Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information

Ovchinnikov S, Kamisetty H, Baker D

Date Published: June 10, 2014

DOI: http://dx.doi.org/10.5061/dryad.s00vr

 

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Title PDB file for TRAP complex
Downloaded 11 times
Description The predicted complex of the tripartite ATP-independent periplasmic (TRAP) transporter. It is composed of three proteins: two integral membrane proteins YIAM and YIAN, and one periplasmic protein YIAO. The PDB file was sampled using UniProt E. coli sequences of YIAM_ECOLI, YIAN_ECOLI and YIAO_ECOLI.
Download YIA_MNO.pdb (1.108 Mb)
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Title PDB file for D-methionine transport system
Downloaded 7 times
Description Predicted complex of the D-methionine transporter. It is an ATP-driven transport system that transports methionine. The PDB file was sampled using UniProt E. coli sequences of METI_ECOLI and METQ_ECOLI.
Download METI_METQ.pdb (854.7 Kb)
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Title PDB file for Tripartite efflux system
Downloaded 18 times
Description Predicted complex for the Tripartite efflux pump. This family of complexes spans both the inner and outer membrane, and are widely used in bacteria to pump toxic compounds out of the cell. The PDB file was modeled using E. coli sequences of MDTP_ECOLI and MDTN_ECOLI.
Download MDTP_MDTN.pdb (3.417 Mb)
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Title PDB file for PFL Complex
Downloaded 10 times
Description Predicted complex of Pyruvate formate lyase-activating enzyme. Pyruvate formate-lyase (PFL) catalyzes the reaction of acetyl-CoA and formate from pyruvate and CoA in the Fermentation pathway. The PDB file was sampled using the E. coli sequences of PFLA_ECOLI and PFLB_ECOLI.
Download PFLA_PFLB.pdb (1.280 Mb)
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Title Ribosome 50S alignments
Downloaded 34 times
Description Multiple sequence alignments used in the Ribosome 50S analysis. Each fasta file begins with the T. thermophilus amino acid sequence pair, with other homologous sequences trimmed to match its length. For an interactive list, please visit: http://gremlin.bakerlab.org/cplx.php?mode=ribo
Download ribosome_50S_alignments.zip (72.64 Mb)
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Title E. coli paired alignments
Downloaded 31 times
Description Multiple sequence alignments used in E. coli gene pair analysis. Each fasta file begins with the E. coli amino acid sequence pair, with other homologous sequences trimmed to match its length. For an interactive list, please visit: http://gremlin.bakerlab.org/cplx.php?mode=ecoli
Download ecoli_paired_alignments.zip (177.3 Mb)
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Title PDB benchmark alignments
Downloaded 44 times
Description Multiple sequence alignments used for the PDB benchmark set. Each fasta file begins with the PDB amino acid sequence pair, with other homologous sequences trimmed to match its length. For an interactive list, please visit: http://gremlin.bakerlab.org/cplx.php?mode=pdb
Download PDB_benchmark_alignments.zip (11.92 Mb)
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Title PDB benchmark alignments NDX
Downloaded 32 times
Description Multiple sequence alignments used for the PDB benchmark set. This set is restricted to the NADH dehydrogenase complex. Each fasta file begins with the T. thermophilus amino acid sequence pair, with other homologous sequences trimmed to match its length. For an interactive list, please visit: http://gremlin.bakerlab.org/cplx.php?mode=ndx
Download PDB_benchmark_alignments_NDX.zip (47.52 Mb)
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When using this data, please cite the original publication:

Ovchinnikov S, Kamisetty H, Baker D (2014) Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 3: e02030. http://dx.doi.org/10.7554/eLife.02030

Additionally, please cite the Dryad data package:

Ovchinnikov S, Kamisetty H, Baker D (2014) Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.s00vr
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