The Impact of Structural Genomics: Expectations and Outcomes

By John-Marc Chandonia, Steven E. Brenner. Science, 2005

393 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/073ad57320d36a21e446758709ebbb3a4418d714

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Citations in the corpus

Computational design of a protein crystal (2012, background): “Crystals of proteins and other biomacromolecules are widely studied, and they play a crucial role in structural biology, where realization of diffraction-quality crystals is often the bottleneck of structural genomics efforts (10, 11).”
The Protein Structure Initiative: achievements and visions for the future (2012, background): “Major recent advances Several recent reviews have outlined the progress and achievements of the PSI program [3-9].”
Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “New Context for Modeling Provided by the Protein Structure Initiative AstimulatingcatalystformolecularmodelingistheProteinStruc-ture Initiative (PSI), which aims to determine representative atomic structures of most major protein families by X-ray crystal-lography and nuclear magnetic resonance (NMR”
ProteinNet: a standardized data set for machine learning of protein structure (2019, background): “3), likely reflecting the end of the Structural Genomics Initiative (Chandonia and Brenner, 2006) which crystallized a large number of proteins of known folds.”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Structural genomics is an international effort to determine the 3-D shapes of all important biological macromolecules, with a primary focus on proteins [67–72].”
Three-dimensional reconstruction of protein networks provides insight into human genetic disease (2012, background): “We used both iPfam 17 and 3did 18 to identify the interfaces of two interacting proteins by mapping them to known atomic-resolution 3D structures of interactions in the Protein Data Bank (PDB) 19 ( Fig.”
Improving structure-based function prediction using molecular dynamics (2009, background): “Since the initiation of the structural genomics (SG) efforts, the number of solved structures in the Protein Data Bank (PDB) (Berman et al., 2000) with unknown function is increasing (Chandonia and Brenner, 2006; Levitt, 2007; Terwilliger, 2004).”
Advances in Protein Chemistry and Structural Biology (2010, background): “The structural genomics projects have made significant contributions to our current body of knowledge of protein structures (Chandonia and Brenner, 2006).”
Machine Learning Methods for Protein Structure Prediction (2008, neutral): “from primary sequences [16].”
Data growth and its impact on the SCOP database: new developments (2007, background): “A large proportion of new structures come from worldwide Structural Genomics initiatives, which are producing them at an increasing rate (6,7).”
Progress and challenges in protein structure prediction. (2008, background): “Introduction In recent years, despite many debates, structure genomics is probably one of the most noteworthy efforts in protein structure determination, which aims to obtain 3D models of all proteins by an optimized combination of experimental structure solution and computer-based structure predict”
Protein Structure Prediction: Is It Useful? (2009, background): “Considering that traditional structural biology has contributed roughly the same number of novel structures as the SG centers in the past two years [49,51 ], it will take about one more decade to determine”
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction (2006, background): “However, with the gradual growth in structural data likely to be generated from the various structural genomics projects [38,39], multiple structure representatives should become available for many more superfamilies.”
CATHEDRAL: A Fast and Effective Algorithm to Predict Folds and Domain Boundaries from Multidomain Protein Structures (2007, background): “…solved by the structural genomics initiatives—which are frequently targeted because they have no clear sequence similarity to existing structures and may adopt novel folds—show that approximately 90% are similar to those already observed in the PDB through sequence or structure comparison [21,22].”
Nature of the protein universe (2009, neutral): “Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures.”
An estimated 5% of new protein structures solved today represent a new Pfam family (2013, background): “…how close we are to the goal of structurally covering the proteinsequence space; that is, of having the structure of a homologue for each (or, more realistically, most) of the protein sequences available (Chothia, 1992; Yan & Moult, 2005; Chandonia & Brenner, 2006; Levitt, 2007; Nair et al., 2009).”
SCOPe: Manual Curation and Artifact Removal in the Structural Classification of Proteins – extended Database (2016, result): “These results are similar to the novelty of newly classified structures in SCOP ten to twenty years ago, for structures that did not have significant sequence similarity with previously classified structures [25,26].”