How SWISS-MODEL works
| Search for suitable templates | Check sequence identity with target | Create ProModII jobs | Generate models with ProModII | Energy minimisation with Gromos96 | ||
| Step | Program/Method | Database | Action |
| 1 | BLASTP2 | ExNRL-3D | Will find all similarities of target sequence with sequences of known structure. |
| 2 | SIM | - | Will select all templates with sequence identities above 25% and projected model size larger than 20 residues. Furthermore, this step will detect domains which can be modelled based on unrelated templates |
| 3 | - | - | Generate ProModII input files |
| 4 | ProModII | ExPDB | Generate all models |
| 5 | Gromos96 | - | Energy minimsation of all models |
Obtained: Two models
One for the DEATH domain (intracellular) and one for the ligand domain (extracellular)
| 1 | AlignMaster output ============================================================ Length of target sequence: 335 residues Searching sequences of known 3D structures Found 11DDF.pdb with P(N)=3.4e-59 Found 11CDF.pdb with P(N)=1.6e-13 Found 11EXT.pdb with P(N)=1.5e-09 Found 21EXT.pdb with P(N)=1.5e-09 Found 21NCF.pdb with P(N)=1.5e-09 Found 21TNR.pdb with P(N)=1.5e-09 Found 11NCF.pdb with P(N)=1.5e-09 Extracting template sequences |
| 2 | Running pair-wise alignments with target sequence Sequence identity of templates with target: 11DDF.pdb: 100 % identity 11CDF.pdb: 37.33 % identity 11EXT.pdb: 26.4 % identity 21EXT.pdb: 26.4 % identity 21NCF.pdb: 26.4 % identity 21TNR.pdb: 26.4 % identity 11NCF.pdb: 26.4 % identity Looking for template groups Global alignment overview: Taget Sequence: |=======================================================| 11DDF.pdb | ------------------- 11CDF.pdb | --------------- 11EXT.pdb | ------------- 21EXT.pdb | ------------- 21NCF.pdb | ------------- 21TNR.pdb | ------------- 11NCF.pdb | ------------- |
| 3 | AlignMaster found 2 regions to model separately: 1: Using template(s) 11DDF.pdb 2: Using template(s) 11CDF.pdb 11EXT.pdb 11NCF.pdb 21EXT.pdb 21NCF.pdb 21TNR.pdb Creating Batch files for ProMod (if any): Exiting AlignMaster |
| 4 | ProModII trace log for Batch.1 ============================================================ SPDBV: Loading Template SPDBV: Loading Raw Sequence SPDBV: Generating Structural Alignment SPDBV: Aligning Raw Sequence SPDBV: Refining Raw Sequence Alignment SPDBV: Averaging Sidechains SPDBV: Adding Missing Sidechains SPDBV: Dumping Sequence Alignment SPDBV: Dumping Preliminary Model SPDBV: Done. ProModII trace log for Batch.2 ============================================================ SPDBV: Loading Template SPDBV: Loading Template SPDBV: Loading Template SPDBV: Loading Template SPDBV: 