DOI: 10.5061/dryad.s00vr
title: Data from: Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information

description: Do the amino acid sequence identities of residues that make contact across
 protein interfaces covary during evolution? If so, such covariance could
 be used to predict contacts across interfaces and assemble models of
 biological complexes. We find that residue pairs identified using a
 pseudo-likelihood based method to covary across protein-protein interfaces
 in the 50S ribosomal unit and 28 additional bacterial protein complexes
 with known structure are almost always in contact in the complex provided
 that the number of aligned sequences is greater than the average of the
 lengths of the two proteins. We use this method to make subunit contact
 predictions for an additional 36 protein complexes with unknown
 structures, and present models based on these predictions for the
 tripartite ATP-independent periplasmic (TRAP) transporter, the tripartite
 efflux system, the pyruvate formate lyase-activating enzyme complex, and
 the methionine ABC transporter.
description: PDB file for TRAP
 complexThe 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.YIA_MNO.pdbPDB file for D-methionine transport systemPredicted 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.METI_METQ.pdbPDB file for Tripartite efflux systemPredicted 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.MDTP_MDTN.pdbPDB file for PFL ComplexPredicted 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.PFLA_PFLB.pdbRibosome 50S alignmentsMultiple 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=riboribosome_50S_alignments.zipE. coli paired alignmentsMultiple 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=ecoliecoli_paired_alignments.zipPDB benchmark alignmentsMultiple 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=pdbPDB_benchmark_alignments.zipPDB benchmark alignments NDXMultiple 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=ndxPDB_benchmark_alignments_NDX.zip