Ras DI Score Configuration

Protein := P01112 In Membrane? := no Coupling Scoring := DI Compute Structures? := yes Known Structure := 5p21 Your Job Name := ras_h Your Email := alexander.betz@gmail.com Domain/Family Name := (Generate Alignment) Tool For Generating Alignment := hhblits (Generate Alignment) Start offset in Sequence := 1 (Generate Alignment) End offset in Sequence := (Generate Alignment) E-Value := -3 (Generate Alignment) Match Column Gap Pct Limit := 50 (Upload Alignment) Alignment File := (Lookup Alignment) PFAM Accession := PF00071 PFAM Member Selector := RASH_HUMAN Alignment Member Gap Pct Limit := 70 Constraint Count List := 76 123 189 Structure Variant Count := 5 Contact Map EC Counts := Residue Contact Proximity Threshold := 5 Residue Contact Proximity Measure := nearest_atom Overlay Computed Structure EC Count := Overlay Computed Structure Variant := False Positive Plot EC Count := 300 (Secondary Structure) Flanking Upstream Residues := 7 (Secondary Structure) Flanking Downstream Residues := 7 Membrane Helix Topology Override := Psipred Helix Override := Psipred Strand Override := High Conservation Filter Threshold := 100 High Conservation Filter Excludes Gaps? := no Generate Constraints for Side Chains? := yes Constraint Minimum Residue Offset Distance := 5 Constraint Rank Weight Function := none N Over I Weight Numerator := 10 Tanh Weight Global := 20 Tanh Weight Count := 400 Tanh Weight Steepness := 1 Tanh Weight Epsilon := 0.3 NormCDF Weight Mean := 50 NormCDF Weight STDDEV := 25 SS Distance Weight := 5 Allowable Mismatch Offset List := Gap Count Limit := 3 Identical Dist := 0 Correct Ambiguous Dist := 1 Ambiguous Ambiguous Dist := 2 Other Ambiguous Dist := 4 Mismatch Dist := 34 Unaligned Residue Dist := 10 Internal Gap Open Dist := 3 Peripheral Gap Open Dist := 1 Maximum Distance Cutoff Sequence Length Denominator := 16 Maximum Distance Cutoff Absolute Minimum := 4 Substantial Coverage After Gap := 4 Suggestion Gap Count := 2 MSA Member Weighting Distance Threshold := 0.1 EC Pseudocount Adjustment := 0.5 EC Method To Resolve Ambiguous Residues := suppress_member Maximum Domain Width := 500 Minimum Domain Width := 30 Minimum Alignment Member Count := 300 Minimum Alignment Match Col Pct := 30 PLM Field Coefficient := 0.01 PLM Coupling Coefficient := 0.01 Add Upstream Flanking Residues For Modeling := 0 Add Downstream Flanking Residues For Modeling := 0 Apply Distance Constraints := yes Apply Angle Constraints := yes Alpha Helix Phi Angle Degrees := -57.0 Alpha Helix Phi Angle Range := 7.0 Alpha Helix Phi Energy Constant := 0.5 Alpha Helix Phi Exponent := 2 Alpha Helix Psi Angle Degrees := -47.0 Alpha Helix Psi Angle Range := 7.0 Alpha Helix Psi Energy Constant := 0.5 Alpha Helix Psi Exponent := 2 Beta Sheet Phi Angle Degrees := -127.0 Beta Sheet Phi Angle Range := 20.0 Beta Sheet Phi Energy Constant := 0.5 Beta Sheet Phi Exponent := 2 Beta Sheet Psi Angle Degrees := 122.0 Beta Sheet Psi Angle Range := 20.0 Beta Sheet Psi Energy Constant := 0.5 Beta Sheet Psi Exponent := 2