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| Target PDB Monitor (TPM) |
What is TPMHow to use TPMAcknowledgementAbout TPMTarget PDB Monitor (TPM) displays the updated PDB coverage for JCSG targets. After a target enters high-throughput pipeline of structure determination, we update its current state of PDB coverage and check if it keeps as a potential new fold. The PDB coverages of targets are calculated based on PDB biological macromolecular structure database and JCSG tracking and annotation database.Structure Resources The set of PDB structures includes PDB released structures and JCSG structures that have been solved and go for PDB deposition and release. Methodology The sequence alignmnet program BLAST from NCBI BLAST is used to search homologous sequences between targets and PDB sequences with Expect (Evalue cut-off) at 0.001 and at least 20 of aligned residues within target sequence. For a target, we scan all of PDB unique sequences to check if this target is covered by PDB structures. If there is at least one PDB sequence that satisfies the criteria of PDB coverage (Identity>=85% or Identity>=30% plus Covergage>=50%), we say this target is covered by PDB structures. Structural Coverage Classification Based on the similarity of Blast search, we classify the structural coverages of targets into four groups. A simple color system is used to represent this classification system (red:In-PDB, yellow:HIGH, green:LOW, no: NO-HIT). - IN-PDB: Identity >= 85% and Residues >= 25 - High-Similarity: Identity >= 30% and Coverage >= 50% - Low-Similarity: Evalue <= 0.001 and Residues >= 25 - NO-HIT: no hit coverage (%) = (number of aligned residues within targeted subsequence)/(length of targeted subsequence) * 100% How To Use TPMA TPM user interface is provided to retrieve targets for PDB coverage. There are several ways to search targets. The operators AND (two words separated by whitespace) and OR (two words separated by comma) are supported in fields of keyword search.- Using Target-ID - Using Protein Accession - Using Filter - Uploading Target List You can upload a tab-delimited text file of target list. You need to specify the TID source as the column of TID and the TID type (internal target ID or protein accession). If the target filter is enabled, it will be used for the target list. Target Filter - Target Options Work Status: active or stop Target Stage: the pipeline stage Species Set: species or kingdom - Structure Coverage Classification: In-PDB (red), High-similarity (yellow), Low-similarity (green), No-hit () Resource: PDB, JCSG AcknowledgementThe PDB sequences and structure data are downloaded from PDB FTP server.Protein target information is from JCSG target tracking and annotation system. Protein sequence information contains the annotations from both of JCSG and SWISS-PROT databases. The SWISS-PROT annotation page is accessed from SWALL database. If you have any comment or question, please contact Jie Ouyang at Joint Ceneter for Structural Genomics (JCSG) Bioinformatics Core. |