21NCF : some amino acids sidechain atoms are missing --> reconstructing concerned sidechains. SPDBV: Loading Template SPDBV: 21TNR : some amino acids sidechain atoms are missing --> reconstructing concerned sidechains. SPDBV: Loading Raw Sequence SPDBV: Iterative Template Fitting SPDBV: Iterative Template Fitting SPDBV: Iterative Template Fitting SPDBV: Iterative Template Fitting SPDBV: Generating Structural Alignment SPDBV: Aligning Raw Sequence SPDBV: Refining Raw Sequence Alignment SPDBV: Weighting Backbones SPDBV: Averaging Sidechains SPDBV: Adding Missing Sidechains SPDBV: Trying Ligating from residue 137 to 139 SPDBV: Trying Ligating from residue 137 to 140 SPDBV: Number of Ligations found: (2) SPDBV: Trying Ligating from residue 153 to 155 SPDBV: Trying Ligating from residue 153 to 156 SPDBV: Number of Ligations found: (1) SPDBV: Trying Ligating from residue 159 to 161 SPDBV: Trying Ligating from residue 158 to 161 SPDBV: Number of Ligations found: (1) SPDBV: Building CSP loop from residue 88 to 90 SPDBV: Building CSP loop from residue 87 to 90 SPDBV: Building CSP loop from residue 87 to 91 SPDBV: Dumping Sequence Alignment SPDBV: Dumping Preliminary Model SPDBV: Done. |
| 5 | Gromos96 trace log for Batch.1 ============================================================ Now running PROCS1 on file batch-procs0.dat ... Done. Now running PROCS2 on file batch-procs1.dat ... Done. Now running PROGMT on file batch-procs2.dat ... Done. Now running PROGCH on file batch-procs2.dat ... Done. Now running PROMD on file batch-progch.dat ... Done. Now running PROMD on file batch-promd0.dat ... Done. Detection of SS-Bonds within batch ... Gromos96 trace log for Batch.2 ============================================================ Now running PROCS1 on file batch-procs0.dat ... Done. Now running PROCS2 on file batch-procs1.dat ... Done. Now running PROGMT on file batch-procs2.dat ... Done. Now running PROGCH on file batch-procs2.dat ... Done. Now running PROMD on file batch-progch.dat ... Done. Now running PROMD on file batch-promd0.dat ... Done. Detection of SS-Bonds within batch ... >SS-Bonds detection: #1: 91 <-> 105 >SS-Bonds detection: #2: 66 <-> 81 >SS-Bonds detection: #3: 69 <-> 89 >SS-Bonds detection: #4: 25 <-> 44 >SS-Bonds detection: #5: 47 <-> 63 |
| HEADER | Header line. |
| TITLE | User-supplied title or SWISS-PROT entry DE line. |
| EXPDTA | Always THEORETICAL MODEL. |
| JRNL | Please site these references in case of publication |
| REMARK 3 | Brief description of modelling method and minimisation parameters. |
| REMARK 5 | Description of the templates used to build the model. |
| REMARK 999 | Description of model sequence with respect to corresponding SWISS-PROT entry. |
