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Decoy models

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20 sequences were randomly selected from the Fischer set of 68 pairs of remotely related protein structures from 51 to 568 residues in size. For each sequence, 300 comparative models were built using its closest structurally related sequence as the template. The models were built using alignments that shared no more than 95% of identically aligned positions or had at least 5 different alignment positions. A single comparative model of the target sequence that contains all non-hydrogen atoms was built for each alignment by MODELLER-6, applying the default model building routine .model. with fast refinement.

The alignments were obtained by a genetic algorithm protocol (John, B and Sali, A in press) that produced alignments uniformly spanning from 0 to 100% of correctly aligned positions with respect to the CE structure-based alignment.

Directory Structure:

Each subdirectory under John-2002 contains models numbered from 1-301 *. model 1.pdb.NATIVE is the native structure (X-ray) for the region modeled ( models 1-301). The name of the subdirectory is the PDB code of the modeled sequence. In addition, the file .list-with-native. contains the C-alpha RMSD of the models with respect to their X-ray structures (there is a description in the file too). *4 of the subdirectories have more than 300 models, please ignore models above 301.

The models can be downloaded at:https://salilab.org/ftp/decoys/comp_models.tar.gz

Publication:Comparative Protein Structure Modeling by Iterative Alignment, Model Building, and Model Assessment


* 4 of the subdirectories have more than 300 models, please ignore models above 301