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Protein Data Integration and Interrogation header

Day 1 | Day 2Download Brochure 

Conference Short Courses*View Details 

Sunday, January 9 - 3:00 pm - 6:00 pm

  • Protein Crystallization - Delineating Protein Structure
  • DoE and QbD: Tools for Optimizing the Bioprocess

Thursday, January 13 - 6:30 pm - 9:00 pm

  • Rational Design of Protein Solutions



1:30 pm Conference Registration

2:00 BuzZ Session ABuzz 

2:45 Refreshment Break, Exhibit Viewing and Poster Awards

3:30 BuzZ Session BBuzz 

4:15 End of Day

4:30 Dinner Short Courses 


7:00 am Conference Registration

7:30 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee



8:15 Chairperson’s Opening Remarks

Keynote Speaker:

8:20 Identifying and Understanding Proteomes: HTP Proteomics Meets Extra-Scale Computing and Extremely Large Databases

Eugene KolkerEugene Kolker, Ph.D., Chief Data Officer, Center for Developmental Therapeutics, Children’s Hospital Seattle

Modern discovery and targeted proteomics enable us to detect thousands of expressed peptides and proteins per single experiment.  For the first time, these high-throughput approaches allow us to formulate the question: “Can we identify and understand proteomes?” This presentation will address this question by reviewing capabilities and limitations of modern proteomics, focusing on its data analysis aspects and the biomedical implications.

Click here to download podcast - Topic: The New Paradigm of Data Intensive/Data Rich Protein Informatics

9:00 Dynameomics

Valerie Daggett, Ph.D., Professor, Bioengineering, University of Washington

The goal of Dynameomics is to perform atomistic molecular dynamics simulations of representative proteins from all known folds in explicit water. We began by creating a Consensus Domain Dictionary---a list of metafolds for systematic coverage of fold space, of which there are 807 ‘simulatable’, autonomous protein domains. The simulations are now complete and mining of this >100 TB dataset is underway.

9:30 Data Integration at the RCSB Protein Data Bank

Andreas Prlic, Ph.D., Senior Scientist, RCSB PDB Protein Data Bank, University of California, San Diego

The RCSB PDB web site is a primary resource for accessing atomic level resolution data for experimentally-determined structures of proteins, nucleic acids, and complex assemblies. Over the last two years we have introduced a number of new tools on the web site that allow for a variety of new analyses. Here we will discuss these tools as well as various data integration strategies and interfaces that are available to the public.

10:00 Coffee Break, Exhibit and Poster Viewing

10:45 Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database

Natalie Castellana, Ph.D. Candidate, Computer Science and Engineering, University of California, San Diego

Standard mass spectrometry-based tools for sequencing proteins fail to deliver when the protein of interest is absent from the database or present in a mutated form. Template proteogenomics uses the database merely as a “template” and combines techniques from database search and de novo sequencing to overcome the problem of incorrect or incomplete databases.

11:15 Using Bioinformatics to Characterize Protein Mutations in Disease and their Molecular Effects

Sean Mooney, Ph.D., Associate Professor & Director, Bioinformatics, Buck Institute for Age Research

There are now hundreds of thousands of known genetic variants in genes that likely alter the sequence of their protein product.  Development of new tools that can identify variants in proteins that disrupt biochemical function or cause disease remains an important endeavor.  The MutDB suite of tools enables the identification of protein variants that disrupt known or predicted protein functions such as post translational modifications, catalysis, protein interactions or protein structure.    The resulting analysis of large databases of protein mutants reveals hypotheses about the underlying causes of both somatic and inherited genetic diseases.

11:45 Exploration of Uncharted Regions of the Protein Universe

Adam Godzik, Ph.D., Program Director & Professor, Bioinformatics and Systems Biology, Sanford Burnham Institute for Research

12:15 pm Close of Morning Session

12:30 Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own


Linking Structure to Function

2:00 Chairperson’s Remarks

2:05 Prediction and Recognition of Protein Functions from Sequences by Measuring Features of Sequence Fragments: Application to G Protein Coupled Receptors

Huixiao Hong, Ph.D., Senior Computational Scientist, Center for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, U.S. F.D.A.

G protein coupled receptors (GPCRs) are the targets of a large number of therapeutic agents, about 50% of the drugs on the market. Therefore, there is a considerable interest in developing methods that can effectively predict and recognize the function of a GPCR from its primary amino acid sequence. This presentation will demonstrate a sequence alignment free method for accurately prediction and recognition of subfamilies of GPCRs from their sequences.

2:35 Application of Protein Structure Prediction in Biomedicine

Dong Xu, Ph.D., Professor, Computer Science, University of Missouri, Columbia

The three-dimensional structure of a protein often provides a basis for understanding its function and drug development. Protein structure prediction is becoming an effective way for studying a broad range of proteins. Towards achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. We have applied protein structure prediction in studying therapeutics targets, such as cancer-related proteins.

3:05 A Comprehensive Array of Mass Spectrometric Assays for the Systematic Measurement of the Transcription Factor Proteome

Hamid Mirzaei, Ph.D., Research Scientist, Institute for Systems Biology

Here we introduce a comprehensive set of Selected Reaction Monitoring (SRM) assays for the sensitive, quantitative, and reproducible measurement of four hundred and sixty four proteins with known or suspected roles in transcriptional regulation of RNA polymerase II (Pol II) transcribed genes in yeast. By deploying the assay to systematically identify DNA binding transcriptional regulators that interact with the unusually large FLO11 promoter in cell extracts, we identified 65 regulators that bound specifically to distinct regions along ~2 kb of the regulatory sequence.  We further validated the utility of the approach by demonstrating that a number of SRM identified factors either localize to the FLO11 promoter in vivo and/or are required for proper FLO11 expression.  These results demonstrate the power of the SRM-based approach to systematically decipher the composition of transcriptional regulatory complexes.

3:35 Sponsored Presentation (Opportunity Available)

3:50 Networking Refreshment Break

4:30 Benefits from a Workflow Integrating Different Methods on Protein Structure Analysis

Zoe Lacroix, Ph.D., Associate Professor, Research; Head, Scientific Data Management Lab, Electrical Engineering, Arizona State University; Associate Investigator, Cancer and Cell Biology, TGen

The analysis of the structure of proteins often provides key information on their functions. A very large number of methods, applications, and databases were developed to analyze proteins structures. Although each resource provides a critical piece of information regarding protein structure and its impact on the function, the integration of various viewpoints into an automated workflow may provide added value to the scientist. We illustrate this approach with the Structural Prediction for pRotein fOlding UTility (SPROUT) workflow that automatically runs methods that correlate static and dynamic properties of protein structure. They include the prediction of special positions and stability under the effect of a point mutation. It is a unique resource to visualize characteristics of protein folding and analyze the effect of point mutations on protein structure and to provide experimentalists with the information needed to avoid mutations at positions suspected to be critical for the folding nucleus.

5:00 Interactive Panel Discussion with Afternoon Speakers

5:30 Reception in the Exhibit Hall

6:30 Close of Day


Day 1 | Day 2Download Brochure 

Links to Companion Meetings

Pipeline 1

Protein Purification & Recovery 

Protein Computational Tools