| SEQALI | Sequence alignment generated by ProModII. |
HEADER SWISS-MODEL (Automated Protein Modelling Server) ACCODE P25445_C00002 DATE 19-FEB-1998 TITLE FASL RECEPTOR PRECURSOR (APOPTOSIS-MEDIATING SURFACE ANTIGEN FAS) TITLE 2 (APO-1 ANTIGEN) (CD95 ANTIGEN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: FASL RECEPTOR PRECURSOR (APOPTOSIS-MEDIATING SURFACE ANTIGEN FAS); COMPND 3 GENE NAME: APT1 OR FAS; SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS ; SOURCE 3 ORGANISM_COMMON: HUMAN; KEYWDS APOPTOSIS; RECEPTOR; GLYCOPROTEIN; TRANSMEMBRANE; REPEAT; SIGNAL. EXPDTA THEORETICAL MODEL AUTHOR ProMod (SEE REFERENCE IN JRNL Records) JRNL 1 AUTH M.C.PEITSCH JRNL 1 TITL PROTEIN MODELING BY EMAIL JRNL 1 REF BIO/TECHNOLOGY V. 13 658 1995 JRNL 1 REFN ISSN 0733-222X JRNL 2 AUTH M.C.PEITSCH JRNL 2 TITL PROMOD AND SWISS-MODEL: INTERNET-BASED TOOLS FOR JRNL 2 TITL 2 AUTOMATED COMPARATIVE PROTEIN MODELLING. JRNL 2 REF BIOCHEM. SOC. TRANS. V. 24 274 1996 JRNL 3 AUTH M.C.PEITSCH,N.GUEX JRNL 3 TITL LARGE-SCALE COMPARATIVE PROTEIN MODELLING. JRNL 3 REF PROTEOME RESEARCH: NEW FRONTIERS IN FUNCTIONAL JRNL 3 REF 2 GENOMICS. 177 1997 JRNL 4 AUTH M.C.PEITSCH,N.GUEX JRNL 4 TITL SWISS-MODEL AND THE SWISS-PDBVIEWER: AN JRNL 4 TITL 2 ENVIRONMENT FOR COMPARATIVE PROTEIN MODELLING JRNL 4 REF ELECTROPHORESIS V. 18 2714 1997 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. SEE REMARK 4. REMARK 3 REMARK 3 REFINEMENT. NONE. REMARK 3 REMARK 3 MODELLING METHOD. REMARK 3 PROGRAM : PROMOD 2.0 REMARK 3 AUTHORS : N.GUEX,M.C.PEITSCH REMARK 3 REMARK 3 ENERGY MINIMSATION. REMARK 3 PROGRAM : GROMOS96 REMARK 3 AUTHORS : VAN GUNSTEREN REMARK 3 PARAMETER : IFP43B1 REMARK 3 TOPOLOGY FILE : MTB43B1 REMARK 3 METHOD 1 : STEEPEST DESCENT REMARK 3 CYCLES 1 : 200 REMARK 3 CONSTRAINTS 1 : 25 / C-FACTORS REMARK 3 METHOD 2 : CONJUGATE GRADIENT REMARK 3 CYCLES 2 : 300 REMARK 3 CONSTRAINTS 2 : 2500 / C-FACTORS REMARK 3 REMARK 4 REMARK 4 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 4 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT *CRYST1* AND REMARK 4 *SCALE* RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 4 RECORDS ARE MEANINGLESS. REMARK 5 REMARK 5 THIS MODEL IS BASED UPON THE COORDINATES OF: REMARK 5 REMARK 5 PDB ENTRY 1CDF.pdb REMARK 5 RECEPTOR 26-MAR-96 REMARK 5 THREE-DIMENSIONAL THEORETICAL MODEL OF THE LIGAND BINDING REMARK 5 DOMAIN OF THE HUMAN B CELL RECPTOR CD40 REMARK 5 REMARK 5 PDB ENTRY 1EXT.pdb CHAIN A REMARK 5 SIGNALLING PROTEIN 03-JUL-96 REMARK 5 EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR REMARK 5 RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21. REMARK 5 REMARK 5 PDB ENTRY 1EXT.pdb CHAIN B REMARK 5 SIGNALLING