Large-scale determination of previously unsolved protein structures using evolutionary information

TM-align: a protein structure alignment algorithm based on the TM-score

Zhang, Y. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki524 · Cited by 3,774 · see citing works

Structure and function of the global ocean microbiome

Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., et al. (2015) · Science · doi:10.1126/science.1261359 · Cited by 2,945 · see citing works

Scoring function for automated assessment of protein structure template quality

Zhang, Y., & Skolnick, J. (2004) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.20264 · Cited by 2,392 · see citing works

Protein homology detection by HMM–HMM comparison

Söding, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti125 · Cited by 2,381 · see citing works

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

Remmert, M., Biegert, A., Hauser, A., & Söding, J. (2012) · Nature Methods · doi:10.1038/nmeth.1818 · Cited by 2,288 · see citing works

Activities at the Universal Protein Resource (UniProt)

The UniProt Consortium (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1140 · Cited by 1,736 · see citing works

Protein Structure Prediction Using Rosetta

Rohl, C. A., Strauss, C. E. M., Misura, K. M. S., & Baker, D. A. (2004) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(04)83004-0 · Cited by 1,711 · see citing works

PISCES: a protein sequence culling server

Wang, G., & Dunbrack, R. L. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg224 · Cited by 1,664 · see citing works

UniRef: comprehensive and non-redundant UniProt reference clusters

Suzek, B. E., Huang, H., McGarvey, P., Mazumder, R., & Wu, C. H. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm098 · Cited by 1,613 · see citing works

X-ray structure of a ClC chloride channel at 3.0 Å reveals the molecular basis of anion selectivity

Dutzler, R., Campbell, E., Cadene, M., Chait, B., & MacKinnon, R. (2002) · Nature · doi:10.1038/415287a · Cited by 1,567 · see citing works

Expanded microbial genome coverage and improved protein family annotation in the COG database

Galperin, M. Y., Makarova, K. S., Wolf, Y. I., & Koonin, E. V. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1223 · Cited by 1,547 · see citing works

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Morcos, F., Pagnani, A., Lunt, B., Bertolino, A., Marks, D. S., Sander, C., Zecchina, R., Onuchic, J. N., Hwa, T., & Weigt, M. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1111471108 · Cited by 1,434 · see citing works

Molecules as documents of evolutionary history

Zuckerkandl, E., & Pauling, L. C. (1965) · Journal of Theoretical Biology · doi:10.1016/0022-5193(65)90083-4 · Cited by 1,359 · see citing works

A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE

Eddy, S. R. (2009) · International Conference on Genome Informatics (GIW) · doi:10.1142/9781848165632_0019 · Cited by 1,275 · see citing works

Protein 3D Structure Computed from Evolutionary Sequence Variation

Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144 · see citing works

High-Resolution Comparative Modeling with RosettaCM

Song, Y., DiMaio, F., Wang, R. Y., Kim, D. E., Miles, C., Brunette, T., Thompson, J., & Baker, D. A. (2013) · Structure · doi:10.1016/j.str.2013.08.005 · Cited by 1,079 · see citing works

Macromolecular Modeling with Rosetta

Das, R., & Baker, D. A. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.77.062906.171838 · Cited by 995 · see citing works

Structure of a glutamate transporter homologue from Pyrococcus horikoshii

Yernool, D., Boudker, O., Jin, Y., & Gouaux, E. (2004) · Nature · doi:10.1038/nature03018 · Cited by 784 · see citing works

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

Jones, D. T., Buchan, D. W. A., Cozzetto, D., & Pontil, M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr638 · Cited by 760 · see citing works

Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era

Kamisetty, H., Ovchinnikov, S., & Baker, D. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1314045110 · Cited by 672 · see citing works

Lipid–protein interactions in double-layered two-dimensional AQP0 crystals

Gonen, T., Cheng, Y., Piotr Sliz, A., Hiroaki, Y., Fujiyoshi, Y., Harrison, S. C., & Walz, T. (2005) · Nature · doi:10.1038/nature04321 · Cited by 663 · see citing works

Improved contact prediction in proteins: using pseudolikelihoods to infer Potts models

Ekeberg, M., Lövkvist, C., Lan, Y., Weigt, M., & Aurell, E. (2013) · Physical Review E · doi:10.1103/physreve.87.012707 · Cited by 661 · see citing works

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

Ovchinnikov, S., Kamisetty, H., & Baker, D. (2014) · eLife · doi:10.7554/elife.02030 · Cited by 629 · see citing works

Protein structure prediction from sequence variation

Marks, D. S., Hopf, T. A., & Sander, C. (2012) · Nature Biotechnology · doi:10.1038/nbt.2419 · Cited by 622 · see citing works

AL2CO: calculation of positional conservation in a protein sequence alignment

Pei, J.-M., & Grishin, N. (2001) · Bioinform. · doi:10.1093/bioinformatics/17.8.700 · Cited by 518 · see citing works

