Enhancement of protein modeling by human intervention in applying the automatic programs 3D‐JIGSAW and 3D‐PSSM

By Paul A. Bates, Lawrence A. Kelley, Robert M. MacCallum, Michael J.E. Sternberg. Proteins: Structure, Function, and Bioinformatics, 2001

593 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b038f14cfb05f915a4d2eda65f537d622e0787ce

How researchers see this paper

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

In Materials Chemistry

1. Ben M. Webb
2. Andrej Sali
3. Min-Yi Shen
4. David Eramian
5. Narayanan Eswar
6. Yang Zhang
7. Mallur Srivatsan Madhusudhan
8. Marc A. Martí-Renom

In Molecular Biology

1. Ben M. Webb
2. Andrej Sali
3. Yang Zhang
4. Min-Yi Shen
5. David Eramian
6. Narayanan Eswar
7. Torsten Schwede
8. Mallur Srivatsan Madhusudhan

Citations in the corpus

• SWISS-MODEL: an automated protein homology-modeling server (2003, unknown): “uk/~3djigsaw/) (15), ESyPred3D (http://www.”
• MEDELLER: homology-based coordinate generation for membrane proteins (2010, background): “Membrane proteins (MP) constitute about 30% of all known proteins and are one of the largest classes of drug targets.”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “Three other programs that implement this method are 3D-JIGSAW (Bates et al., 2001), RosettaCM (Song et al., 2013), and SWISSMODEL (Schwede et al., 2003).”
• Comparative Protein Structure Modeling Using Modeller (2006, methodology): “Three other programs that implement this method are 3D-JIGSAW (Bates et al., 2001), RosettaCM (Song et al., 2013), and SWISS-MODEL (Schwede et al., 2003).”
• Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. (2004, methodology): “Three-dimensional models of MYB domains were built using the 3D-Jigsaw server [Bates et al. (2001), http://www.”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “Three other programs that implement this method are 3D-JIGSAW (Bates et al., 2001), RosettaCM (Song et al., 2013), and SWISS-MODEL (Schwede et al., 2003).”
• The properties of protein family space depend on experimental design (2005, background): “Examples are the Superfamily database (11), Gene3D (11), 3D-PSSM (12) and others.”
• Comparative Protein Structure Modeling Using MODELLER (2007, methodology): “By scanning the database of alignments, tables quantifying various correlations were obtained, such as the correlations between two equivalent C α -”
• EVA: evaluation of protein structure prediction servers (2003, background): “3D-Jigsaw http://www.bmm.icnet.uk/servers/3djigsaw/ PA Bates, P Fitzjohn and BC Moreira ( 26 ,27) CPHModels http://www.cbs.dtu.dk/services/CPHmodels/ S Brunak et al. (28) ESyPred3D http://www.fundp.ac.be/urbm/bioinfo/esypred/ C Lambert (29) SDSC1 http://cl.sdsc.edu/hm.html IN Shindyalov and PE Bourn”