References
- Jalili V, Afgan E, Gu Q, Clements D, Blankenberg D, Goecks J, Taylor J, Nekrutenko A. The Galaxy Platform for Accessible, Reproducible and Collaborative Biomedical Analyses: 2020 Update. Nucleic Acids Res. 2021;48(W1):W395–W402. DOI: 10.1093/nar/gkaa434
- Berthold MR, Cebron N, Dill F, Gabriel TR, Kötter T, Meinl T, Ohl P, Thiel K, Wiswedel B. KNIME-the Konstanz Information Miner: Version 2.0 and Beyond. AcM SIGKDD Explor. Newsl. 2009;11(1):26–31. DOI: 10.1145/1656274.1656280
- Hassan M, Brown RD, Varma-O’Brien S, Rogers D. Cheminformatics Analysis and Learning in a Data Pipelining Environment. Mol. Divers. 2006;10(3):283–299. DOI: 10.1007/s11030-006-9041-5
- Warr WA. Scientific Workflow Systems: Pipeline Pilot and KNIME. DOI: 10.1007/s10822-012-9577-7
- Deelman E, Vahi K, Juve G, Rynge M, Callaghan S, Maechling PJ, Mayani R, Chen W, Ferreira Da Silva R, Livny M, Wenger K. Pegasus, a Workflow Management System for Science Automation. Futur. Gener. Comput. Syst. 2015;46:17–35. DOI: 10.1016/j.future.2014.10.008
- Senapathi T, Bray S, Barnett CB, Grüning B, Naidoo KJ. Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE). Bioinformatics. 2019;35(18):3508–3509. DOI: 10.1093/bioinformatics/btz107
- Dakka J, Farkas-Pall K, Turilli M, Wright DW, Coveney PV, Jha S. Concurrent and Adaptive Extreme Scale Binding Free Energy Calculations. In Proceedings – IEEE 14th International Conference on eScience, e-Science; 2018. pp. 189–200. DOI: 10.1109/eScience.2018.00034
- Doerr S, Harvey MJ, Noé F, De Fabritiis G. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput. 2016;12(4):1845–1852. DOI: 10.1021/acs.jctc.6b00049
- Balasubramanian V, Treikalis A, Weidner O, Jha S. Ensemble Toolkit: Scalable and Flexible Execution of Ensembles of Tasks. In Proceedings of the International Conference on Parallel Processing; 2016. DOI: 10.1109/ICPP.2016.59
- Hedges L, Mey A, Laughton C, Gervasio F, Mulholland A, Woods, C, Michel J. BioSimSpace: An Interoperable Python Framework for Biomolecular Simulation. J. Open Source Softw. 2019;4(43):1831. DOI: 10.21105/joss.01831
- Huber GA, Kim S. Weighted-Ensemble Brownian Dynamics Simulations for Protein Association Reactions. Biophys. J. 1996;70(1):97–110. DOI: 10.1016/S0006-3495(96)79552-8
- Fukunishi H, Watanabe O, Takada S. On the Hamiltonian Replica Exchange Method for Efficient Sampling of Biomolecular Systems: Application to Protein Structure Prediction. J. Chem. Phys. 2002;116(20):9058–9067. DOI: 10.1063/1.1472510
- Chen YZ, Zhi DG. Ligand – Protein Inverse Docking and Its Potential Use in the Computer Search of Protein Targets of a Small Molecule. Proteins Struct. Funct. Genet. 2001;43(2):217–226. DOI: 10.1002/1097-0134(20010501)43:2<;217::AID-PROT1032>3.0.CO;2-G
- Rocklin M. Dask: Parallel Computation with Blocked Algorithms and Task Scheduling. In Proceedings of the 14th Python in Science Conference; 2015. pp. 126–132. DOI: 10.25080/Majora-7b98e3ed-013
- Salomon-Ferrer R, Case DA, Walker RC. An Overview of the Amber Biomolecular Simulation Package. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2013;3(2):198–210. DOI: 10.1002/wcms.1121
- Oleinikovas V, Saladino G, Cossins BP, Gervasio FL. Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations. J. Am. Chem. Soc. 2016;138(43):14257–14263. DOI: 10.1021/jacs.6b05425
- Arkin MR, Randal M, DeLano WL, Hyde J, Luong TN, Oslob JD, Raphael DR, Taylor L, Wang J, McDowell RS, Wells JA, Braisted AC. Binding of Small Molecules to an Adaptive Protein-Protein Interface. Proc. Natl. Acad. Sci. U. S. A. 2003;100(4):1603–1608. DOI: 10.1073/pnas.252756299
- Zwier MC, Adelman JL, Kaus JW, Pratt AJ, Wong KF, Rego NB, Suárez E, Lettieri S, Wang DW, Grabe M, Zuckerman DM, Chong LT. WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis. J. Chem. Theory Comput. 2015;11(2):800–809. DOI: 10.1021/ct5010615
- Bogetti AT, Mostofian B, Dickson A, Pratt A, Saglam AS, Harrison PO, Adelman JL, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Zwier MC, Zuckerman DM, Chong LT. A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]. Living J. Comput. Mol. Sci. 2019.1(2):10607–10607. DOI: 10.33011/livecoms.1.2.10607
- Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J. Mol. Biol. 2016;428(4):709–719. DOI: 10.1016/j.jmb.2016.01.029