Homology Modelling

SWISS-MODEL
SWISS-MODEL is an automated comparative modelling server (ExPASy, CH)

SDSC1
Protein structure homology modelling server (San Diego, USA)

3D-JIGSAW
Automated system for 3D models for proteins (Cancer Research UK)

WHATIF
WHAT IF Web interface: homology modelling, drug docking, electrostatics calculations, structure validation and visualisation. You have to provide your own alignments to build models.

ROBETTA
Robetta is a full-chain protein structure prediction server. It divides protein chains into domains, and models them by either homology modelling or ab initio modelling.

SQUARE
A server that will check how good your homology modelling or fold recogniton alignment is (CNB, Madrid).

Loops Database
A table of five protein loop classes. (Cancer Research UK)

BIOTECH Validation Suite
An evaluation suite that uses three widely available validation programs (PROCHECK, PROVE and WHAT IF - may not be available)

Verify3D
A tool designed to help in the refinement of crystallographic structures. It also provides a visual analysis of model quality.

PDG-MAMMOTH
A local method for evaluating RMSD between model and the actual target protein

1.-This is the target sequence:

>target sequence

TQALVTLTSACADSSPSCDLFKNQGYCGEKFFDWMRKNCAKTCGFCGTGGGAETGGSDGVCGKTSVQQSR
IISGTNARPGAWPWMASLYMLSRSHICGGSLLNSRWILTASHCVVGTGATTKNLVIKLGEHDHYDKDGFE
QQFDVEKIIPHPAYKRGPLKNDIALIKLKTPARINKRVKTICLPKKGSAPSVGSRECYLAGWGSIRHPGG
SYHTLQQAMLPVVSYTNCHNQKNFVCAGFGKSSLTNACRGDSGGPLMCRKSDGSWEQHGIASFVVEYCKY
YTAFTPVANYIDWINQHINK

2.- First: Submit the sequence to the SWISS-MODEL program:

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Then you'll receive an e-mail with all the proccesses conducted by SWISS-MODEL

1. SWISS-MODEL search for structural homologues. It uses "BLASTP2" in "ExNRL-3D" Database. Results are shown according to P(N) from BLAST
AlignMaster output
============================================================
Length of target sequence: 300 residues

    Searching sequences of known 3D structures

    Found 1bruP.pdb with P(N)=2e-40
    Found 4chaB.pdb with P(N)=5e-38
    Found 1choE.pdb with P(N)=5e-38
    Found 1gmh_.pdb with P(N)=6e-38
    Found 8gch_.pdb with P(N)=6e-38
    Found 1gcd_.pdb with P(N)=6e-38
    Found 1pytC.pdb with P(N)=6e-38
    Found 3gch_.pdb with P(N)=8e-38
    Found 5gch_.pdb with P(N)=8e-38
    Found 4gch_.pdb with P(N)=8e-38
    Found 1gmcA.pdb with P(N)=8e-38
    Found 2gmt_.pdb with P(N)=8e-38
     ........ (cutfor clarity)


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2. With the "SIM" program all the "templates" (3D structures used to model) with an id% > 25% more than 25 residues length will be retrieved. In addition, this program can recognise different domains. For example ...:

"Extracting template sequences
"Running pair-wise alignments with target sequence
"Sequence identity of templates with target:

    1bruP.pdb:44.98 % identity
    4chaB.pdb:36.14 % identity
    1choE.pdb:36.14 % identity
    1gmh_.pdb:36.6 % identity
    8gch_.pdb:36.6 % identity
    1gcd_.pdb:36.6 % identity
    1pytC.pdb:40.96 % identity
    3gch_.pdb:30.78 % identity
    5gch_.pdb:30.78 % identity

"Looking for template groups "Global alignment overview:
    Taget Sequence:|==================================================|
    1bruP.pdb| --------------------------------------
    4chaB.pdb| ---------------------------------------
    1choE.pdb| ---------------------------------------
    1gmh_.pdb| ---------------------------------------
    8gch_.pdb| ---------------------------------------
    1gcd_.pdb| ---------------------------------------
    1pytC.pdb| --------------------------------------
    3gch_.pdb| ---------------------------------------
    5gch_.pdb| ---------------------------------------
    4gch_.pdb| ---------------------------------------
    1gmcA.pdb| ---------------------------------------
    2gmt_.pdb| ---------------------------------------
    etc etc...............................

