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Protein structural diversity analysis

Workflow

Protein structural diversity analysis

Protein X ray structures are extracted from different sources and analyzed. They are aligned by structure and the sequences are renumbered accordingly. The statistical analysis of Ramachandran angles used as alignment free descriptors is performed as well as the selection of the most meaningful descriptors. Most significant angles are projected onto protein structure.

This workflow was developed by Marc Bianciotto at Sanofi.

[Requires: Prime, Vernalis extensions and R extensions (with CircStats library). Optional: Erlwood extensions]

Real WorldPrimeR ExtensionsErlwood ExtensionsVernalis Extensions
Structures from PDB : gathering and preparation Protein structural diversity analysisProtein X ray structures are extracted from different sources and analyzed. They are aligned by structure and the sequences are renumbered accordingly. The statistical analysis ofRamachandran angles used as alignment free descriptors is performed as well as the selection of the most meaningful descriptors. Most significant angles are projected ontoprotein structure.This workflow was developed by Marc Bianciotto at Sanofi.[Requires: Prime, Vernalis extensions and R extensions (with CircStats library). Optional: Erlwood extensions] To install CircStats run:In KNIME installation\plugins\org.knime.ext.r3.bin.win32.x86_3.0.3.0047858\R-Inst\bin\R.exeIn the console opened run:install.packages("CircStats", dependencies = TRUE) Additional structures : preparation Structures preprocessing Structural descriptors generation Structure information in PDB connector node output canbe expanded in the node Report option tab.Filtered outstructures ASL configurableDihedral angle matrix Inspect structures(aligned in Maestro) Most significant angles projected onto protein structureGreen Psi varies significantlyRed PhiBlue Phi and Psi Protein (text search),Xray Protein and atom number range Alignmenttemplate Residue range Extra structuresStructureinformationProtein size filter XML query from a PDB interactive first Post processing:Source = humanTitle contains the protein name[you can add more filters] Protein Post processing:Title contains the protein name[you can add more filters]Filtered outstructuresSplit by chainand filter by size and RMSD filteringRejectedstructures Extra structuresto filter outDistribution of thenumber of atoms Distribution statisticsfor the each angleSplit by chainand filter by size First structuresFirst structures Alignment inspection and possibly other structures to filter out Atom number range Alignment template(execute the node torefresh the list), Alignment RMSD and scrore thresholdSpecific fixVernalis OK 50 first structuresfor the sake oftime and size Table Viewer Renumber sequences Pivoting Report dihedrals Table Viewer Run Maestro Run Maestro MISSING PDB Connector(deprecated) Workflowconfiguration Rule-basedRow Splitter Parsing Delete first andlast residues Workflowconfiguration Table Viewer Table Viewer MISSING PDB Connector (XMLQuery String) (deprecated) Rule-basedRow Splitter Concatenate Workflowconfiguration Rule-basedRow Splitter Table Viewer Protein preparation Angle distributionstatistics Structuralalignment Table Viewer Row Splitter Histogram Chart(JFreeChart) Table Viewer Protein preparation Row Filter Row Filter Run Maestro Read PDB files Workflowconfiguration Workflowconfiguration Title Get PDB Row Filter Structures from PDB : gathering and preparation Protein structural diversity analysisProtein X ray structures are extracted from different sources and analyzed. They are aligned by structure and the sequences are renumbered accordingly. The statistical analysis ofRamachandran angles used as alignment free descriptors is performed as well as the selection of the most meaningful descriptors. Most significant angles are projected ontoprotein structure.This workflow was developed by Marc Bianciotto at Sanofi.[Requires: Prime, Vernalis extensions and R extensions (with CircStats library). Optional: Erlwood extensions] To install CircStats run:In KNIME installation\plugins\org.knime.ext.r3.bin.win32.x86_3.0.3.0047858\R-Inst\bin\R.exeIn the console opened run:install.packages("CircStats", dependencies = TRUE) Additional structures : preparation Structures preprocessing Structural descriptors generation Structure information in PDB connector node output canbe expanded in the node Report option tab.Filtered outstructures ASL configurableDihedral angle matrix Inspect structures(aligned in Maestro) Most significant angles projected onto protein structureGreen Psi varies significantlyRed PhiBlue Phi and Psi Protein (text search),Xray Protein and atom number range Alignmenttemplate Residue range Extra structuresStructureinformationProtein size filter XML query from a PDB interactive first Post processing:Source = humanTitle contains the protein name[you can add more filters] Protein Post processing:Title contains the protein name[you can add more filters]Filtered outstructuresSplit by chainand filter by size and RMSD filteringRejectedstructures Extra structuresto filter outDistribution of thenumber of atoms Distribution statisticsfor the each angleSplit by chainand filter by size First structuresFirst structures Alignment inspection and possibly other structures to filter out Atom number range Alignment template(execute the node torefresh the list), Alignment RMSD and scrore thresholdSpecific fixVernalis OK 50 first structuresfor the sake oftime and size Table Viewer Renumber sequences Pivoting Report dihedrals Table Viewer Run Maestro Run Maestro MISSING PDB Connector(deprecated) Workflowconfiguration Rule-basedRow Splitter Parsing Delete first andlast residues Workflowconfiguration Table Viewer Table Viewer MISSING PDB Connector (XMLQuery String) (deprecated) Rule-basedRow Splitter Concatenate Workflowconfiguration Rule-basedRow Splitter Table Viewer Protein preparation Angle distributionstatistics Structuralalignment Table Viewer Row Splitter Histogram Chart(JFreeChart) Table Viewer Protein preparation Row Filter Row Filter Run Maestro Read PDB files Workflowconfiguration Workflowconfiguration Title Get PDB Row Filter

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Nodes

Protein structural diversity analysis consists of the following 187 nodes(s):

Plugins

Protein structural diversity analysis contains nodes provided by the following 14 plugin(s):