Sequence co-evolution gives 3D contacts and structures of protein complexes

Hopf, T. A., Schärfe, C. P. I., Rodrigues, J. P. G. L. M., Green, A. G., Kohlbacher, O., Sander, C., Bonvin, A. M. J. J., & Marks, D. S. (2014) · eLife · doi:10.7554/elife.03430 · Cited by 515 · see citing works

Structure prediction for CASP8 with all‐atom refinement using Rosetta

Raman, S., Vernon, R. M., Thompson, J., Tyka, M. D., Sadreyev, R. I., Pei, J., Kim, D. E., Kellogg, E. H., DiMaio, F., Lange, O. F., et al. (2009) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.22540 · Cited by 511 · see citing works

The cytochrome bd respiratory oxygen reductases

Borisov, V. B., Gennis, R. B., Hemp, J., & Verkhovsky, M. I. (2011) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2011.06.016 · Cited by 508 · see citing works

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

Hopf, T. A., Colwell, L. J., Sheridan, R., Rost, B., Sander, C., & Marks, D. S. (2012) · Cell · doi:10.1016/j.cell.2012.04.012 · Cited by 501 · see citing works

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

Seemayer, S., Gruber, M., & Söding, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu500 · Cited by 416 · see citing works

Common structural features of mapeg—a widespread superfamily of membrane associated proteins with highly divergent functions in eicosanoid and glutathione metabolism

Jakobsson, P., Morgenstern, R., Mancini, J. A., Ford‐Hutchinson, A. W., & Persson, B. (1999) · Protein Science · doi:10.1110/ps.8.3.689 · Cited by 366 · see citing works

Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates

Yang, Y., Faraggi, E., Zhao, H., & Zhou, Y. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr350 · Cited by 325 · see citing works

Learning generative models for protein fold families

Balakrishnan, S., Kamisetty, H., Carbonell, J. G., Lee, S., & Langmead, C. J. (2011) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.22934 · Cited by 316 · see citing works

Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2

Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., & Gray, J. J. (2011) · PLoS ONE · doi:10.1371/journal.pone.0022477 · Cited by 306 · see citing works

A two-domain elevator mechanism for sodium/proton antiport

Lee, C., Kang, H. J., von Ballmoos, C., Newstead, S. L., Uzdavinys, P., Dotson, D., Iwata, S., Beckstein, O., Cameron, A. D., & Drew, D. (2013) · Nature · doi:10.1038/nature12484 · Cited by 252 · see citing works

Improved molecular replacement by density- and energy-guided protein structure optimization

DiMaio, F., Terwilliger, T. C., Read, R. J., Wlodawer, A., Oberdorfer, G., Wagner, U. G., Valkov, E., Alon, A., Fass, D., Axelrod, H. L., et al. (2011) · Nature · doi:10.1038/nature09964 · Cited by 246 · see citing works

Genomics-aided structure prediction

Sulkowska, J. I., Morcos, F., Weigt, M., Terence Hwa, B., & Onuchic, J. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207864109 · Cited by 226 · see citing works

Antiparallel EmrE exports drugs by exchanging between asymmetric structures

Morrison, E. A., DeKoster, G. T., Dutta, S., Vafabakhsh, R., Clarkson, M. W., Bahl, A., Kern, D., Ha, T., & Henzler‐Wildman, K. A. (2011) · Nature · doi:10.1038/nature10703 · Cited by 218 · see citing works

<i>Tara</i> Oceans studies plankton at planetary scale

Bork, P., Bowler, C., de Vargas, C., Gorsky, G., Karsenti, E., & Wincker, P. (2015) · Science · doi:10.1126/science.aac5605 · Cited by 217 · see citing works

Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples

Lange, O. F., Rossi, P., Sgourakis, N. G., Song, Y., Lee, H., Aramini, J. M., Ertekin, A., Xiao, R., Acton, T., Montelione, G. T., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1203013109 · Cited by 209 · see citing works

Identification and evolution of dual-topology membrane proteins

Rapp, M., Granseth, E., Seppälä, S., & von HEIJNE, G. (2006) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1057 · Cited by 204 · see citing works

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

Theobald, D. L., & Wuttke, D. S. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl332 · Cited by 194 · see citing works

GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli

Hommais, F., Krin, E., Coppée, J., Lacroix, C., Yeramian, E., Danchin, A., & Bertin, P. (2003) · Microbiology · doi:10.1099/mic.0.26659-0 · Cited by 182 · see citing works

Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis

Nugent, T., & Jones, D. T. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120036109 · Cited by 174 · see citing works

Identification of Multiple Genes Encoding Membrane Proteins with Undecaprenyl Pyrophosphate Phosphatase (UppP) Activity in Escherichia coli

Ghachi, M. E., Derbise, A., Bouhss, A., & Mengin‐Lecreulx, D. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m412277200 · Cited by 173 · see citing works

Mechanism of farnesylated CAAX protein processing by the intramembrane protease Rce1

Manolaridis, I., Kulkarni, K. A., Dodd, R. B., Ogasawara, S., Zhang, Z., Bineva‐Todd, G., O’Reilly, N., Hanrahan, S. J., Thompson, A., Cronin, N., et al. (2013) · Nature · doi:10.1038/nature12754 · Cited by 169 · see citing works

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases.

