Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Shao, Chenghua; Liu, Zonghong; Yang, Huanwang; Wang, Sijian; Burley, Stephen K.

doi:10.1038/sdata.2018.293

Title: Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Journal Article · Tue Dec 11 00:00:00 EST 2018 · Scientific Data

DOI:https://doi.org/10.1038/sdata.2018.293· OSTI ID:1624556

Shao, Chenghua ^[1]; Liu, Zonghong ^[1]; Yang, Huanwang ^[1]; Wang, Sijian ^[1]; Burley, Stephen K. ^[2]

Rutgers Univ., Piscataway, NJ (United States)
Rutgers Univ., Piscataway, NJ (United States); Univ. of California San Diego, La Jolla, CA (United States)

Outlier analyses are central to scientific data assessments. Conventional outlier identification methods do not work effectively for Protein Data Bank (PDB) data, which are characterized by heavy skewness and the presence of bounds and/or long tails. We have developed a data-driven nonparametric method to identify outliers in PDB data based on kernel probability density estimation. Unlike conventional outlier analyses based on location and scale, Probability Density Ranking can be used for robust assessments of distance from other observations. Analyzing PDB data from the vantage points of probability and frequency enables proper outlier identification, which is important for quality control during deposition-validation-biocuration of new three-dimensional structure data. Ranking of Probability Density also permits use of Most Probable Range as a robust measure of data dispersion that is more compact than Interquartile Range. The Probability-Density-Ranking approach can be employed to analyze outliers and data-spread on any large data set with continuous distribution.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Rutgers Univ., Piscataway, NJ (United States)

Sponsoring Organization:: USDOE; National Science Foundation (NSF); National Institute of General Medical Sciences (NIGMS); National Cancer Institute (NCI)

Grant/Contract Number:: NSF-DBI 1338415

OSTI ID:: 1624556

Journal Information:: Scientific Data, Vol. 5, Issue 1; ISSN 2052-4463

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

References (51)

Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive Shao, Chenghua; Yang, Huanwang; Westbrook, John D. Structure, Vol. 25, Issue 3 https://doi.org/10.1016/j.str.2017.01.013	journal	March 2017
Hibernating Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture) Yonath, Ada Angewandte Chemie International Edition, Vol. 49, Issue 26 https://doi.org/10.1002/anie.201001297	journal	June 2010
PDBe: improved accessibility of macromolecular structure data from PDB and EMDB Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes Nucleic Acids Research, Vol. 44, Issue D1 https://doi.org/10.1093/nar/gkv1047	journal	October 2015
Announcing the worldwide Protein Data Bank Berman, Helen; Henrick, Kim; Nakamura, Haruki Nature Structural & Molecular Biology, Vol. 10, Issue 12 https://doi.org/10.1038/nsb1203-980	journal	December 2003
Serial femtosecond crystallography: A revolution in structural biology Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse Archives of Biochemistry and Biophysics, Vol. 602 https://doi.org/10.1016/j.abb.2016.03.036	journal	July 2016
Crystal and NMR Structures of a Peptidomimetic β-Turn That Provides Facile Synthesis of 13-Membered Cyclic Tetrapeptides Cameron, Alan J.; Squire, Christopher J.; Edwards, Patrick J. B. Chemistry - An Asian Journal, Vol. 12, Issue 24 https://doi.org/10.1002/asia.201701422	journal	November 2017
A New Generation of Crystallographic Validation Tools for the Protein Data Bank Read, Randy J.; Adams, Paul D.; Arendall, W. Bryan Structure, Vol. 19, Issue 10 https://doi.org/10.1016/j.str.2011.08.006	journal	October 2011
RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education: RCSB Protein Data Bank Burley, Stephen K.; Berman, Helen M.; Christie, Cole Protein Science, Vol. 27, Issue 1 https://doi.org/10.1002/pro.3331	journal	November 2017
Potassium Channels and the Atomic Basis of Selective Ion Conduction (Nobel Lecture) MacKinnon, Roderick Angewandte Chemie International Edition, Vol. 43, Issue 33 https://doi.org/10.1002/anie.200400662	journal	August 2004
OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang Structure, Vol. 25, Issue 3 https://doi.org/10.1016/j.str.2017.01.004	journal	March 2017
Retrieval of Crystallographically-Derived Molecular Geometry Information Bruno, Ian J.; Cole, Jason C.; Kessler, Magnus Journal of Chemical Information and Computer Sciences, Vol. 44, Issue 6 https://doi.org/10.1021/ci049780b	journal	November 2004
From the Structure and Function of the Ribosome to New Antibiotics (Nobel Lecture) Steitz, Thomas A. Angewandte Chemie International Edition, Vol. 49, Issue 26 https://doi.org/10.1002/anie.201000708	journal	June 2010
X-ray Crystallographic Studies of Proteins Matthews, B. W. Annual Review of Physical Chemistry, Vol. 27, Issue 1 https://doi.org/10.1146/annurev.pc.27.100176.002425	journal	October 1976
Unraveling the Structure of the Ribosome (Nobel Lecture) Ramakrishnan, V. Angewandte Chemie International Edition, Vol. 49, Issue 26 https://doi.org/10.1002/anie.201001436	journal	June 2010
Stereochemistry of polypeptide chain configurations Ramachandran, G. N.; Ramakrishnan, C.; Sasisekharan, V. Journal of Molecular Biology, Vol. 7, Issue 1 https://doi.org/10.1016/S0022-2836(63)80023-6	journal	July 1963
Accurate bond and angle parameters for X-ray protein structure refinement Engh, R. A.; Huber, R. Acta Crystallographica Section A Foundations of Crystallography, Vol. 47, Issue 4 https://doi.org/10.1107/S0108767391001071	journal	July 1991
Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection Reddy, V. S.; Nemerow, G. R. Proceedings of the National Academy of Sciences, Vol. 111, Issue 32 https://doi.org/10.1073/pnas.1408462111	journal	July 2014
Analysis of solvent content and oligomeric states in protein crystals-does symmetry matter? Chruszcz, Maksymilian; Potrzebowski, Wojciech; Zimmerman, Matthew D. Protein Science, Vol. 17, Issue 4 https://doi.org/10.1110/ps.073360508	journal	April 2008
Detect, correct, retract: How to manage incorrect structural models Wlodawer, Alexander; Dauter, Zbigniew; Porebski, Przemyslaw J. The FEBS Journal, Vol. 285, Issue 3 https://doi.org/10.1111/febs.14320	journal	November 2017
Mutagenic conformation of 8-oxo-7,8-dihydro-2′-dGTP in the confines of a DNA polymerase active site Batra, Vinod K.; Beard, William A.; Hou, Esther W. Nature Structural & Molecular Biology, Vol. 17, Issue 7 https://doi.org/10.1038/nsmb.1852	journal	June 2010
On the Development of Electron Cryo-Microscopy (Nobel Lecture) Dubochet, Jacques Angewandte Chemie International Edition, Vol. 57, Issue 34 https://doi.org/10.1002/anie.201804280	journal	July 2018
NMR Studies of Structure and Function of Biological Macromolecules (Nobel Lecture) Wüthrich, Kurt Angewandte Chemie International Edition, Vol. 42, Issue 29 https://doi.org/10.1002/anie.200300595	journal	July 2003
Biased and Unbiased Cross-Validation in Density Estimation Scott, David W.; Terrell, George R. Journal of the American Statistical Association, Vol. 82, Issue 400 https://doi.org/10.1080/01621459.1987.10478550	journal	December 1987
Mise of kernel estimates of a density and its derivatives Singh, Radhey S. Statistics & Probability Letters, Vol. 5, Issue 2 https://doi.org/10.1016/0167-7152(87)90072-1	journal	March 1987
The Molecular Basis of Eukaryotic Transcription (Nobel Lecture) Kornberg, Roger Angewandte Chemie International Edition, Vol. 46, Issue 37 https://doi.org/10.1002/anie.200701832	journal	September 2007
Identification of the Proton Channel to the Active Site Type 2 Cu Center of Nitrite Reductase: Structural and Enzymatic Properties of the His254Phe and Asn90Ser Mutants ^† ^, ^‡ Hough, Michael A.; Eady, Robert R.; Hasnain, S. Samar Biochemistry, Vol. 47, Issue 51 https://doi.org/10.1021/bi801369y	journal	December 2008