AlignMaster found 1 regions to model separately: 1: Using template(s)

1a0lA.pdb   1a0lB.pdb  1a0lC.pdb  1a0lD.pdb  1a3bH.pdb 1a3eH.pdb   1a61H.pdb  1abiH.pdb
1acbE.pdb  1ad8H.pdb  1ae8H.pdb  1afeH.pdb  1ahtH.pdb 1ai8H.pdb   1aixH.pdb  1amhA.pdb
--------  ETC etc..





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3. Now batch files are created for ProMod to generate a model

Batch.1: residues 56 - 300 of submitted sequence.

Exiting AlignMaster


ProModII trace log for Batch.1
============================================================

ProModII: 3.70 (SP3)
ProModII: Loading Template: 1bruP.pdb
ProModII: Loading Template: 4chaB.pdb
ProModII: Loading Template: 1choE.pdb
ProModII: Loading Template: 1gmh_.pdb
ProModII: Loading Template: 8gch_.pdb
ProModII: Loading Raw Sequence
ProModII: Iterative Template Fitting
ProModII: Iterative Template Fitting
ProModII: Iterative Template Fitting
ProModII: Iterative Template Fitting
ProModII: Generating Structural Alignment
ProModII: Aligning Raw Sequence
ProModII: Refining Raw Sequence Alignment
ProModII: ProModII: doing complex assignment of backbone
ProModII: N-terminal overhang trimmed for chain ' '. Start at residue: 16
ProModII: ProModII: adding blocking groups
ProModII: Weighting Backbones
ProModII: Src residue is not amino-acid
ProModII: Src residue is not amino-acid
ProModII: Averaging Sidechains
ProModII: Adding Missing Sidechains
ProModII: Trying Ligating with anchor residues SER 32 and MET 35
ProModII: Trying Ligating with anchor residues SER 32 and LEU 36
ProModII: connectivity problem --> including residue LEU 22
ProModII: Trying Ligating with anchor residues SER 32 and SER 37
ProModII: connectivity problem --> including residue SER 23
ProModII: Trying Ligating with anchor residues SER 32 and ARG 38
ProModII: connectivity problem --> including residue ARG 24
ProModII: Trying Ligating with anchor residues SER 32 and SER 39
ProModII: Number of Ligations found: 500
ProModII: ACCEPTING loop 378: clash= 0 FF= 195.4 PP= -7.00
ProModII: Small Ligation (C-N < 3.0A) ignored;
ProModII: GROMOS will repair it at residue SER 25
ProModII: connectivity problem (C-N > 3.0A) at residue: 71
ProModII: Trying Ligating with anchor residues GLY 83 and GLN 86
ProModII: Number of Ligations found: 3
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues ASP 82 and GLN 86
ProModII: Number of Ligations found: 22
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues LYS 81 and GLN 86
ProModII: Number of Ligations found: 500
ProModII: ACCEPTING loop 230: clash= 0 FF= -17.5 PP= -2.00
ProModII: connectivity problem (C-N > 3.0A) at residue: 91
ProModII: Trying Ligating with anchor residues PRO 103 and ASN 106
ProModII: Number of Ligations found: 12
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues GLY 102 and ASN 106
ProModII: Number of Ligations found: 14
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues GLY 102 and ASP 107
ProModII: connectivity problem --> including residue ASP 93
ProModII: Trying Ligating with anchor residues GLY 102 and ILE 108
ProModII: Trying Ligating with anchor residues ARG 101 and ILE 108
ProModII: Number of Ligations found: 273
ProModII: ACCEPTING loop 218: clash= 0 FF= 1486.4 PP= 0.00
ProModII: Trying Ligating with anchor residues ASN 175 and ASN 178
ProModII: Trying Ligating with anchor residues HIS 174 and ASN 178
ProModII: Number of Ligations found: 22
ProModII: ACCEPTING loop 10: clash= 0 FF= -294.1 PP= -3.00
ProModII: Trying Ligating with anchor residues GLY 183 and LYS 186
ProModII: Trying Ligating with anchor residues ALA 182 and LYS 186
ProModII: Trying Ligating with anchor residues ALA 182 and SER 187
ProModII: Trying Ligating with anchor residues CYS 181 and SER 187
ProModII: Trying Ligating with anchor residues CYS 181 and SER 188
ProModII: Trying Ligating with anchor residues VAL 180 and SER 188
