Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure…

By E. Krissinel', K. Henrick

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Citations in the corpus

RUPEE: A fast and accurate purely geometric protein structure search (2018, neutral): “We end with a comparison of results against the 34 mTM-align structure search [5], the secondary structure matching (SSM) search [6], and 35 the CATHEDRAL structural scan [7] available at the CATH website.”
Features and development of Coot (2010, neutral): “In addition, Coot depends upon open-source crystallographic software components including the Clipper libraries (Cowtan, 2003), the MMDB library (Krissinel et al. , 2004), the SSM library (Krissinel & Henrick, 2004) and the CCP 4 libraries.”
BALBES: a molecular-replacement pipeline (2007, methodology): “Quality factors (Q-factors) were calculated using the procedure described by Krissinel & Henrick (2004).”
ASH structure alignment package: Sensitivity and selectivity in domain classification (2007, methodology): “Four external structure alignment programs were used directly in this study: DaliLite[11] was downloaded from the FSSP server[12]; STRUCTAL[13] was taken from the STRUCTAL download page[14]; FAST[15] was taken from the FAST server[16]; SSM [17] was taken from the SSM download center[18].”
Searching protein structure databases with DaliLite v.3 (2008, methodology): “SSM server (http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver; Krissinel and Henrick, 2004) parameters were set to 10:10 and highest precision.”
Intricate Knots in Proteins: Function and Evolution (2006, methodology): “Applying this analysis, we discovered 241 knotted structures in the Protein Data Bank.”
Structural and immunologic characterization of bovine, horse, and rabbit serum albumins (2012, methodology): “Sequence and structure analysis The PDBeFold (Krissinel and Henrick, 2004) service was used to search for human serum albumin structures that adopt conformations most similar to those of BSA, ESA, or RSA, and calculate the root-mean-square deviations (RMSDs) between them.”
Structural Characterization of the glycoprotein GP2 Core Domain from the CAS Virus, a Novel Arenavirus-like Species (2013, methodology): “LSQKAB and SSM algorithms were used for structural superpositions [47,52].”
Advances and pitfalls of protein structural alignment. (2009, unknown): “3D N(2)e NANBð1þðrmsd=3Þ(2)Þ Q-score SSM [40]”