Structure validation by Cα geometry: ϕ,ψ and Cβ deviation Lovell, Simon C.; Davis, Ian W.; Arendall, W. Bryan Proteins: Structure, Function, and Bioinformatics, Vol. 50, Issue 3 https://doi.org/10.1002/prot.10286	journal	January 2003
Solvent content of protein crystals Matthews, B. W. Journal of Molecular Biology, Vol. 33, Issue 2 https://doi.org/10.1016/0022-2836(68)90205-2	journal	April 1968
The future of biocuration Howe, Doug; Costanzo, Maria; Fey, Petra Nature, Vol. 455, Issue 7209 https://doi.org/10.1038/455047a	journal	September 2008
The FAIR Guiding Principles for scientific data management and stewardship Wilkinson, Mark D.; Dumontier, Michel; Aalbersberg, IJsbrand Jan Scientific Data, Vol. 3, Issue 1 https://doi.org/10.1038/sdata.2016.18	journal	March 2016
BioMagResBank Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm957	journal	December 2007
Validation of Structures in the Protein Data Bank Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M. S. Structure, Vol. 25, Issue 12 https://doi.org/10.1016/j.str.2017.10.009	journal	December 2017
Cryocrystallography of biological macromolecules: a generally applicable method Hope, H. Acta Crystallographica Section B Structural Science, Vol. 44, Issue 1 https://doi.org/10.1107/S0108768187008632	journal	February 1988
Control of the negative IRES trans -acting factor KHSRP by ubiquitination Kung, Yu-An; Hung, Chuan-Tien; Chien, Kun-Yi Nucleic Acids Research, Vol. 45, Issue 1 https://doi.org/10.1093/nar/gkw1042	journal	November 2016
Outlier Analyses of the Protein Data Bank Archive Using a Probability-Density-Ranking Approach Burley, Stephen K.; Shao, Chenghua; Yang, Huanwang Figshare https://doi.org/10.6084/m9.figshare.c.4148975	collection	January 2018
Serial femtosecond crystallography of soluble proteins in lipidic cubic phase Fromme, Raimund; Ishchenko, Andrii; Metz, Markus IUCrJ, Vol. 2, Issue 5, p. 545-551 https://doi.org/10.1107/S2052252515013160	journal	August 2015
Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures Kinjo, Akira R.; Bekker, Gert-Jan; Suzuki, Hirofumi Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw962	journal	October 2016
Phi/Psi-chology: Ramachandran revisited Kleywegt, Gerard J.; Jones, T. Alwyn Structure, Vol. 4, Issue 12 https://doi.org/10.1016/S0969-2126(96)00147-5	journal	December 1996
The Protein Data Bank Berman, H. M. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.235	journal	January 2000
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures Brünger, Axel T. Nature, Vol. 355, Issue 6359 https://doi.org/10.1038/355472a0	journal	January 1992
Single-Particle Reconstruction of Biological Molecules-Story in a Sample (Nobel Lecture) Frank, Joachim Angewandte Chemie International Edition, Vol. 57, Issue 34 https://doi.org/10.1002/anie.201802770	journal	July 2018
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals Kantardjieff, Katherine A.; Rupp, Bernhard Protein Science, Vol. 12, Issue 9 https://doi.org/10.1110/ps.0350503	journal	September 2003
From Electron Crystallography to Single Particle CryoEM (Nobel Lecture) Henderson, Richard Angewandte Chemie International Edition, Vol. 57, Issue 34 https://doi.org/10.1002/anie.201802731	journal	July 2018
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data Young, Jasmine Y.; Westbrook, John D.; Feng, Zukang Database, Vol. 2018 https://doi.org/10.1093/database/bay002	journal	January 2018
Identification of Outliers Hawkins, D. M. Monographs on Statistics and Applied Probability https://doi.org/10.1007/978-94-015-3994-4	book	January 1980
Improved amino acid flexibility parameters Smith, David K.; Radivojac, Predrag; Obradovic, Zoran Protein Science, Vol. 12, Issue 5 https://doi.org/10.1110/ps.0236203	journal	May 2003
ChemInform Abstract: Polar Bears, Antibiotics, and the Evolving Ribosome (Nobel Lecture) Yonath, A. ChemInform, Vol. 41, Issue 40 https://doi.org/10.1002/chin.201040269	journal	September 2010
A note on modified cross-validation in density estimation Feluch, W.; Koronacki, J. Computational Statistics & Data Analysis, Vol. 13, Issue 2 https://doi.org/10.1016/0167-9473(92)90002-w	journal	March 1992
Modified cross-validation in density estimation Stute, W. Journal of Statistical Planning and Inference, Vol. 30, Issue 3 https://doi.org/10.1016/0378-3758(92)90157-n	journal	March 1992
Multivariate analyses of quality metrics for crystal structures in the PDB archive Shao, Chenghua; Yang, Huanwang; Westbrook, John D. Acta Crystallographica Section A Foundations and Advances, Vol. 73, Issue a1 https://doi.org/10.1107/s0108767317098142	journal	May 2017
RCSB Protein Data Bank: sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education Zardecki, Christine; Berman, Helen M.; Christie, Cole Acta Crystallographica Section A Foundations and Advances, Vol. 74, Issue a1 https://doi.org/10.1107/s0108767318098811	journal	July 2018

Figures / Tables (5)

Similar Records

Protein Data Bank: the single global archive for 3D macromolecular structure data

Journal Article · Wed Oct 24 00:00:00 EDT 2018 · Nucleic Acids Research · OSTI ID:1624556

Burley, Stephen K.; Berman, Helen M.; Bhikadiya, Charmi; +79 more

Validation of Structures in the Protein Data Bank

Journal Article · Fri Dec 01 00:00:00 EST 2017 · Structure · OSTI ID:1624556

Gore, Swanand; Sanz García, Eduardo; Hendrickx, Pieter M. S.; +31 more

Investigation of protein quaternary structure via stoichiometry and symmetry information

Journal Article · Mon Jun 04 00:00:00 EDT 2018 · PLoS ONE · OSTI ID:1624556

Korkmaz, Selcuk; Duarte, Jose M.; Prlić, Andreas; +5 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
science and technology
data processing
databases
protein databases
statistical methods
x-ray crystallography

Title: Outlier analyses of the Protein Data Bank archive using a probability-density-ranking approach

Citation Formats

References (51)

Linked Research (1)

Figures / Tables (5)

Similar Records

Related Subjects