Verification of protein structures : Side-chain planarity

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Increasing the precision of comparative models with YASARA NOVA—a self‐parameterizing force field (2002, methodology): “These are extracted from the 25 highest resolution X-ray structures in the PDB, with (cid:7) 30% sequence identity, obtained from the PDB-SELECT algorithm 13 (a list with PDBID codes of all proteins used in this work is available from http://www.yasara.com/nova).”
Objectively judging the quality of a protein structure from a Ramachandran plot (1997, methodology): “The Ramachandran plot quality analysis is available as part of the WHAT_CHECK program (Hooft et al., 1996b).”
A series of PDB-related databanks for everyday needs (2014, background): “The single way of accessing PDB SELECT lists is through the PDB SELECT pages.”
Making optimal use of empirical energy functions: Force‐field parameterization in crystal space (2004, background): “20 The top 50 structures were chosen and divided into optimization (even numbers) and validation sets (uneven numbers).”