Anantharaman, V., Koonin, E. V., & Aravind, L. (2002) · PubMed · Cited by 146 · see citing works

Discontinuous membrane helices in transport proteins and their correlation with function

Screpanti, E., & Hunte, C. (2007) · Journal of Structural Biology · doi:10.1016/j.jsb.2007.01.011 · Cited by 139 · see citing works

Quasi-symmetry in the Cryo-EM Structure of EmrE Provides the Key to Modeling its Transmembrane Domain

Fleishman, S. J., Harrington, S. E., Enosh, A., Halperin, D., Tate, C. G., & Ben‐Tal, N. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.08.072 · Cited by 127 · see citing works

Evidence for a novel protease governing regulated intramembrane proteolysis and resistance to antimicrobial peptides in Bacillus subtilisPreprint

Ellermeier, C. D., & Losick, R. M. (2006) · Genes & Development · doi:10.1101/gad.1440606 · Cited by 125 · see citing works

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

Hopf, T. A., Morinaga, S., Ihara, S., Touhara, K., Marks, D. S., & Benton, R. (2015) · Nature Communications · doi:10.1038/ncomms7077 · Cited by 118 · see citing works

The integral membrane FtsW protein and peptidoglycan synthase PBP3 form a subcomplex in Escherichia coli

Fraipont, C., Alexeeva, S., Wolf, B., van der Ploeg, R., Schloesser, M., den Blaauwen, T., & Nguyen‐Distèche, M. (2010) · Microbiology · doi:10.1099/mic.0.040071-0 · Cited by 116 · see citing works

Crystal structures of an archaeal oligosaccharyltransferase provide insights into the catalytic cycle of N-linked protein glycosylation

Matsumoto, S., Shimada, A., Nyirenda, J., Igura, M., Kawano, Y., & Kohda, D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1309777110 · Cited by 105 · see citing works

Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation

Tian, P., Boomsma, W., Wang, Y., Otzen, D. E., Jensen, M. H., & Lindorff‐Larsen, K. (2014) · Journal of the American Chemical Society · doi:10.1021/ja5093634 · Cited by 105 · see citing works

Prediction of loop geometries using a generalized born model of solvation effects

Rapp, C. S., & Friesner, R. A. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990501)35:2 · Cited by 103 · see citing works

Crystal Structures of Aconitase with Trans-aconitate and Nitrocitrate Bound

Lauble, H., Kennedy, M. C., Beinert, H., & Stout, C. D. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1246 · Cited by 93 · see citing works

One contact for every twelve residues allows robust and accurate topology‐level protein structure modeling

Kim, D. E., DiMaio, F., Wang, R. Y., Song, Y., & Baker, D. A. (2013) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24374 · Cited by 90 · see citing works

A structural model of the active ribosome-bound membrane protein insertase YidC

Wickles, S., Singharoy, A., Andréani, J., Seemayer, S., Bischoff, L., Berninghausen, O., Söding, J., Schulten, K. J., van der Sluis, E. O., & Beckmann, R. (2014) · eLife · doi:10.7554/elife.03035 · Cited by 86 · see citing works

CREST - a large and diverse superfamily of putative transmembrane hydrolases

Pei, J., Millay, D. P., Olson, E. N., & Grishin, N. V. (2011) · Biology Direct · doi:10.1186/1745-6150-6-37 · Cited by 84 · see citing works

Amino acid preferences at protein binding sites

Villar, H. O., & Kauvar, L. M. (1994) · FEBS Letters · doi:10.1016/0014-5793(94)00648-2 · Cited by 83 · see citing works

SATP (YaaH), a succinate–acetate transporter protein in Escherichia coli

Sá‐Pessoa, J., Paiva, S., Ribas, D. M. N., Silva, I. J., Viegas, S. C., Arraiano, C. M., & Casal, M. (2013) · Biochemical Journal · doi:10.1042/bj20130412 · Cited by 80 · see citing works

Expansion of Type II CAAX Proteases Reveals Evolutionary Origin of γ-Secretase Subunit APH-1

Pei, J., Mitchell, D. A., Dixon, J. E., & Grishin, N. V. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.04.066 · Cited by 68 · see citing works

Contributions to the NIH-NIGMS Protein Structure Initiative from the PSI Production Centers

Burley, S. K., Joachimiak, A., Montelione, G. T., & Wilson, I. A. (2008) · Structure · doi:10.1016/j.str.2007.12.002 · Cited by 67 · see citing works

Computation and Functional Studies Provide a Model for the Structure of the Zinc Transporter hZIP4

Antala, S., Ovchinnikov, S., Kamisetty, H., Baker, D. A., & Dempski, R. E. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.617613 · Cited by 65 · see citing works

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

Thomas, A. M., Hinsen, K., Field, M. J., & Pérahia, D. (1999) · Proteins Structure Function and Bioinformatics · doi:10.1002/(sici)1097-0134(19990101)34:1 · Cited by 64 · see citing works

Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB

Xu, Q., & Dunbrack, R. L. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts533 · Cited by 64 · see citing works

All-atom 3D structure prediction of transmembrane β-barrel proteins from sequences

Hayat, S., Sander, C., Marks, D. S., & Elofsson, A. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419956112 · Cited by 50 · see citing works

Phosphatidylglycerol::Prolipoprotein Diacylglyceryl Transferase (Lgt) of Escherichia coli Has Seven Transmembrane Segments, and Its Essential Residues Are Embedded in the Membrane

Pailler, J., Aucher, W., Pires, M., & Buddelmeijer, N. (2012) · Journal of Bacteriology · doi:10.1128/jb.06641-11 · Cited by 50 · see citing works

INVERTED TOPOLOGIES IN MEMBRANE PROTEINS: A MINI-REVIEW

Duran, A. M., & Meiler, J. (2013) · Computational and Structural Biotechnology Journal · doi:10.5936/csbj.201308004 · Cited by 43 · see citing works

Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase from Escherichia coli

Chang, H. Y., Chou, C., Hsu, M.-F., & Wang, A. H. ‐. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.575076 · Cited by 42 · see citing works

Identification of the L-tartrate dehydratase genes (ttdA and ttdB) of Escherichia coli and evolutionary relationship with the Class I fumarase genes

Reaney, S. K., Begg, C. B., Bungard, S. J., & Guest, J. R. (1993) · Journal of General Microbiology · doi:10.1099/00221287-139-7-1523 · Cited by 40 · see citing works

The structure of membrane associated proteins in eicosanoid and glutathione metabolism as determined by electron crystallography

Hebert, H., & Jegerschöld, C. (2007) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2007.07.008 · Cited by 31 · see citing works

Homology relationship between the messenger RNA and heterogenous nuclear RNA of mouse L cells. A DNA excess hybridization study

HAMES, B. D., & Perry, R. P. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80022-3 · Cited by 31 · see citing works

Analysis of two domains with novel RNA-processing activities throws light on the complex evolution of ribosomal RNA biogenesis

Burroughs, A. M., & Aravind, L. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00424 · Cited by 27 · see citing works

JDet: interactive calculation and visualization of function-related conservation patterns in multiple sequence alignments and structures

Muth, T., García-Martín, J. A., Rausell, A., Juan, D., Valencia, A., & Pazos, F. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr688 · Cited by 23 · see citing works

Conserved evolutionary units in the heme‐copper oxidase superfamily revealed by novel homologous protein families

Pei, J., Li, W., Kinch, L. N., & Grishin, N. V. (2014) · Protein Science · doi:10.1002/pro.2503 · Cited by 11 · see citing works

Homology- and coevolution-consistent structural models of bacterial copper-tolerance protein CopM support a ‘metal sponge’ function and suggest regions for metal-dependent protein-protein interactionsPreprint

Abriata, L. A. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/013581 · Cited by 9 · see citing works

Climate science: Rising tide

Jones, N. (2013) · Nature · doi:10.1038/501300a · Cited by 6 · see citing works

Data from: Large scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L. N., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. A. (2015) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.987j0 · Cited by 1 · see citing works

Highly accurate protein structure prediction for the human proteome

Tunyasuvunakool, K., Adler, J., Wu, Z., Green, T., Zielinski, M., Žídek, A., Bridgland, A., Cowie, A., Meyer, C., Laydon, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03828-1 · Cited by 3,025 · see citing works

The coming of age of de novo protein design

Huang, P.-S., Boyken, S. E., & Baker, D. (2016) · Nature · doi:10.1038/nature19946 · Cited by 1,478 · see citing works

Unified rational protein engineering with sequence-based deep representation learning

Alley, E. C., Khimulya, G., Biswas, S., AlQuraishi, M., & Church, G. M. (2019) · Nature Methods · doi:10.1038/s41592-019-0598-1 · Cited by 1,131 · see citing works

Advances in protein structure prediction and design

Kuhlman, B., & Bradley, P. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0163-x · Cited by 806 · see citing works

Mutation effects predicted from sequence co-variation

Hopf, T. A., Ingraham, J. B., Poelwijk, F. J., Schärfe, C. P. I., Springer, M., Sander, C., & Marks, D. S. (2017) · Nature Biotechnology · doi:10.1038/nbt.3769 · Cited by 775 · see citing works

Deep generative models of genetic variation capture the effects of mutations

Riesselman, A. J., Ingraham, J. B., & Marks, D. S. (2018) · Nature Methods · doi:10.1038/s41592-018-0138-4 · Cited by 601 · see citing works

Epistasis in protein evolution

Starr, T. N., & Thornton, J. W. (2016) · Protein Science · doi:10.1002/pro.2897 · Cited by 575 · see citing works

Sampling alternative conformational states of transporters and receptors with AlphaFold2

del Alamo, D., Sala, D., Mchaourab, H. S., & Meiler, J. (2022) · eLife · doi:10.7554/elife.75751 · Cited by 511 · see citing works

