diff --git a/TeachingMaterials/tertiary_structure_pred.md b/TeachingMaterials/tertiary_structure_pred.md index 665856f05b8ece0f67e34757b1ac792420941ba4..261952b08fbcc243a2c586afb8343846e4aa4b32 100644 --- a/TeachingMaterials/tertiary_structure_pred.md +++ b/TeachingMaterials/tertiary_structure_pred.md @@ -1,49 +1,6 @@ ## Computational structure prediction of proteins -### Secondary structure prediction - -**Tool used in this course**: [JPred](http://www.compbio.dundee.ac.uk/jpred/) - -JPred is a protein secondary structure prediction tool. It also makes predictions on Solvent Accessibility and Coiled-coil regions. It first searches the query sequence in PDB to identify homologous structure, if not available it predicts structure using Jnet algorithm, which uses neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences. - -- Example using their default example protein -- There is a limit of sequence length to 800 aa, however the sequence can be split and used at batch mode - -- Run Jpred (click the `Make Prediction`) -- It immediately opens a list of PDB tht matches the query - - One can either explore those proteins individually using the PDB linkout - - Or, submit the job to identify a more accurate secondary structure assignment. - - the result page shows the predicted components of secondary structures - -Default query using default parameters: -```` -MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC -```` -[result page](http://www.compbio.dundee.ac.uk/jpred4/results/jp_1Xqh2hJ/jp_1Xqh2hJ.results.html) - - -Long sequence of Toll-like receptor 4 split into multiple fragments (advanced search): - -```` ->sp|O00206|TLR4_HUMAN Toll-like receptor 4 OS=Homo sapiens GN=TLR4 PE=1 SV=2 -MMSASRLAGTLIPAMAFLSCVRPESWEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLD -LSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALG -AFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHL -DLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSL -NVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDI -IDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTS -NKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLG -LEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAG -NSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPY -KCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQL -LVEVERMECATPSDKQGMPVLSLNITCQMNKTIIGVSVLSVLVVSVVAVLVYKFYFHLML -LAGCIKYGRGENIYDAFVIYSSQDEDWVRNELVKNLEEGVPPFQLCLHYRDFIPGVAIAA -NIIHEGFHKSRKVIVVVSQHFIQSRWCIFEYEIAQTWQFLSSRAGIIFIVLQKVEKTLLR -QQVELYRLLSRNTYLEWEDSVLGRHIFWRRLRKALLDGKSWNPEGTVGTGCNWQEATSI -```` -[Result page]() - -### Tertiary structure prediction +### Secondary and tertiary structure prediction **Tool used in this course**: [Phyre2](http://www.sbg.bio.ic.ac.uk/phyre2/index.cgi) @@ -179,6 +136,60 @@ Intensive mode often creates excellent full length models that cannot be achieve Example: Human Toll like receptor 4 +```` +>sp|O00206|TLR4_HUMAN Toll-like receptor 4 OS=Homo sapiens GN=TLR4 PE=1 SV=2 +MMSASRLAGTLIPAMAFLSCVRPESWEPCVEVVPNITYQCMELNFYKIPDNLPFSTKNLD +LSFNPLRHLGSYSFFSFPELQVLDLSRCEIQTIEDGAYQSLSHLSTLILTGNPIQSLALG +AFSGLSSLQKLVAVETNLASLENFPIGHLKTLKELNVAHNLIQSFKLPEYFSNLTNLEHL +DLSSNKIQSIYCTDLRVLHQMPLLNLSLDLSLNPMNFIQPGAFKEIRLHKLTLRNNFDSL +NVMKTCIQGLAGLEVHRLVLGEFRNEGNLEKFDKSALEGLCNLTIEEFRLAYLDYYLDDI +IDLFNCLTNVSSFSLVSVTIERVKDFSYNFGWQHLELVNCKFGQFPTLKLKSLKRLTFTS +NKGGNAFSEVDLPSLEFLDLSRNGLSFKGCCSQSDFGTTSLKYLDLSFNGVITMSSNFLG +LEQLEHLDFQHSNLKQMSEFSVFLSLRNLIYLDISHTHTRVAFNGIFNGLSSLEVLKMAG +NSFQENFLPDIFTELRNLTFLDLSQCQLEQLSPTAFNSLSSLQVLNMSHNNFFSLDTFPY +KCLNSLQVLDYSLNHIMTSKKQELQHFPSSLAFLNLTQNDFACTCEHQSFLQWIKDQRQL +LVEVERMECATPSDKQGMPVLSLNITCQMNKTIIGVSVLSVLVVSVVAVLVYKFYFHLML +LAGCIKYGRGENIYDAFVIYSSQDEDWVRNELVKNLEEGVPPFQLCLHYRDFIPGVAIAA +NIIHEGFHKSRKVIVVVSQHFIQSRWCIFEYEIAQTWQFLSSRAGIIFIVLQKVEKTLLR +QQVELYRLLSRNTYLEWEDSVLGRHIFWRRLRKALLDGKSWNPEGTVGTGCNWQEATSI +```` + +### Secondary structure prediction + +[JPred](http://www.compbio.dundee.ac.uk/jpred/) + +JPred is a protein secondary structure prediction tool. It also makes predictions on Solvent Accessibility and Coiled-coil regions. It first searches the query sequence in PDB to identify homologous structure, if not available it predicts structure using Jnet algorithm, which uses neural network secondary structure prediction algorithm with different types of multiple sequence alignment profiles derived from the same sequences. + +- Example using their default example protein +- There is a limit of sequence length to 800 aa, however the sequence can be split and used at batch mode + +- Run Jpred (click the `Make Prediction`) +- It immediately opens a list of PDB tht matches the query + - One can either explore those proteins individually using the PDB linkout + - Or, submit the job to identify a more accurate secondary structure assignment. + - the result page shows the predicted components of secondary structures + +Default query using default parameters: +```` +MQVWPIEGIKKFETLSYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHRSPGYYDGRYWTMWKLPMFGCTDATQVLKELEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGC +```` +[result page](http://www.compbio.dundee.ac.uk/jpred4/results/jp_1Xqh2hJ/jp_1Xqh2hJ.results.html) + +Long sequence of Toll-like receptor 4 split into multiple fragments (advanced search): + +**Result:** + +An archive with all the results can be downloaded from the following link: +http://www.compbio.dundee.ac.uk/jpred4/results/jp_batch_1478672019__YtqOUQg/jp_batch_1478672019__ALL_JOBS_ARCHIVE.tar.gz + +Results for individual queries are available from the links below: +SUCCESS TLR4_HUMAN3 Link to results: http://www.compbio.dundee.ac.uk/jpred4/results/jp_batch_1478672019__mUJGlod +SUCCESS TLR4_HUMAN1 Link to results: http://www.compbio.dundee.ac.uk/jpred4/results/jp_batch_1478672019__6tFSD1_ +SUCCESS TLR4_HUMAN2 Link to results: http://www.compbio.dundee.ac.uk/jpred4/results/jp_batch_1478672019__YtqOUQg + + +### Secondary structure prediction + 1. [I-TASSER](http://zhanglab.ccmb.med.umich.edu/I-TASSER/) Requires registration and submission permission