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P01112 EVfold Configuration PLM - Revision history
2024-03-28T10:48:16Z
Revision history for this page on the wiki
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Gerkej: Created page with " Protein := <User Supplied Sequence> In Membrane? := no Coupling Scoring := PLM Compute Structures? := yes Known Structure := 121p Your Job Name := ev_ras_PLM_ca Your Email…"
2013-09-03T16:45:28Z
<p>Created page with " Protein := <User Supplied Sequence> In Membrane? := no Coupling Scoring := PLM Compute Structures? := yes Known Structure := 121p Your Job Name := ev_ras_PLM_ca Your Email…"</p>
<p><b>New page</b></p><div> Protein := <User Supplied Sequence><br />
In Membrane? := no<br />
Coupling Scoring := PLM<br />
Compute Structures? := yes<br />
Known Structure := 121p<br />
Your Job Name := ev_ras_PLM_ca<br />
Your Email := julia.gerke@t-online.de<br />
Domain/Family Name := <br />
(Generate Alignment) Tool For Generating Alignment := hhblits<br />
(Generate Alignment) Start offset in Sequence := 1<br />
(Generate Alignment) End offset in Sequence := <br />
(Generate Alignment) E-Value := -3<br />
(Generate Alignment) Match Column Gap Pct Limit := 50<br />
(Upload Alignment) Alignment File := <br />
(Lookup Alignment) PFAM Accession := PF00071<br />
PFAM Member Selector := RASH_HUMAN<br />
Alignment Member Gap Pct Limit := 70<br />
Constraint Count List := <br />
Structure Variant Count := 5<br />
Contact Map EC Counts := <br />
Residue Contact Proximity Threshold := 5<br />
Residue Contact Proximity Measure := carbon_alpha<br />
Overlay Computed Structure EC Count := <br />
Overlay Computed Structure Variant := <br />
False Positive Plot EC Count := 300<br />
(Secondary Structure) Flanking Upstream Residues := 7<br />
(Secondary Structure) Flanking Downstream Residues := 7<br />
Membrane Helix Topology Override := <br />
Psipred Helix Override := <br />
Psipred Strand Override := <br />
High Conservation Filter Threshold := 100<br />
High Conservation Filter Excludes Gaps? := no<br />
Generate Constraints for Side Chains? := yes<br />
Constraint Minimum Residue Offset Distance := 5<br />
Constraint Rank Weight Function := none<br />
N Over I Weight Numerator := 10<br />
Tanh Weight Global := 20<br />
Tanh Weight Count := 400<br />
Tanh Weight Steepness := 1<br />
Tanh Weight Epsilon := 0.3<br />
NormCDF Weight Mean := 50<br />
NormCDF Weight STDDEV := 25<br />
SS Distance Weight := 5<br />
Allowable Mismatch Offset List := <br />
Gap Count Limit := 3<br />
Identical Dist := 0<br />
Correct Ambiguous Dist := 1<br />
Ambiguous Ambiguous Dist := 2<br />
Other Ambiguous Dist := 4<br />
Mismatch Dist := 34<br />
Unaligned Residue Dist := 10<br />
Internal Gap Open Dist := 3<br />
Peripheral Gap Open Dist := 1<br />
Maximum Distance Cutoff Sequence Length Denominator := 16<br />
Maximum Distance Cutoff Absolute Minimum := 4<br />
Substantial Coverage After Gap := 4<br />
Suggestion Gap Count := 2<br />
MSA Member Weighting Distance Threshold := 0.1<br />
EC Pseudocount Adjustment := 0.5<br />
EC Method To Resolve Ambiguous Residues := suppress_member<br />
Maximum Domain Width := 500<br />
Minimum Domain Width := 30<br />
Minimum Alignment Member Count := 300<br />
Minimum Alignment Match Col Pct := 30<br />
PLM Field Coefficient := 0.01<br />
PLM Coupling Coefficient := 0.01<br />
Add Upstream Flanking Residues For Modeling := 0<br />
Add Downstream Flanking Residues For Modeling := 0<br />
Apply Distance Constraints := yes<br />
Apply Angle Constraints := yes<br />
Alpha Helix Phi Angle Degrees := -57.0<br />
Alpha Helix Phi Angle Range := 7.0<br />
Alpha Helix Phi Energy Constant := 0.5<br />
Alpha Helix Phi Exponent := 2<br />
Alpha Helix Psi Angle Degrees := -47.0<br />
Alpha Helix Psi Angle Range := 7.0<br />
Alpha Helix Psi Energy Constant := 0.5<br />
Alpha Helix Psi Exponent := 2<br />
Beta Sheet Phi Angle Degrees := -127.0<br />
Beta Sheet Phi Angle Range := 20.0<br />
Beta Sheet Phi Energy Constant := 0.5<br />
Beta Sheet Phi Exponent := 2<br />
Beta Sheet Psi Angle Degrees := 122.0<br />
Beta Sheet Psi Angle Range := 20.0<br />
Beta Sheet Psi Energy Constant := 0.5<br />
Beta Sheet Psi Exponent := 2</div>
Gerkej