Molecular Mechanisms of Two-Component Signal Transduction

Zschiedrich, C. P., Keidel, V., & Szurmant, H. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.08.003 · Cited by 540 · see citing works

Protein structure determination using metagenome sequence data

Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science · doi:10.1126/science.aah4043 · Cited by 520 · see citing works

FtsW is a peptidoglycan polymerase that is functional only in complex with its cognate penicillin-binding protein

Taguchi, A., Welsh, M. A., Marmont, L. S., Lee, W., Sjodt, M., Kruse, A. C., Kahne, D. E., Bernhardt, T. G., & Walker, S. (2019) · Nature Microbiology · doi:10.1038/s41564-018-0345-x · Cited by 335 · see citing works

Protein interaction networks revealed by proteome coevolution

Cong, Q., Anishchenko, I., Ovchinnikov, S., & Baker, D. (2019) · Science · doi:10.1126/science.aaw6718 · Cited by 241 · see citing works

The EVcouplings Python framework for coevolutionary sequence analysis

Hopf, T. A., Green, A. G., Schubert, B., Mersmann, S., Schärfe, C., Ingraham, J., Tóth-Petróczy, Á., Brock, K. P., Riesselman, A. J., Palmedo, P., et al. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty862 · Cited by 286 · see citing works

The electron's spin and molecular chirality – how are they related and how do they affect life processes?

Michaeli, K., Kantor-Uriel, N., Naaman, R., & Waldeck, D. H. (2016) · Chemical Society Reviews · doi:10.1039/c6cs00369a · Cited by 291 · see citing works

Crystal structure of the human sterol transporter ABCG5/ABCG8

Lee, J., Kinch, L. N., Borek, D., Wang, J., Wang, J., Urbatsch, I. L., Xie, X., Grishin, N. V., Cohen, J. C., Otwinowski, Z., et al. (2016) · Nature · doi:10.1038/nature17666 · Cited by 271 · see citing works

Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex

Wu, X., Siggel, M., Ovchinnikov, S., Mi, W., Svetlov, V. V., Nudler, E., Liao, M., Hummer, G., & Rapoport, T. A. (2020) · Science · doi:10.1126/science.aaz2449 · Cited by 236 · see citing works

Architectures of Lipid Transport Systems for the Bacterial Outer Membrane

Ekiert, D. C., Bhabha, G., Isom, G. L., Greenan, G. A., Ovchinnikov, S., Henderson, I. R., Cox, J. S., & Vale, R. D. (2017) · Cell · doi:10.1016/j.cell.2017.03.019 · Cited by 221 · see citing works

Chirality-induced spin polarization places symmetry constraints on biomolecular interactions

Kumar, A., Capua, E., Kesharwani, M., Martin, J. M. L., Sitbon, E., Waldeck, D., & Naaman, R. (2017) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1611467114 · Cited by 210 · see citing works

Protocols for Molecular Modeling with Rosetta3 and RosettaScripts

Bender, B. J., Cisneros, A., Duran, A. M., Finn, J. A., Fu, D., Lokits, A. D., Mueller, B. K., Sangha, A. K., Sauer, M. F., Sevy, A. M., et al. (2016) · Biochemistry · doi:10.1021/acs.biochem.6b00444 · Cited by 206 · see citing works

Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3

Schoebel, S., Mi, W., Stein, A., Ovchinnikov, S., Pavlovicz, R. E., DiMaio, F., Baker, D. A., Chambers, M. G., Su, H., Li, D., et al. (2017) · Nature · doi:10.1038/nature23314 · Cited by 196 · see citing works

Structures of the stator complex that drives rotation of the bacterial flagellum

Deme, J. C., Johnson, S., Vickery, O. N., Aron, A., Monkhouse, H., Griffiths, T., James, R. H., Berks, B. C., Coulton, J. W., Stansfeld, P. J., et al. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0788-8 · Cited by 196 · see citing works

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures

Kappel, K., Zhang, K., Su, Z., Watkins, A. M., Kladwang, W., Li, S., Pintilie, G. D., Topkar, V. V., Rangan, R., Zheludev, I. N., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0878-9 · Cited by 182 · see citing works

RodA as the missing glycosyltransferase in Bacillus subtilis and antibiotic discovery for the peptidoglycan polymerase pathway

Emami, K., Guyet, A., Kawai, Y., Devi, J., Wu, L. J., Allenby, N., Daniel, R. A., & Errington, J. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.253 · Cited by 187 · see citing works

Origins of coevolution between residues distant in protein 3D structures

Anishchenko, I., Ovchinnikov, S., Kamisetty, H., & Baker, D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1702664114 · Cited by 185 · see citing works

Structure of the core of the type III secretion system export apparatus

Kuhlen, L., Abrusci, P., Johnson, S., Gault, J., Deme, J. C., Caesar, J. J. E., Dietsche, T., Mebrhatu, M. T., Ganief, T. A., Maček, B., et al. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0086-9 · Cited by 175 · see citing works

