VADAR: a web server for quantitative evaluation of protein structure quality

By Leigh Willard, Anuj Ranjan, Haiyan Zhang, H. Monzavi, Robert F. Boyko, B. Sykes, David S. Wishart. Nucleic Acids Res., 2003

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SuperPose: a simple server for sophisticated structural superposition (2004, methodology): “If the pairwise sequence identity falls below the default threshold (25%), SuperPose determines the secondary structure using VADAR (volume, area, dihedral angle reproter) (9) and performs a secondary structure alignment using a modified Needleman–Wunsch algorithm.”
GOMoDo: A GPCRs Online Modeling and Docking Webserver (2013, methodology): “directly submitted to the VADAR model quality assessment server [30].”
SHIFTX2: significantly improved protein chemical shift prediction (2011, methodology): “) each protein structure in the training data set was further processed by VADAR (Willard et al. 2003), SHIFTX (Neal et al. 2003), PROSESS (Berjanskii et al. 2010) and other in-house programs.”
BASys: a web server for automated bacterial genome annotation (2005, methodology): “If the sequence has sufﬁcient similarity to a sequence represented in the PDB database, then BASys may use HOMODELLER (X. Dong, unpublished data) to generate a homology model and subsequently perform a structural analysis using VADAR (18).”