PROTEIN 03-JUL-96 REMARK 5 EXTRACELLULAR DOMAIN OF THE 55KDA TUMOR NECROSIS FACTOR REMARK 5 RECEPTOR. CRYSTALLIZED AT PH3.7 IN P 21 21 21. REMARK 5 REMARK 5 PDB ENTRY 1NCF.pdb CHAIN B REMARK 5 SIGNALLING PROTEIN 12-OCT-94 REMARK 5 REMARK 5 PDB ENTRY 1TNR.pdb CHAIN R REMARK 5 COMPLEX(LYMPHOKINE/RECEPTOR) 09-MAY-94 REMARK 5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 P25445_C00002 SWS P25445 1 - 38 NOT IN ATOMS LIST REMARK 999 P25445_C00002 SWS P25445 200 - 335 NOT IN ATOMS LIST DBREF P25445_C00002 1 161 SWS P25445 FASA_HUMAN 39 199 SEQALI SEQALI P25445 1 MLGIWTLLPL VLTSVARLSS KSVNAQVTDI NSKGLELRKT VTTVETQNLE SEQALI 11CDF 1 TACREKQYLI SEQALI 11EXT 1 SVCPQGKYIH SEQALI 21EXT 1 MD SVCPQGKYIH SEQALI 21NCF 1 VCPQGKYIH SEQALI 21TNR 1 CPQGKYIH SEQALI . . SEQALI P25445 sssss SEQALI 11CDF sssss SEQALI 11EXT sssss SEQALI 21EXT sssss SEQALI 21NCF sssss SEQALI 21TNR sss SEQALI SEQALI SEQALI P25445 51 GLHHDGQFCH KPCPPGERKA RDCTVNGDEP DCVPCQEGKE YTDKAHFSSK SEQALI 11CDF 11 ---NS-Q-CC SLCQPGQKLV SDCTEF-TET ECLPCGES-E FLDTWNRETH SEQALI 11EXT 11 PQNNS-I-CC TKCHKGTYLY NDCPGPGQDT DCRECESG-S FTASENHLRH SEQALI 21EXT 13 PQ-NNSI-CC TKCHKGTYLY NDCPGPGQDT DCRECESG-S FTASENHLRH SEQALI 21NCF 10 --PQNNSICC TKCHKGTYLY NDCPGPGQDT DCRECESG-S FTASENHLRH SEQALI 21TNR 9 P-QNN-SICC TKCHKGTYLY NDCPGPGQDT DCRECESG-S FTASENHLRH SEQALI * * * ** . .* * . . . SEQALI P25445 sss ss sssss sssss SEQALI 11CDF s ss ss sssss sssss SEQALI 11EXT s ss ss sssss sssss s s s SEQALI 21EXT s ss ss sssss sssss s s s SEQALI 21NCF sss ss sssss sssss s s s SEQALI 21TNR s ss sssss sssss s s s SEQALI SEQALI SEQALI P25445 101 CRRCRLCDEG HGLEVEINCT RTQNTKCRCK PNFFCNST-- VCEHCDPCTK SEQALI 11CDF 54 CHQHKYCDPN LGLRVQQKGT SETDTICTCE EGWHCTSE-- ACESCVLHRS SEQALI 11EXT 58 CLSCSKCRKE MGQVEISSCT VDRDTVCGCR KNQYRHYWSE NLFQCFNCSL SEQALI 21EXT 60 CLSCSKCRKE MGQVEISSCT VDRDTVCGCR KNQYRHYWSE NLFQCFNCSL SEQALI 21NCF 57 CLSCSKCRKE MGQVEISSCT VDRDTVCGCR KNQYRHYWSE NLFQCFNCSL SEQALI 21TNR 56 CLSCSKCRKE MGQVEISSCT VDRDTVCGCR KNQYRHYWSE NLFQCFNCSL SEQALI * * * * .* * * * SEQALI P25445 sss sss sssss sssss SEQALI 11CDF sss sss sss sss SEQALI 11EXT sss sss sss sssssss sssssss SEQALI 21EXT sss sss sss sssssss sssssss SEQALI 21NCF sss sss sss sssssss sssssss SEQALI 21TNR sss sss sss sssssss sssssss SEQALI SEQALI SEQALI P25445 149 CEHGI-IKEC TLT-SNTKCK EEGSRSNLGW LCLLLLPIPL IVWVKRKEVQ SEQALI 11CDF 102 CSPGFGVKQI ATGVSDTICE ---------- ---------- ---------- SEQALI 11EXT 108 CLNGTVHLSC QEKQNTVCTC HAGFFLRENE CVSCSNCKKS LECTKLCLPQ SEQALI 21EXT 110 CLNGTVHLSC QEKQNTVCTC HAGFFLRENE CVSCSNCKKS LECTKLCLP- SEQALI 21NCF 107 CLN-GTVHLS CQEKQNTVCT CHAGFFLREN ECVSCSN--- ---------- SEQALI 21TNR 106 CLNG------ -------TVH LSCQEKQNTV CTCHAGFFLR