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases

Safarian, S., Rajendran, C., Müller, H., Preu, J., Langer, J. D., Ovchinnikov, S., Hirose, T., Kusumoto, T., Sakamoto, J., & Michel, H. (2016) · Science · doi:10.1126/science.aaf2477 · Cited by 163 · see citing works

Inferring protein 3D structure from deep mutation scans

Rollins, N. J., Brock, K. P., Poelwijk, F. J., Stiffler, M. A., Gauthier, N. P., Sander, C., & Marks, D. S. (2019) · Nature Genetics · doi:10.1038/s41588-019-0432-9 · Cited by 163 · see citing works

Deep Learning in Proteomics

Wen, B., Zeng, W., Liao, Y., Shi, Z., Savage, S. R., Jiang, W., & Zhang, B. (2020) · PROTEOMICS · doi:10.1002/pmic.201900335 · Cited by 152 · see citing works

Determining protein structures using deep mutagenesis

Schmiedel, J. M., & Lehner, B. (2019) · Nature Genetics · doi:10.1038/s41588-019-0431-x · Cited by 145 · see citing works

Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness

Levy, R. M., Haldane, A., & Flynn, W. F. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.11.004 · Cited by 134 · see citing works

Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis

Sjodt, M., Brock, K. P., Dobihal, G. S., Rohs, P. D. A., Green, A. G., Hopf, T. A., Meeske, A. J., Srisuknimit, V., Kahne, D. E., Walker, S., et al. (2018) · Nature · doi:10.1038/nature25985 · Cited by 132 · see citing works

Harnessing Conformational Plasticity to Generate Designer Enzymes

Crean, R., Gardner, J. M., & Kamerlin, S. C. L. (2020) · Journal of the American Chemical Society · doi:10.1021/jacs.0c04924 · Cited by 129 · see citing works

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Safarian, S., Hahn, A. S., Mills, D. J., Radloff, M., Eisinger, M., Nikolaev, A., Meier‐Credo, J., Melin, F., Miyoshi, H., Gennis, R. B., et al. (2019) · Science · doi:10.1126/science.aay0967 · Cited by 127 · see citing works

A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW

Yang, X., McQuillen, R. J., Lyu, Z., Phillips‐Mason, P. J., Cruz, A. D. L., McCausland, J. W., Liang, H., DeMeester, K. E., Santiago, C. C., Grimes, C. L., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-020-00853-0 · Cited by 115 · see citing works

Large-scale discovery of protein interactions at residue resolution using co-evolution calculated from genomic sequences

Green, A. G., Elhabashy, H., Brock, K. P., Maddamsetti, R., Kohlbacher, O., & Marks, D. S. (2021) · Nature Communications · doi:10.1038/s41467-021-21636-z · Cited by 114 · see citing works

Interplay between Penicillin-binding proteins and SEDS proteins promotes bacterial cell wall synthesis

Leclercq, S., Derouaux, A., Olatunji, S., Fraipont, C., Egan, A. J. F., Vollmer, W., Breukink, E. J., & Terrak, M. (2017) · Scientific Reports · doi:10.1038/srep43306 · Cited by 113 · see citing works

Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta

Ovchinnikov, S., Kim, D. E., Wang, R. Y., Liu, Y., DiMaio, F., & Baker, D. A. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24974 · Cited by 111 · see citing works

Molecular structure of the intact bacterial flagellar basal body

Johnson, S., Furlong, E., Deme, J. C., Nord, A. L., Caesar, J. J. E., Chevance, F. F. V., Berry, R. M., Hughes, K. T., & Lea, S. M. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00895-y · Cited by 109 · see citing works

Large-scale identification of coevolution signals across homo-oligomeric protein interfaces by direct coupling analysis

Uguzzoni, G., Lovis, S. J., Oteri, F., Schug, A. H., Szurmant, H., & Weigt, M. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1615068114 · Cited by 108 · see citing works

Deciphering protein evolution and fitness landscapes with latent space models

Ding, X., Zou, Z., & Brooks III, C. L. (2019) · Nature Communications · doi:10.1038/s41467-019-13633-0 · Cited by 106 · see citing works

Protein structure prediction using Rosetta in CASP12

Ovchinnikov, S., Park, H., Kim, D. E., DiMaio, F., & Baker, D. A. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25390 · Cited by 105 · see citing works

Biogenesis and functions of aminocarboxypropyluridine in tRNA

Takakura, M., Ishiguro, K., Akichika, S., Miyauchi, K., & Suzuki, T. (2019) · Nature Communications · doi:10.1038/s41467-019-13525-3 · Cited by 94 · see citing works

Assessment of hard target modeling in CASP12 reveals an emerging role of alignment‐based contact prediction methods

Abriata, L. A., Tamò, G. E., Monastyrskyy, B., Kryshtafovych, A., & Peraro, M. D. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25423 · Cited by 90 · see citing works

Protein contact prediction using metagenome sequence data and residual neural networks

