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Table 1: Common uses of comparative protein structure models. A list of our papers using MODELLER to address practical problems in collaboration with experimentalists can be obtained at URL http://guitar.rockefeller.edu/publications/ref/ref.html.

Designing (site-directed) mutants to test hypotheses about function

Identifying active and binding sites

Searching for ligands of a given binding site

Designing and improving ligands of a given binding site

Modeling substrate specificity

Predicting antigenic epitopes

Protein-protein docking simulations

Inferring function from calculated electrostatic potential around the protein

Molecular replacement in X-ray structure refinement

Refining models against NMR dipolar coupling data

Testing a given sequence - structure alignment

Rationalizing known experimental observations

Planning new experiments

 

 

Table 2: Web sites useful for comparative modeling.

Databases
NCBI	www.ncbi.nlm.nih.gov/
PDB	www.rcsb.org/
MSD	www.rcsb.org/databases.html
CATH	www.biochem.ucl.ac.uk/bsm/cath/
TrEMBL	srs.ebi.ac.uk/
SCOP	scop.mrc-lmb.cam.ac.uk/scop/
PRESAGE	presage.stanford.edu
MODBASE	guitar.rockefeller.edu/modbase/
GeneCensus	bioinfo.mbb.yale.edu/genome
GeneBank	www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
PSI	www.structuralgenomics.org
Template search, fold assignment
PDB-Blast	bioinformatics.burnham-inst.orgpdb_blast
BLAST	www.ncbi.nlm.nih.gov/BLAST/
FastA	www.dna.affrc.go.jp/htdocs/Blast/fasta.html
DALI	www2.ebi.ac.uk/dali/
PhD, TOPITS	www.embl-heidelberg.de/predictprotein/predictprotein.html
THREADER	insulin.brunel.ac.uk/
123D	genomic.sanger.ac.uk/123D/run123D.html
UCLA-DOE	www.doe-mbi.ucla.edu/people/frsvr/frsvr.html
PROFIT	lore.came.sbg.ac.at/
MATCHMAKER	www.tripos.com/software/mm.html
3D-PSSM	www.bmm.icnet.uk/ 3dpssm/html/ffrecog.html
BIOINGBGU	www.cs.bgu.ac.il/ bioinbgu/
FUGUE	www-cryst.bioc.cam.ac.uk/ fugue
LOOPP	ser-loopp.tc.cornell.edu/loopp.html
FASS	bioinformatics.burnham-inst.org/FFAS/index.html
SAM-T99/T98	www.cse.ucsc.edu/research/compbio/sam.html

Comparative modeling
3D-JIGSAW	www.bmm.icnet.uk/servers/3djigsaw/
CPH-Models	www.cbs.dtu.dk/services/CPHmodels/
COMPOSER	www-cryst.bioc.cam.ac.uk/
FAMS	physchem.pharm.kitasato-u.ac.jp/FAMS/fams.html
MODELLER	guitar.rockefeller.edu/modeller/modeller.html
PrISM	honiglab.cpmc.columbia.edu/
SWISS-MODEL	www.expasy.ch/swissmod/SWISS-MODEL.html
SDSC1	cl.sdsc.edu/hm.html
WHAT IF	www.cmbi.kun.nl/bioinf/predictprotein/
ICM	www.molsoft.com/
SCWRL	www.fccc.edu/research/labs/dunbrack/scwrl/
InsightII	www.accelrys.com
SYBYL	www.tripos.com
Model evaluation
PROCHECK	www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
WHATCHECK	www.cmbi.kun.nl/swift/whatcheck/
ProsaII	www.came.sbg.ac.at
BIOTECH	biotech.embl-ebi.ac.uk:8400/
VERIFY3D	www.doe-mbi.ucla.edu/Services/Verify_3D/
ERRAT	www.doe-mbi.ucla.edu/Services/Errat.html
ANOLEA	guitar.rockefeller.edu/ fmelo/anolea/anolea.html
AQUA	urchin.bmrb.wisc.edu/ jurgen/Aqua/server/
SQUID	www.yorvic.york.ac.uk/~oldfield/squid
PROVE	www.ucmb.ulb.ac.be/UCMB/PROVE/

 Table 2 continued.

  

Figure 1: Steps in comparative protein structure modeling. See text for description of each step.

  

Figure 2: Comparative model building by program MODELLER. First, homology-derived spatial restraints on many atom-atom distances and dihedral angles are extracted from the template structure(s). The alignment is used to determine equivalent residues between the target and the template. The homology-derived and stereochemical restraints are combined into an objective function. Finally, the model of the target is optimized until a model that best satisfies the spatial restraints is obtained. This procedure is similar to the one used in structure determination by NMR spectroscopy.

  

Figure 3: Average model accuracy as a function of sequence identity. As the sequence identity between the target sequence and the template structure decreases, the average structural similarity between the template and the target also decreases (dotted line, open circles). (continued on the next page)

(Figure 3: continued from the previous page)

Structural overlap is defined as the fraction of equivalent $\mbox{C}_\alpha$ atoms. For the comparison of the model with the actual structure (filled circles), two $\mbox{C}_\alpha$ atoms were considered equivalent if they belonged to the same residue and were within 3.5Å of each other after least-squares superposition of all $\mbox{C}_\alpha$ atoms by the ALIGN3D command in MODELLER. For comparison of the template structure with the actual target structure (open circles), two $\mbox{C}_\alpha$ atoms were considered equivalent if they were within 3.5Å of each other after alignment and rigid-body superposition. At high sequence identities, the models are close to the templates and therefore also close to the experimental target structure (solid line, filled circles). At low sequence identities, errors in the target-template alignment become more frequent and the structural similarity of the model with the experimental target structure falls below the target-template structural similarity. The difference between the model and the actual target structure is a combination of the target-template differences (light area) and the alignment errors (dark area). The figure was constructed by calculating 3993 comparative models based on single templates of varying similarity to the targets. All targets had known (experimentally determined) structures and therefore the comparison of the models and templates with the experimental structures was possible [47]. The top part of the figure shows three models (solid line) compared with their corresponding experimental structures (dotted line). The models were calculated with MODELLER in a completely automated fashion before the experimental structures were available [43]. The arrows indicate the target-template similarity in each case.

  

Figure 4: PROSAII [45] energy profile for the raw TvLDH model (dashed line), refined TvLDH model (thin line), and the 4mdhA template structure (heavy line) (Examples 1 and 2). The extended peak above the zero line in the region 90-100 and 220-250 of the raw model highlights a possible error in the raw model, significantly improved in the refined model.

  

Figure 5: Superposition of models for six linker segments with lengths from 6 to 9 residues. Towards the C-terminus of the loop, a larger structural variation can be observed, but the dominant conformation is well defined by a cluster of four loops.