ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure

Narunsky, Aya; Ben‐Tal, Nir

doi:10.1186/1471-2105-15-s3-a5

Cited by 2 publications

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“…ConTemplate builds an ensemble of conformations for a query protein that has at least one known structure, using a threestep process (Narunsky and Ben-Tal, 2014): First, it searches for a set of proteins that are structural equivalents of the query, using the structure-aligner GESAMT (Krissinel, 2012) based on preset similarity thresholds ( Figures 3A, 4A, and 4D). For efficiency, the search is only among the structural neighbors of the query, rather than the entire PDB.…”

Section: The Contemplate Methodsmentioning

confidence: 99%

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

et al. 2015

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Protein function involves conformational changes, but often, for a given protein, only some of these conformations are known. The missing conformations could be predicted using the wealth of data in the PDB. Most PDB proteins have multiple structures, and proteins sharing one similar conformation often share others as well. The ConTemplate web server (http://bental.tau.ac.il/contemplate) exploits these observations to suggest conformations for a query protein with at least one known conformation (or model thereof). We demonstrate ConTemplate on a ribose-binding protein that undergoes significant conformational changes upon substrate binding. Querying ConTemplate with the ligand-free (or bound) structure of the protein produces the ligand-bound (or free) conformation with a root-mean-square deviation of 1.7 Å (or 2.2 Å); the models are derived from conformations of other sugar-binding proteins, sharing approximately 30% sequence identity with the query. The calculation also suggests intermediate conformations and a pathway between the bound and free conformations.

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Section: The Contemplate Methodsmentioning

confidence: 99%

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

et al. 2015

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“…We developed the ConTemplate method to exploit the richness of the Protein Data Bank (PDB)[ 1 ] for this purpose. ConTemplate uses a three-step process to suggest alternative conformations for a query protein with one known conformation [ 2 ]. First, ConTemplate uses GESAMT to scan the PDB for proteins that share structural similarity with the query [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

et al. 2015

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ConTemplate: exploiting the protein databank to propose ensemble of conformations of a query protein of known structure

Cited by 2 publications

References 5 publications

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

Using ConTemplate and the PDB to explore conformational space: on the detection of rare protein conformations

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