20 Bursulaya BD, Totrov M, Abagyan R, Brooks CL 3rd.Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. Flexible protein–ligand docking by global energy optimization in internal coordinates. Improved protein–ligand docking using GOLD. 17 Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD.Method and assessment of docking accuracy. Glide: a new approach for rapid, accurate docking and scoring. 16 Friesner RA, Banks JL, Murphy RB et al.15 Mcgann MR, Almond HR, Nicholls A, Grant JA, Brown FK.Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking. DOCK 6: combining techniques to model RNA-small molecule complexes. 13 Lang PT, Brozell SR, Mukherjee S et al.Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. 12 Morris GM, Goodsell DS, Halliday RS et al.Structure-based drug design: docking and scoring. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. 10 Moitessier N, Englebienne P, Lee D, Lawandi J, Corbeil CR.A critical assessment of docking programs and scoring functions. 9 Warren GL, Andrews CW, Capelli AM et al.Docking and scoring in virtual screening for drug discovery: methods and applications. 8 Kitchen DB, Decornez H, Furr JR, Bajorath J.Molecular recognition and docking algorithms. Computer tools in the discovery of HIV-1 integrase inhibitors. Combining docking with pharmacophore filtering for improved virtual screening. Quo Vadis, virtual screening? A comprehensive survey of prospective applications. 4 Ripphausen P, Nisius B, Peltason L, Bajorath J.Complementarity between a docking and a high-throughput screen in discovering new cruzain inhibitors.

3 Ferreira RS, Simeonov A, Jadhav A et al.What has computer-aided molecular design ever done for drug discovery? Expert Opin. Successful applications of computer aided drug discovery: moving drugs from concept to the clinic. Capabilities in Jmol enabled by Jmol SMILES and Jmol SMARTS include efficient MMFF94 atom typing, conformational identification, SMILES comparisons without canonicalization, identification of stereochemical relationships, quantitative comparison of 3D structures from different sources (including differences in Kekulization), conformational flexible fitting, and atom mapping used to synchronize interactive displays of 2D structures, 3D structures, and spectral correlations, where data are being drawn from multiple sources. Together they have proven exceptionally capable in extracting valuable information from 3D structural models, as demonstrated in Jmol. Jmol SMILES and Jmol SMARTS add value to standard SMILES and SMARTS. While developed specifically for Jmol, these dialects of SMILES and SMARTS are independent of the Jmol application itself. The result is an expansion of the capabilities of SMILES and SMARTS primarily for use in 3D molecular analysis, allowing a broader range of matching involving any combination of 3D molecular structures, SMILES strings, and SMARTS patterns. Jmol SMARTS similarly adds these same modifications to OpenSMARTS, but also adds a number of additional 'primitives' and elements of syntax tuned to matching 3D molecular structures and selecting their atoms. Jmol SMILES is a superset of OpenSMILES, allowing a freer format, including whitespace and comments, the addition of 'processing directives' that modify the meaning of certain aspects of SMILES processing such as aromaticity and stereochemistry, a more extensive treatment of stereochemistry, and several minor additions. The dialects most closely resemble OpenSMILES and OpenSMARTS. The specifications of 'Jmol SMILES' and 'Jmol SMARTS' are described. Over the past 10 years, from 2007 to 2016, work on Jmol has included the development of dialects of SMILES and SMARTS that incorporate novel aspects that allow new and powerful applications.

Jmol is a widely used open-source molecular visualization and analysis tool written in Java and implemented in both Java and JavaScript. SMILES and SMARTS are two well-defined structure matching languages that have gained wide use in cheminformatics.

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