Homology modeling
From Christoph's Personal Wiki
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "template"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.[1]
Contents
Popular Web servers for remote homology/fold recognition
| Homology modeling servers | |||
|---|---|---|---|
| Server name | Consensus/ single |
Model building/ confidence measure |
FR/ ab initio |
| Phyre | Single | Model + confidence | FR |
| I-TASSER | Single | Model + confidence | FR + ab initio |
| SAM-T06 | Single | Model + confidence | FR |
| HHpred | Single | Confidence | FR |
| GenThreader | Single | P-value | FR |
| PCONS | Consensus | Model + Pcons score | FR |
| Bioinfo | Consensus | Model + E-value | FR |
| FFAS | Single | FFAS score | FR |
| Robetta | Single | Model + confidence | FR + ab initio |
| SP4 | Single | Model + Z-score | FR |
"Consensus" indicates that the server collates results from multiple independent servers to form a final prediction, whereas "single" indicates that a server uses only its own local methods. The Model building/confidence measure column indicates whether a server provides as output 3D coordinates of a potential model ("Model") and a score indicating the confidence in the model (Z-score, P-value, E-value and so on). The "FR/ab initio" column indicates whether the server can produce results based only on remote homology/fold recognition ("FR") or can additionally build models in the absence of a template ("ab initio").[2]
See also
- wikipedia:Category:Molecular modelling software
- wikipedia:Homology modeling
- WHAT IF
- Biskit — written in Python
- NOCH (or NOC)
- Jmol
- PyMOL
- RasMol
References
- ↑ Chothia, C; Lesk, AM (1986). "The relation between the divergence of sequence and structure in proteins". EMBO J 5 (4): 823–6. PMC 1166865. PMID 3709526.
- ↑ Kelley LA, Sternber MJE (2009). "Protein structure prediction on the Web: a case study using the Phyre server". Nature Protocols 4: 363-371. DOI:10.1038/nprot.2009.2
External links
- 3D-Coffee and Expresso — a special mode of T-Coffee that uses structural information
- SWISS-MODEL - automated model construction server
- 3D-JIGSAW - automated model construction server
- PHYRE – automated model construction server, replace 3D-PSSM.
- MODELLER – widely used standalone program using the spatial restraints method
- ModBase – database for homology models
- LiveBench – continuous benchmark for automated prediction servers
- EVA – continuous benchmark for automated prediction servers
- Consensus – Alignment of a sequence (target) to its closest homolog in PDB (template) using a consensus of other alignment methods
- MolIDE – Open-source cross-platform graphical environment for homology modeling
- WHAT IF – free servers for structure and model analysis, validation, and visualisation.
- PDBREPORT – lists of errors in PDB files.
- WHAT_CHECK – downloadable software for structure and model validation.
- SUPERFAMILY – Hidden Markov model library offering remote homology detection at the Structural_Classification_of_Proteins (SCOP)
- HOMSTRAD (Homologous Structure Alignment Database) — a curated database of structure-based alignments for homologous protein families.
- PDBeFold (Structure Similarity; SSM) — an interactive service for comparing protein structures in 3D (pdbe.org/fold)
