The penultimate rotamer library

By S. Lovell, J. Word, Jane S. Richardson, David C Richardson. 2000

1,031 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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. Paul D. Adams
2. David Baker
3. Randy J. Read
4. Pavel V. Afonine
5. Torsten Schwede
6. T. C. Terwilliger
7. Ben M. Webb
8. Yang Zhang

In Molecular Biology

1. David Baker
2. Torsten Schwede
3. Paul D. Adams
4. Randy J. Read
5. Yang Zhang
6. Ben M. Webb
7. Andrej Sali
8. T. C. Terwilliger

Citations in the corpus

• Features and development of Coot (2010, neutral): “The rotamer statistics are generated from an analysis of the nearest conformation in the MolProbity rotamer probability distribution (Lovell et al. , 2000) and displayed as a bar chart.”
• Alternate states of proteins revealed by detailed energy landscape mapping (2010, positive): “To assess recapitulation of side-chain rotamers, each side chain in the low-energy models and deposited crystal structures was first assigned to a named rotamer 32 using the smoothed, multidimensional χ -angle distributions ( B - factor and resolution-filtered) in MolProbity.”
• A Generic Program for Multistate Protein Design (2011, neutral): “‘‘rotamers’’ [20–22] and are typically represented with all their”
• SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling (2008, methodology): “Residues with high B-factors or atomic clashes were removed from the data set, as suggested by Lovell et al”
• A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, background): “…can be distorted by systematic errors caused by fitting the end of a side chain 180 backward into its local electron density (as happened to the Thr in Figure 1A); these are not entirely removed by applying d min and B-factor filters to the reference data (Lovell et al., 2000; Headd et al., 2009).”
• UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “…2009), SAXS profile fitting by IMP FoXS (Forster et al., 2008; Schneidman-Duhovny et al., 2010), and evaluation of sidechain conformations from backbone-dependent and backbone-independent rotamer libraries (Dunbrack, 2002; Lovell et al., 2000) into the UCSF Chi-mera molecular visualization package.”
• SWISS-MODEL: an automated protein homology-modeling server (2003, background): “Possible side chain conformations are selected from a backbone dependent rotamer library, which has been constructed carefully taking into account the quality of the source structures (25).”
• MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004, background): “Ramachandran plot criteria (16) and side chain rotamer distributions ( 17 ) have been updated and improved, and the deviation of C-beta positions from ideal (16) summarizes bond angle distortions around the sensitive C-alpha position.”