Computational Aspects of the Protein Target Selection, Protein Production Management and Structure Analysis Pipeline

Structural genomics has established a pipeline for producing Protein structures

Target Selection Semi-automated Structure determination Automated HT Imaging Structure Validation & Deposition Automated HT Crystal Screening + Data Collection Semi-Auto Publication Automated HT Crystallization Automated HT Purification Parallel HT Expression JCSG DB  Integration of custom and commercial instrumentation a HT pipeline.  Data tracking parallels the pipeline collecting 424 parameters from 28 stages.  Graphical interfaces to the experimental stages.  Feedback to the experimental pipeline and Integrated LIMS.

Cell-based and cell-free protein production Pipeline

Crystal Management Crystal Mounting Crystal Alignment Crystal Description Data Collection Structure Determination ? ASAPASAP Data Collection Pipeline

PDB refinement validation annotation publication phasingtracing SDC software development XpleoXsolve Automatically fill in gaps in initial model to provide most complete model for refinement Optimize quality of initial phasing Using parallel processing Refinement management JCSG refinement guidelines Centralized refinement staff Uniform standards and quality criteria Refinement and QC list Six dedicated scientists Peer review/quality control Peer-peer training Close communication Process ensures high quality “deposition ready” structures are output SSTS database Captures all data and information needed for deposition and mmCIF generation Tracks progress of each target Identifies problems and bottlenecks JCSG structure determination CNSS Build consensus model by combining models all initial models

Structure Pipeline Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication

Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication Day 1: Target to Domain selection Structure Pipeline

Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication Day 2: Introduction to PiMS Information management System and use of xtalPiMS and Xtrack MANAGEMENT of Data and EXPERIMENTS Structure Pipeline

Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication Day 3: Ligands Validation of Ligands Structure Pipeline

Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication Day 4: Structure to Function Although structure does not always elucidate function, in many instances the atomic structure readily provides insight into the function of a protein whose function was previously unknown. Structure Pipeline

Genomic Based Target Selection Crystallomics Data Collection Structure Determination Isolation, Expression, Purification,Crystallization PDB Deposition & Release Functional Annotation Publication Day 5: Structure comparisons Structure Pipeline