Data from: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

Latallo MJ, Cortina GA, Faham S, Nakamoto RK, Kasson P

Date Published: July 25, 2017

DOI: https://doi.org/10.5061/dryad.ck3dh

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Title CTX-M9:meropenem acylenzyme run input file
Downloaded 3 times
Description Gromacs TPR for wild-type CTX-M9 in complex with meropenem
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Title Binding pocket trajectories for CTX-M9
Downloaded 3 times
Description Gromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.
Download ctx_pocket_trajs.tgz (71.44 Mb)
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Title Binding pocket trajectories for CTX-M9 L48A
Downloaded 6 times
Description Gromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.
Download l48a_pocket_trajs.tgz (65.95 Mb)
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Title Binding pocket trajectories for CTX-M9 T165W
Downloaded 3 times
Description Gromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.
Download t165w_pocket_trajs.tgz (75.27 Mb)
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Title Binding pocket trajectories for CTX-M9 S281A
Downloaded 7 times
Description Gromacs trajectory files and reference PDB for drug binding pocket atoms, computed using TPR of the full solvated acylenzyme. These trajectories were used for mutual information feature selection and decision tree calculation.
Download s281a_pocket_trajs.tgz (68.26 Mb)
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Title CTX-M9 L48A:meropenem acylenzyme run input file
Downloaded 6 times
Description Gromacs TPR for CTX-M9 L48A in complex with meropenem
Download ctx_l48a.tpr (3.348 Mb)
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Title CTX-M9 T165W:meropenem acylenzyme run input file
Downloaded 3 times
Description Gromacs TPR for CTX-M9 T165W in complex with meropenem
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Title CTX-M9 S281A:meropenem acylenzyme run input file
Downloaded 7 times
Description Gromacs TPR for CTX-M9 S281A in complex with meropenem
Download ctx_s281a.tpr (3.327 Mb)
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Title PDB file for solvated CTX-M9:meropenem adduct
Downloaded 4 times
Description PDB file corresponding to simulation start state for CTX-M9:meropenem
Download ctx_acyl.pdb (6.908 Mb)
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Title PDB file for solvated CTX-M9 L48A:meropenem adduct
Downloaded 6 times
Description PDB file corresponding to simulation start state for L48A:meropenem acylenzyme.
Download ctx_l48a.pdb (7.661 Mb)
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Title PDB file for solvated CTX-M9 T165W:meropenem adduct
Downloaded 7 times
Description PDB file corresponding to simulation start state for CTX-M9 T165W meropenem acylenzyme
Download ctx_t165w.pdb (7.419 Mb)
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Title PDB file for solvated CTX-M9 S281A:meropenem adduct
Downloaded 10 times
Description PDB file corresponding to simulation start state for CTX-M9 S281A meropenem acylenzyme
Download ctx_s281a.pdb (7.584 Mb)
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Title Residue definitions for meropenem and cefotaxime acylenzymes
Downloaded 6 times
Description Modified GROMACS aminoacids.rtp file for AMBER99SB-ILDN force field containing residue definitions for serine-meropenem adducts and serine-cefotaxime adducts.
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Title atom type file
Downloaded 5 times
Description aminoacids.atp in GROMACS format for modified AMBER99SB-ILDN parameters to describe acylenzymes.
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Title ffnonbonded.itp
Downloaded 4 times
Description Nonbonded parameter file ffnonbonded.itp for modified AMBER99SB-ILDN to define acylenzymes.
Download ffnonbonded.itp (6.529 Kb)
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When using this data, please cite the original publication:

Latallo MJ, Cortina GA, Faham S, Nakamoto RK, Kasson P (2017) Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme. Chemical Science 8(9): 6484-6492. https://doi.org/10.1039/c7sc02676e

Additionally, please cite the Dryad data package:

Latallo MJ, Cortina GA, Faham S, Nakamoto RK, Kasson P (2017) Data from: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme. Dryad Digital Repository. https://doi.org/10.5061/dryad.ck3dh
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