Evaluating protein structures determined by structural genomics consortia

By Aneerban Bhattacharya, R. Tejero, Gaetano T. Montelione. 2006

745 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. Andriy Kryshtafovych
2. Gaetano T. Montelione
3. David Baker
4. Sergey Ovchinnikov
5. Yang Zhang
6. Krzysztof Fidelis
7. Ivan V. Anishchenko
8. Yuanpeng Janet Huang

In Molecular Biology

1. David Baker
2. Sergey Ovchinnikov
3. Andriy Kryshtafovych
4. Gaetano T. Montelione
5. Yang Zhang
6. Debora Marks
7. Ivan V. Anishchenko
8. Krzysztof Fidelis

Citations in the corpus

• Predicting multiple conformations via sequence clustering and AlphaFold2 (2023, neutral): “The final structures were validated using the wwPDB validation tool 79,80 (https://validate-rcsb-east.wwpdb.org/ validservice/) and the Protein Structure Validation Suite (PSVS) 81 .”
• De novo protein design by deep network hallucination (2020, methodology): “The lowest energy 20, of 100 structures calculated, were then refined in explicit water using CNS 50 with the addition of 70 backbone one-bond 1 H-15 N RDCs. Structure quality analyses were performed on the final ensemble of 20 models using RPF and PSVS software 51 (Table S1).”
• Protein structure determination by combining sparse NMR data with evolutionary couplings (2015, positive): “Similar results have also been observed in analyses of the sensitivity of NMR restraint violations for validating NMR-derived structures 17 .”
• Assessment of Prediction Methods for Protein Structures Determined by NMR in CASP14: Impact of AlphaFold2 (2021, positive): “Structure quality statistics for T1027 were analyzed with the PSVS software suite.(22) The resulting structure quality statistics for both the NMR and AF2 model ensembles are summarized in”
• The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data (2016, methodology): “Structural assessment was conducted by the PSVS package (Bhattacharya et al. 2007).”
• Improved Technologies Now Routinely Provide Protein NMR Structures Useful for Molecular Replacement (2011, methodology): “Coordinates of ‘not-well-defined’ residues calculated by PSVS program based on dihedral order parameter values (Bhattacharya et al., 2007; Hyberts et al., 1992) are removed, and surface residues with side chains longer than Ser are truncated to Ser.”
• Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples (2012, neutral): “In the cases where an X-ray structure was not available to evaluate high-resolution accuracy, the RASREC models had the same overall topology as conventionally determined NMR structures but better side-chain and core packing as judged by traditional knowledge-based validation methods (39, 40).”