ProModII: Number of Ligations found: 500
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues VAL 180 and LEU 189
ProModII: Number of Ligations found: 112
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Trying Ligating with anchor residues PHE 179 and LEU 189
ProModII: Number of Ligations found: 500
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: +++ Warning: Ligation Failed, SparePart will be inserted later
ProModII: +++ It is usually the sign that the region is misaligned.
ProModII: connectivity problem (C-N > 3.0A) at residue: 177
ProModII: Trying Ligating with anchor residues LEU 189 and ALA 192
ProModII: Trying Ligating with anchor residues SER 188 and ALA 192
ProModII: Trying Ligating with anchor residues SER 187 and ALA 192
ProModII: Trying Ligating with anchor residues LYS 186 and ALA 192
ProModII: Trying Ligating with anchor residues GLY 185 and ALA 192
ProModII: Trying Ligating with anchor residues PHE 184 and ALA 192
ProModII: Trying Ligating with anchor residues GLY 183 and ALA 192
ProModII: Trying Ligating with anchor residues ALA 182 and ALA 192
ProModII: +++ Warning: Ligation Failed, SparePart will be inserted later
ProModII: +++ It is usually the sign that the region is misaligned.
ProModII: connectivity problem (C-N > 3.0A) at residue: 207
ProModII: Trying Ligating with anchor residues VAL 219 and TYR 222
ProModII: Number of Ligations found: 7
ProModII: ACCEPTING loop 0: clash= 0 FF= -37.3 PP= 1.00
ProModII: Trying Ligating with anchor residues LYS 224 and THR 227
ProModII: Number of Ligations found: 2
ProModII: ACCEPTING loop 1: clash= 0 FF= 261.7 PP= 2.00
ProModII: Building CSP loop with anchor residues VAL 59 and ALA 64
ProModII: Number of Ligations found: 53
ProModII: all loops are bad; continuing CSP with larger segment
ProModII: Building CSP loop with anchor residues VAL 59 and THR 65
ProModII: Number of Ligations found: 119
ProModII: ACCEPTING loop 114: clash= 0 FF= 560.6 PP= 1.00
ProModII: Building CSP loop with anchor residues SER 136 and SER 139
ProModII: Building CSP loop with anchor residues PRO 135 and SER 139
ProModII: Building CSP loop with anchor residues ALA 134 and SER 139
ProModII: Number of Ligations found: 500
ProModII: ACCEPTING loop 22: clash= 0 FF= -38.9 PP= -2.00
ProModII: Finding Spare-Part loop with anchor residues ASN 178 and ASN 191
ProModII: connectivity problem --> including residue ASN 177
ProModII: Finding Spare-Part loop with anchor residues ASN 178 and ALA 192
ProModII: ACCEPTING loop 1 from 4RHV1 Clash= 4 FF= 555.6 PP=-29.69
ProModII: BadPhi= 1 BadGX= 0 BadXP= 0 weakXP= 0 Score= 7.00 rms= 0.00
ProModII: Optimizing Sidechains
ProModII: Dumping Preliminary Model
ProModII: Adding Hydrogens
ProModII: Optimizing loops and OXT (nb = 41)
ProModII: Final Total Energy: 5009.919 KJ/mol
ProModII: Removing Hydrogens
ProModII: Fixing Atom Nomenclature
ProModII: Dumping Sequence Alignment
***

Getting the 3D coordinates from the model

Finally you'll receive an e-mail with the pdb coordinates if your model. Here you can see in the image the model (RED) and one target (1bruP) in grey. These are predictions, so any conclusion must be taken carefully. (HERE Access to an e-mail with the 3D coordinates.). Note that several templates have been selected to generate the model although in the figure only one is represented.

QUICK GUIDES

:::: [BACK TO TOP]

• A QUICK GUIDE TO ANALYSE SWISS MODEL RESULTS


• EXAMPLE OF QUALITY CHECKS: WHATIF & PROSA


• PROTEIN MODELLING AND EVALUATION:


• Comparative protein modelling : framework, loops, side chains, rotamers
  
  [within Principles of Protein Structure , Comparative Protein Modelling and Visualisation (Nicolas Guex and Manuel C. Peitsch)]


• Professional gambling (G. Vriend). A review of homology modelling from template detection to energy refinement.


• The use of position specific rotamers in model building by homology