Chenghua Shao
Assistant Research Professor
RCSB Protein Data Bank
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Road
Piscataway, NJ 08854-8076

Tel: 848-445-4968
Fax: 732-445-4320
Email Address: chenghua@rcsb.rutgers.edu
  Education
Highest Earned Degree
Ph.D., Boston University, Biophysics, 2007
Other Earned Degrees
M.S., Rutgers University, New Brunswick, NJ, Statistics, 2014
M.S., Peking University, (Beijing, China), Biophysics, 2001
B.S., Peking University, (Beijing, China), Physics, 1997
  Research Interests
Professional Identification
Data Curation Specialist
Crystallographer
Structural Biologist
Biophysicist
Statistician
Biologist
Description of Research and Scholarly or Creative Objectives
My research focuses on data curation and analysis at the Protein Data Bank (PDB). PDB provides free public deposition and distribution services on macromolecular 3D structures determined by experimental methods. As PDB data are broadly used in biomedical research, we develop system and methods for data process and validation, to ensure data accuracy and archive consistency. With combination usage of structure biology, biochemistry, and statistics, we also perform data analysis to find trends, patterns, outliers, and the underlying biological explanation, which enables better data collection and curation to improve data quality. In addition, I supervise curation on the structural and chemical data of ligands and drugs to ensure the PDB representation of such compounds is up to the standard for their usage in biomedical research.
  Publications
Articles in Refereed Journals
2017: Shao C, Yang H, Westbrook JD, Young JY, Zardecki C, Burley SK. "Multivariate Analyses of Quality Metrics for Crystal Structures in the PDB Archive". Structure. 2017;25(3):458-468.
2017: Young JY, Westbrook JD, Feng Z, Sala R, Peisach E, Oldfield TJ, Sen S, Gutmanas A, Armstrong DR, Berrisford JM, Chen L, Chen M, Di Costanzo L, Dimitropoulos D, Gao G, Ghosh S, Gore S, Guranovic V, Hendrickx PM, Hudson BP, Igarashi R, Ikegawa Y, Kobayashi N, Lawson CL, Liang Y, Mading S, Mak L, Mir MS, Mukhopadhyay A, Patwardhan A, Persikova I, Rinaldi L, Sanz-Garcia E, Sekharan MR, Shao C, Swaminathan GJ, Tan L, Ulrich EL, van Ginkel G, Yamashita R, Yang H, Zhuravleva MA, Quesada M, Kleywegt GJ, Berman HM, Markley JL, Nakamura H, Velankar S, Burley SK. "OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive." Structure. 2017;25(3):536-545.
2017: Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao YP, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK. "The RCSB protein data bank: integrative view of protein, gene and 3D structural information". Nucleic Acids Res. 2017;45(D1):D271-D281.
2016: Adams PD, Aertgeerts K, Bauer C, Bell JA, Berman HM, Bhat TN, Blaney JM, Bolton E, Bricogne G, Brown D, Burley SK, Case DA, Clark KL, Darden T, Emsley P, Feher VA, Feng Z, Groom CR, Harris SF, Hendle J, Holder T, Joachimiak A, Kleywegt GJ, Krojer T, Marcotrigiano J, Mark AE, Markley JL, Miller M, Minor W, Montelione GT, Murshudov G, Nakagawa A, Nakamura H, Nicholls A, Nicklaus M, Nolte RT, Padyana AK, Peishoff CE, Pieniazek S, Read RJ, Shao C, Sheriff S, Smart O, Soisson S, Spurlino J, Stouch T, Svobodova R, Tempel W, Terwilliger TC, Tronrud D, Velankar S, Ward SC, Warren GL, Westbrook JD, Williams P, Yang H, Young J. "Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop". Structure. 2016;24(4):502-508.
2015: Westbrook JD, Shao C, Feng Z, Zhuravleva M, Velankar S, Young J. "The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank". Bioinformatics. 2015;31(8):1274-8.
2014: Sen S, Young J, Berrisford JM, Chen M, Conroy MJ, Dutta S, Di Costanzo L, Gao G, Ghosh S, Hudson BP, Igarashi R, Kengaku Y, Liang Y, Peisach E, Persikova I, Mukhopadhyay A, Narayanan BC, Sahni G, Sato J, Sekharan M, Shao C, Tan L, Zhuravleva MA. "Small molecule annotation for the Protein Data Bank". Database (Oxford). 2014;2014:bau116.
2014: Dutta S, Dimitropoulos D, Feng Z, Persikova I, Sen S, Shao C, Westbrook J, Young J, Zhuravleva MA, Kleywegt GJ, Berman HM. "Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank". Biopolymers. 2014;101(6):659-68.
2013: Young JY, Feng Z, Dimitropoulos D, Sala R, Westbrook J, Zhuravleva M, Shao C, Quesada M, Peisach E, Berman HM. "Chemical annotation of small and peptide-like molecules at the Protein Data Bank". Database (Oxford). 2013;2013:bat079
2013: Berman HM, Coimbatore Narayanan B, Di Costanzo L, Dutta S, Ghosh S, Hudson BP, Lawson CL, Peisach E, Prlić A, Rose PW, Shao C, Yang H, Young J, Zardecki C. "Trendspotting in the Protein Data Bank". FEBS Lett. 2013;587(8):1036-45.
2009: Shi X, Shao C, Zhang X, Zambonelli C, Redfield AG, Head JF, Seaton BA, Roberts MF. "Modulation of Bacillus thuringiensis phosphatidylinositol-specific phospholipase C activity by mutations in the putative dimerization interface". J Biol Chem. 2009;284(23):15607-18.
2008: Shao C, Novakovic VA, Head JF, Seaton BA, Gilbert GE. "Crystal structure of lactadherin C2 domain at 1.7A resolution with mutational and computational analyses of its membrane-binding motif". J Biol Chem. 2008;283(11):7230-41.
2007: Shao C, Shi X, Wehbi H, Zambonelli C, Head JF, Seaton BA, Roberts MF. "Dimer structure of an interfacially impaired phosphatidylinositol-specific phospholipase C". J Biol Chem. 2007;282(12):9228-35.
2006: Shao C, Zhang F, Kemp MM, Linhardt RJ, Waisman DM, Head JF, Seaton BA. "Crystallographic analysis of calcium-dependent heparin binding to annexin A2". J Biol Chem. 2006;281(42):31689-95.
2002: Shao C, Zhu JP, Cheng Y, Wang JF, Gong WB, Xu Q, Chen ZL, Lu GY. “Sequence-specific Assignments of Proton NMR Resonance Peaks and Analysis of Secondary Structural Elements of LC1, a Novel Antibacterial Polypeptide”. Acta Biochim. Biophys. Sin. 2002;34(4):457-62.
2001: Shao C, Zhou ZH, Lu G. “Three-dimensional Structural of the Inner Core of Rice Dwarf Virus”. Sci. China C Life Sci. 2001;44(2):192-198.