacKerell Jr. Inclusion of multiple fragment types in the Site Identification by Ligand Competitive Saturation (SILCS) approach. J. Chem. Inf. Model., 53(12):3384–3398, December 2013. doi: 10.1021/ci4005628.

20

Geoffrey A Heinzl, Weiliang Huang, Wenbo Yu, Bennett J. Giardina, Yue Zhou, Alexander D MacKerell Jr, Angela Wilks, and Fengtian Xue. Iminoguanidines as allosteric inhibitors of the iron-regulated heme oxygenase (HemO) of Pseudomonas aeruginosa. J. Med. Chem., 59(14):6929–6942, June 2016. doi: 10.1021/acs.jmedchem.6b00757.

21

Maryanna E Lanning, Wenbo Yu, Jeremy L Yap, Jay Chauhan, Lijia Chen, Ellis Whiting, Lakshmi S Pidugu, Tyler Atkinson, Hala Bailey, Willy Li, Braden M Roth, Lauren Hynicka, Kirsty Chesko, Eric A Toth, Paul Shapiro, Alexander D MacKerell Jr, Paul T Wilder, and Steven Fletcher. Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein. Eur. J. Med. Chem., 113:273–292, May 2016. doi: 10.1016/j.ejmech.2016.02.006.

22

Wenbo Yu, Sirish Kaushik Lakkaraju, E Prabhu Raman, Lei Fang, and Alexander D MacKerell Jr. Pharmacophore modeling using Site Identification by Ligand Competitive Saturation (SILCS) with multiple probe molecules. J. Chem. Inf. Model., 55(2):407–420, February 2015. doi: 10.1021/ci500691p.

23

E Prabhu Raman, Kenno Vanommeslaeghe, and Alexander D MacKerell Jr. Site-specific fragment identification guided by Single-Step Free Energy Perturbation calculations. J. Chem. Theory Comput., 8(10):3513–3525, October 2012. doi: 10.1021/ct300088r.

24

E Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah Aldrin Denny, and Alexander D MacKerell Jr. Estimation of relative free energies of binding using pre-computed ensembles based on the Single-Step Free Energy Perturbation and the Site Identification by Ligand Competitive Saturation approaches. J. Comput. Chem., 38(15):1238–1251, October 2016. doi: 10.1002/jcc.24522.

25

Taiji Oashi, Ashley L. Ringer, E. Prabhu Raman, and Alexander D. MacKerell. Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness. J. Chem. Inf. Model., 51:148–158, December 2011. doi: 10.1021/ci100359a.

26

Sirish Kaushik Lakkaraju, Wenbo Yu, E Prabhu Raman, Alena V Hershfeld, Lei Fang, Deepak A Deshpande, and Alexander D MacKerell Jr. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors. J. Chem. Inf. Model., 55(3):700–708, March 2015. doi: 10.1021/ci500729k.

27

Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, and Alexander D. Jr. MacKerell. GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. J. Comput. Chem., 44(20):1719–1732, July 2023. doi:10.1002/jcc.27121.