Completeness in structural genomics

By Dennis Vitkup, Eugene Melamud, John Moult, Christopher Sander. Nature Structural Biology, 2001

359 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/229ea8946152eaa69699d70ed1edd92d6a09b532

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Citations in the corpus

Modeling structurally variable regions in homologous proteins with rosetta (2004, background): “quently, complete three-dimensional (3D) models cannot be generated by homology-based methods alone.(2) Because”
MODBASE: a database of annotated comparative protein structure models and associated resources (2005, background): “We highlight here the increased coverage of the sequence± structure space (31) by the NYSGXRC structures.”
Increasing the Radius of Convergence of Molecular Replacement by Density and Energy Guided Protein Structure Optimization (2011, neutral): “20% sequence identity: the chance there is a structure with a sequence identity of 20% or greater is more than twice that of finding a structure with at least 30% sequence identity 23 .”
Homology Modeling a Fast Tool for Drug Discovery: Current Perspectives (2012, background): “Homology modeling methods use the fact that evolutionary related proteins share a similar structure[2,3].”
ModBase, a database of annotated comparative protein structure models and associated resources (2013, background): “We highlight here the increased coverage of the sequence‐ structure space ( 31 ) by the NYSGXRC structures.”
SWISS-MODEL: an automated protein homology-modeling server (2003, background): “A key to the efficient coverage will be the careful and optimal selection of the proteins for structural genomics (6).”
Tools for comparative protein structure modeling and analysis (2003, background): “Fortunately, domains in protein sequences are gradually evolving entities that can be clustered into a relatively small number of families of domains with similar sequences and structures (that is, folds) (4).”
The structure of the protein universe and genome evolution (2002, background): “This highly skewed distribution of proteins among folds should enable structural genomics research programmes to complete a preliminary tour of the most important part of the protein universe within the next few year”
Toward better refinement of comparative models: Predicting loops in inexact environments (2008, background): “Two requirements for successful comparative model refinement are (1) efficient methods for sampling degrees of freedom that enable near-native configurations to be located from the starting structure; and (2) an energy function capable of identifying near-native conformations.”
3DCoffee: combining protein sequences and structures within multiple sequence alignments. (2004, background): “(a) Each box indicates the average accuracy difference between TC-3D and TCoffee when computing HOM39 MSAs with various structure/sequence ratios: [0–20] (6 values), [21–40] (27 values), [41–60] (44 values), [61–80] (44 values), [81–100] (20 values).”
Template‐based modeling and free modeling by I‐TASSER in CASP7 (2007, background): “If any region with > 80 residues has no aligned residues in at least two strong PPA alignments of Z -score > 8, the target will be judged as a multiple domain protein and domain boundaries are automatically assigned based on the borders of the large gaps.”
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison (2002, background): “To fully realize its potential, structural genomics needs rigorous and fast methods to compare at large scale the vast number of both experimental protein structures and models, involving disparate resolution levels, that will be produced over the next years (Sali 1998; Vitkup et al. 2001).”
The protein folding problem. (2008, background): “Structural genomics is likely to help here (87, 222).”
Protein Structure Prediction: Is It Useful? (2009, background): “It has been estimated [50] that at least 16 000 optimally selected new structures need to be determined so that CM can cover 90% of protein domain families.”