Interview with NCBI Staff Scientist Carol Scott


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Presentation by Katie Rapp for LBSC 690 Information Technology course at the University of Maryland, College Park

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Interview with NCBI Staff Scientist Carol Scott

  1. 1. Interview withCarol ScottPhD, BioengineeringBioinformatics Scientist and CuratorConserved Domain DatabaseA project of the U.S. National Library of Medicine at theNational Institutes of Health,National Center for Biotechnology InformationKatie RappLBSC 690March 1, 2011
  2. 2. Protein is Everything! Every living thing is made up of unique, identifiable proteins Examples: human hemoglobin, insulin, proteins infungus, bacteria, plants Proteins are made of different combinations of amino acids 20 naturally-occurring amino acids; they are like beads in a necklaceand their order determines the type of protein Proteins do the work inside cells Examples: Hemoglobin carries oxygen in the blood, insulin regulatesglucose metabolism
  3. 3. Problems with Proteins Proteins do the work inside cells, so when there areproblems, such as diseases, they are often caused by adefective protein Example: Sickle Cell Anemia (one change in one amino acid inhemoglobin and you go from healthy to ill) Medical researchers study proteins at the molecular level inorder to find cures to diseases
  4. 4. Conserved Domains –Motivation behind thedatabase The amino acid chains that make up proteins are coiled andfolded. Repeated blocks of coiled and folded amino acids arereferred to as “conserved domains.” Conserved domains have specific functions and 3-dimensional shapes It is useful for researchers to be able to compare relatedconserved domains in different proteins, but there was noreal way to do this in the past
  5. 5. Conserved Domain Database -Development This database was developed to meet the needs ofresearchers Project begun in 2001; Carol Scott has worked on it since2002 Worked with software developers to produce highly-interactive database
  6. 6. Conserved Domain DatabaseCurators Carol Scott and other curators create the data in thedatabase from lists of amino acid sequences found in otherdatabases They take amino acid sequences from millions of proteinsand link them based on structural and functional similarities They work with programmers to create the interface andvisual output of the database Curators also find and provide links to information about eachprotein, journal articles and other resources, related proteins
  7. 7. Conserved Domain Database -Challenges Not all amino acid sequence information is reliable – curatorsmust pick and choose where they get the basic data to putinto their database The process of creating the comparisons in the CDD is verycomplex and time-consuming Software exists to help find these comparisons, but muchwork must be done manually based on knowledge of thechemical attributes of the amino acids The project is currently facing budgetary cutbacks whichaffect staffing and perhaps the future of the database
  8. 8. Conserved Domain DatabaseResults Enables scientists to search on specific amino acid chains ofinterest to them Genetic studies, mutation studies, studying size, shape andfunction of proteins They can find and compare similar chemical alignments indifferent proteins These alignments can provide insight into the functions ofdifferent parts of protein molecules
  9. 9. Conserved Domain DatabaseOutput – 3-Dimensional Structures
  10. 10. Conserved Domain DatabaseOutput - Superfamilies
  11. 11. Conserved Domain DatabaseUsers – Who Are They? The database is freely accessible to anyone over the internet It is used frequently by researchers around the world Users include anyone studying proteins – everyone from highschool and college students up to very high level researchersat NIH, pharmaceutical companies, genetic researchers,bioengineering firms, etc. Can be used to spur further research into areas wheredefects in proteins could be repaired using geneticengineering
  12. 12. Conserved Domain Database Questions?