ENECVSC--- SEQALI * SEQALI P25445 sss s sssss ssssss SEQALI 11CDF sss sss SEQALI 11EXT sssss ssss s sssss s ssss hhhhhh SEQALI 21EXT sssss ssss s sssss s ssss hhhhh SEQALI 21NCF s ssss sss ss sssss sssss SEQALI 21TNR ss sss s ssss sssss sssss SEQALI SEQALI SEQALI P25445 197 KTCRKHRKEN QGSHESPTLN PETVAINLSD VDLSKYITTI AGVMTLSQVK SEQALI 11CDF ---------- ---------- ---------- ---------- ---------- SEQALI 11EXT 158 IEN------- ---------- ---------- ---------- ---------- SEQALI 21EXT ---------- ---------- ---------- ---------- ---------- SEQALI 21NCF ---------- ---------- ---------- ---------- ---------- SEQALI 21TNR ---------- ---------- ---------- ---------- ---------- SEQALI SEQALI P25445 SEQALI 11CDF SEQALI 11EXT SEQALI 21EXT SEQALI 21NCF SEQALI 21TNR SEQALI SEQALI SEQALI P25445 247 GFVRKNGVNE AKIDEIKNDN VQDTAEQKVQ LLRNWHQLHG KKEAYDTLIK SEQALI 11CDF ---------- ---------- ---------- ---------- ---------- SEQALI 11EXT ---------- ---------- ---------- ---------- ---------- SEQALI 21EXT ---------- ---------- ---------- ---------- ---------- SEQALI 21NCF ---------- ---------- ---------- ---------- ---------- SEQALI 21TNR ---------- ---------- ---------- ---------- ---------- SEQALI SEQALI P25445 SEQALI 11CDF SEQALI 11EXT SEQALI 21EXT SEQALI 21NCF SEQALI 21TNR SEQALI SEQALI SEQALI P25445 297 DLKKANLCTL AEKIQTIILK DITSDSENSN FRNEIQSLV SEQALI 11CDF ---------- ---------- ---------- --------- SEQALI 11EXT ---------- ---------- ---------- --------- SEQALI 21EXT ---------- ---------- ---------- --------- SEQALI 21NCF ---------- ---------- ---------- --------- SEQALI 21TNR ---------- ---------- ---------- --------- SEQALI SEQALI P25445 SEQALI 11CDF SEQALI 11EXT SEQALI 21EXT SEQALI 21NCF SEQALI 21TNR SEQALI SEQALI SEQRES 1 161 THR VAL THR THR VAL GLU THR GLN ASN LEU GLU GLY LEU SEQRES 2 161 HIS HIS ASP GLY GLN PHE CYS HIS LYS PRO CYS PRO PRO SEQRES 3 161 GLY GLU ARG LYS ALA ARG ASP CYS THR VAL ASN GLY ASP SEQRES 4 161 GLU PRO ASP CYS VAL PRO CYS GLN GLU GLY LYS GLU TYR SEQRES 5 161 THR ASP LYS ALA HIS PHE SER SER LYS CYS ARG ARG CYS SEQRES 6 161 ARG LEU CYS ASP GLU GLY HIS GLY LEU GLU VAL GLU ILE SEQRES 7 161 ASN CYS THR ARG THR GLN ASN THR LYS CYS ARG CYS LYS SEQRES 8 161 PRO ASN PHE PHE CYS ASN SER THR VAL CYS GLU HIS CYS SEQRES 9 161 ASP PRO CYS THR LYS CYS GLU HIS GLY ILE ILE LYS GLU SEQRES 10 161 CYS THR LEU THR SER ASN THR LYS CYS LYS GLU GLU GLY SEQRES 11 161 SER ARG SER ASN LEU GLY TRP LEU CYS LEU LEU LEU LEU SEQRES 12 161 PRO ILE PRO LEU ILE VAL TRP VAL LYS ARG LYS GLU VAL SEQRES 13 161 GLN LYS THR CYS CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 ATOM 1 H1 LYS 1 20.330 -2.680 -25.883 1.00 99.00etc ...
Torsten Schwede , Manuel C. Peitsch & Nicolas Guex.