Wu, Q., Peng, Z., Anishchenko, I. V., Cong, Q., Baker, D. A., & Yang, J. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz477 · Cited by 86 · see citing works

Structure of bacterial phospholipid transporter MlaFEDB with substrate bound

Coudray, N., Isom, G. L., MacRae, M. R., Saiduddin, M. N., Bhabha, G., & Ekiert, D. C. (2020) · eLife · doi:10.7554/elife.62518 · Cited by 76 · see citing works

Computational approaches to investigating allostery

Schueler‐Furman, O., & Wodak, S. J. (2016) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2016.06.017 · Cited by 72 · see citing works

DESTINI: A deep-learning approach to contact-driven protein structure prediction

Gao, M., Zhou, H., & Skolnick, J. (2019) · Scientific Reports · doi:10.1038/s41598-019-40314-1 · Cited by 61 · see citing works

Structure of the type VI secretion system TssK–TssF–TssG baseplate subcomplex revealed by cryo-electron microscopy

Park, Y., LaCourse, K. D., Cambillau, C., DiMaio, F., Mougous, J. D., & Veesler, D. (2018) · Nature Communications · doi:10.1038/s41467-018-07796-5 · Cited by 61 · see citing works

Crystal structure of undecaprenyl-pyrophosphate phosphatase and its role in peptidoglycan biosynthesis

Ghachi, M. E., Howe, N., Huang, C., Oliéric, V., Warshamanage, R., Touzé, T., Weichert, D., Stansfeld, P. J., Wang, M., Kerff, F., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03477-5 · Cited by 58 · see citing works

Structural and Evolutionary Insights Point to Allosteric Regulation of TRP Ion Channels

Hilton, J. K., Kim, M., & Horn, W. D. V. (2019) · Accounts of Chemical Research · doi:10.1021/acs.accounts.9b00075 · Cited by 56 · see citing works

AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures

Tejero, R., Huang, Y. J., Ramelot, T. A., & Montelione, G. T. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.877000 · Cited by 56 · see citing works

Crystal structure of an intramembranal phosphatase central to bacterial cell-wall peptidoglycan biosynthesis and lipid recycling

Workman, S. D., Worrall, L. J., & Strynadka, N. C. J. (2018) · Nature Communications · doi:10.1038/s41467-018-03547-8 · Cited by 54 · see citing works

The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development

Doroshkov, A. V., Konstantinov, D. K., Afonnikov, D. A., & Владимирович, Г. К. (2019) · BMC Plant Biology · doi:10.1186/s12870-019-1640-2 · Cited by 54 · see citing works

Inferring interaction partners from protein sequences using mutual information

Bitbol, A. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006401 · Cited by 54 · see citing works

Assessment of prediction methods for protein structures determined by <scp>NMR</scp> in <scp>CASP14</scp> : Impact of <scp>AlphaFold2</scp>

Huang, Y. J., Zhang, N., Bersch, B., Fidelis, K., Inouye, M., Ishida, Y., Kryshtafovych, A., Kobayashi, N., Kuroda, Y., Liu, G., et al. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26246 · Cited by 49 · see citing works

Structure determination of the HgcAB complex using metagenome sequence data: insights into microbial mercury methylation

Cooper, C. J., Zheng, K., Rush, K. W., Johs, A., Sanders, B., Pavlopoulos, G. A., Kyrpides, N. C., Podar, M., Ovchinnikov, S., Ragsdale, S. W., et al. (2020) · Communications Biology · doi:10.1038/s42003-020-1047-5 · Cited by 53 · see citing works

Enzyme structures of the bacterial peptidoglycan and wall teichoic acid biogenesis pathways

Caveney, N. A., Li, F. K. K., & Strynadka, N. C. J. (2018) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2018.05.002 · Cited by 53 · see citing works

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

Shamsi, Z., Moffett, A. S., & Shukla, D. (2017) · Scientific Reports · doi:10.1038/s41598-017-12874-7 · Cited by 60 · see citing works

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

Berman, H. M., Adams, P. D., Bonvin, A. M. J. J., Burley, S. K., Carragher, B. O., Chiu, W., DiMaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., et al. (2019) · Structure · doi:10.1016/j.str.2019.11.002 · Cited by 49 · see citing works

Crystal structure of the bacterial acetate transporter SatP reveals that it forms a hexameric channel

Sun, P., Li, J., Zhang, X., Guan, Z., Xiao, Q., Zhao, C., Song, M., Zhou, Y., Mou, L., Ke, M., et al. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.003876 · Cited by 47 · see citing works

Genetic analysis of the septal peptidoglycan synthase FtsWI complex supports a conserved activation mechanism for SEDS-bPBP complexes

Li, Y., Gong, H., Zhan, R., Ouyang, S., Park, K., Lutkenhaus, J., & Du, S. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009366 · Cited by 46 · see citing works

A Slippery Scaffold: Synthesis and Recycling of the Bacterial Cell Wall Carrier Lipid

Workman, S. D., & Strynadka, N. C. J. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.03.025 · Cited by 45 · see citing works

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

Chan, Y. H., Venev, S. V., Zeldovich, K. B., & Matthews, C. R. (2017) · Nature Communications · doi:10.1038/ncomms14614 · Cited by 44 · see citing works

Complex Relationships between Chromatin Accessibility, Sequence Divergence, and Gene Expression in Arabidopsis thaliana

Alexandre, C. M., Urton, J. R., Jean-Baptiste, K., Huddleston, J., Dorrity, M. W., Cuperus, J. T., Sullivan, A. M., Bemm, F., Jolić, D., Arsovski, A. A., et al. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx326 · Cited by 44 · see citing works

Protein sequence‐to‐structure learning: Is this the end(‐to‐end revolution)?

