Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

By Ajay N. Jain. J. Comput. Aided Mol. Des., 2007

573 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0401c86fd549dbc72f0202e7f5b3207a708e7e8d

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Citations in the corpus

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go (2008, unknown): “…et al ., 2003; Schulz-Gasch and Stahl, 2003; Wang et al ., 2003, 2004; Ferrara et al ., 2004; Kellenberger et al ., 2004; Kontoyianni et al ., 2004; Kroemer et al ., 2004; Perola et al ., 2004, 2007; Chen et al ., 2006; Cummings et al ., 2005; Kontoyianni et al ., 2005; Warren et al ., 2006).”
Challenges and advances in computational docking: 2009 in review (2011, methodology): “Within Surﬂex (37,38), each pose is re-scored using all of the provided receptor conformations (39), while the evolution implementation of Flexibility Induced Through Targeted Evolutionary Description (FITTED) allows for cross-over and mutations of multiple side chain and backbone conformations…”
Key Topics in Molecular Docking for Drug Design (2019, background): “Surflex Fragmentation and alignment to idealised molecule (Protomol) + BFGS optimisation Empirical Commercial Jain, 2003; Jain 2007 [39,40]”
Assessing protein–ligand interaction scoring functions with the CASF-2013 benchmark (2018, background): “Today’s docking programs, such as DOCK 8,9 , AutoDock 10,11 , GOLD 12 , Glide 13,14 , and Surflex-Dock 15,16 , all rely on scoring functions for evaluating protein–ligand interactions.”
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis (2009, background): “1 [42] were selected due to their relatively fast speed, high accuracy and ease of automation in large-scale docking studies.”
Virtual screening strategies in drug discovery: a critical review. (2013, background): “Surflex [55] No http://www.”
Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways (2013, methodology): “Surflex 2.6(24) and OMEGA 2.4.6 were used for small molecule docking and ROCS 3.1.2 was used to generate overlap scores for chemotype clustering.”