Recognition of errors in three‐dimensional structures of proteins

By Manfred J. Sippl. 1993

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

Citations in the corpus

Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, neutral): “2006; Sippl, 1993; Wallner and Elofsson, 2003).”
A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “…Beyer, 1994; Casari and Sippl, 1992; Gatchell et al., 2000; Hendlich et al., 1990; Samudrala and Moult, 1998; Simons et al., 1999; Vendruscolo et al., 2000), and protein model quality assessment (Jones and Thornton, 1996; Panchenko et al., 2000; Peng and Xu, 2010; Reva et al., 1997; Sippl, 1993).”
Comparative protein structure modeling by iterative alignment, model building and model assessment. (2003, background): “Fortunately, there is a great variety of model assessment methods, which can sometimes detect some errors in the assessed models (15–17).”
Modeling and Docking Studies on Novel Mutants (K71L and T204V) of the ATPase Domain of Human Heat Shock 70 kDa Protein 1 (2014, methodology): “Keywords: adenovirus; Hsp70; PROCHECK; ProQ; ERRAT; Verify 3D; ProSA; docking”
The utility of comparative models and the local model quality for protein crystal structure determination by Molecular Replacement (2012, methodology): “In order to operate, MetaMQAP combines the output from a number of model quality assessment programs (MQAPs), including VERIFY3D [18], PROSA [19], BALA-SNAPP [20], ANO-LEA [21], PROVE [22], TUNE [23], REFINER [24], and PROQRES [25].”
Comparative Protein Structure Modeling Using Modeller (2006, methodology): “template was used for the modeling. correct equivalences, that is, They include VERIFY3D (Luthy et al., 1992), Prosa2003 (Sippl, 1993; Wiederstein and Sippl, 2007), HARMONY (Topham et al., 1994), ANOLEA (Melo and Feytmans, 1998), DFIRE (Zhou and Zhou, 2002), DOPE (Shen and Sali, 2006), SOAP (Dong et”
New statistical potential for quality assessment of protein models and a survey of energy functions (2010, unknown): “…as potentials proposed in this work, “ RF_CB_SRS_OD ” , “ RF_CB_OD ” , “ RF_CB_SRS ” , “ RF_CB ” , and (iii) composite potentials: “ PROSA-pair ” , “ PROSA-combined ” [57], “ Rosetta ” [44], “ Shortle2005 ” [32], “ QMEAN6 ” [28,46], “ OPUS_CA ” [41], “ VSCORE-combined ” [38], and “ PC2CA ” [34].”
The Arabidopsis CORONATINE INSENSITIVE1 Protein Is a Jasmonate Receptor[C][W] (2009, background): “Verify3D,WHATIF, PROCHECK, andProSA2003 were used to evaluate the quality of the acquired structure.”
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction (2002, background): “2001), and validations (Luthy et al. 1992; Sippl 1993; MacArthur et al. 1994; Rojnuckarin and Subramaniam 1999), docking and binding (Pellegrini et al.”
The Victor/FRST Function for Model Quality Estimation (2005, unknown): “…RAPDF (Samudrala et al. , 1998), AKBP (Lu et al. , 2001), DFIRE (Zhou et al. , 2002; Zhang et al. , 2004), SNAPP (Krishnamoorthy et al. , 2003), Errat (Colovos et al. , 1993), Prosa II (Sippl, 1993b), Verify3D (Luthy et al. , 1992; Eisenberg et al. , 1997), and ProQ (Wallner et al. , 2003).”
Tools for comparative protein structure modeling and analysis (2003, methodology): “The accuracy of comparative models calculated by MODWEB, MOULDER and those in MODBASE can be judged by a variety of criteria (7,10), including percentage sequence identity on which the models are based (12) and various model assessment scores (25, 33 ).”