Laine, E., Eismann, S., Elofsson, A., & Grudinin, S. (2021) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.26235 · Cited by 44 · see citing works

Applications of contact predictions to structural biology

Šimkovic, F., Ovchinnikov, S., Baker, D. A., & Rigden, D. J. (2017) · IUCrJ · doi:10.1107/s2052252517005115 · Cited by 42 · see citing works

Protein structural motifs in prediction and design

Mackenzie, C. O., & Grigoryan, G. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.03.012 · Cited by 42 · see citing works

Large-scale structure prediction by improved contact predictions and model quality assessment

Michel, M., Hurtado, D. M., Uziela, K., & Elofsson, A. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx239 · Cited by 41 · see citing works

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter

Davies, J. S., Currie, M. J., North, R. A., Scalise, M., Wright, J. D., Copping, J. M., Remus, D. M., Gulati, A., Morado, D. R., Jamieson, S. A., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-36590-1 · Cited by 34 · see citing works

Aeromonas species isolated from aquatic organisms, insects, chicken, and humans in India show similar antimicrobial resistance profiles

Dubey, S., Ager-Wick, E., Kumar, J., Karunasagar, I., Karunasagar, I., Peng, B., Evensen, Ø., Sørum, H. R., & Munang’andu, H. M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1008870 · Cited by 39 · see citing works

A lipophilicity-based energy function for membrane-protein modelling and design

Weinstein, J. J., Elazar, A., & Fleishman, S. J. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1007318 · Cited by 38 · see citing works

Mi3-GPU: MCMC-based inverse Ising inference on GPUs for protein covariation analysis

Haldane, A., & Levy, R. M. (2020) · Computer Physics Communications · doi:10.1016/j.cpc.2020.107312 · Cited by 38 · see citing works

The FtsLB subcomplex of the bacterial divisome is a tetramer with an uninterrupted FtsL helix linking the transmembrane and periplasmic regions

Condon, S. G. F., Mahbuba, D., Armstrong, C. R., Vázquez, G. D., Craven, S. J., LaPointe, L. M., Khadria, A. S., Chadda, R., Crooks, J. A., Rangarajan, N., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000426 · Cited by 35 · see citing works

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Sahoo, A., Khare, S., Devanarayanan, S., Jain, P. C., & Varadarajan, R. (2015) · eLife · doi:10.7554/elife.09532 · Cited by 36 · see citing works

Big-data approaches to protein structure prediction

Söding, J. (2017) · Science · doi:10.1126/science.aal4512 · Cited by 35 · see citing works

Inner membrane proteins YgdD and SbmA are required for the complete susceptibility of Escherichia coli to the proline-rich antimicrobial peptide arasin 1(1–25)

Paulsen, V. S., Mardirossian, M., Blencke, H., Benincasa, M., Runti, G., Nepa, M., Haug, T., Stensvåg, K., & Scocchi, M. (2016) · Microbiology · doi:10.1099/mic.0.000249 · Cited by 34 · see citing works

Topology Prediction Improvement of α-helical Transmembrane Proteins Through Helix-tail Modeling and Multiscale Deep Learning Fusion

Feng, S., Zhang, W.-X., Yang, J., Yang, Y., & Shen, H. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.12.007 · Cited by 33 · see citing works

Blind assessment of monomeric AlphaFold2 protein structure models with experimental NMR data

Li, E. H., Spaman, L. E., Tejero, R., Huang, Y. J., Ramelot, T. A., Fraga, K. J., Prestegard, J. H., Kennedy, M. A., & Montelione, G. T. (2023) · Journal of Magnetic Resonance · doi:10.1016/j.jmr.2023.107481 · Cited by 33 · see citing works

Modeling of protein conformational changes with Rosetta guided by limited experimental data

Sala, D., del Alamo, D., Mchaourab, H. S., & Meiler, J. (2022) · Structure · doi:10.1016/j.str.2022.04.013 · Cited by 30 · see citing works

Molecular basis of polyspecificity of the Small Multidrug Resistance Efflux Pump AbeS from Acinetobacter baumannii

Lytvynenko, I., Brill, S., Oswald, C., & Pos, K. M. (2015) · Journal of Molecular Biology · doi:10.1016/j.jmb.2015.12.006 · Cited by 31 · see citing works

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

Vorberg, S., Seemayer, S., & Söding, J. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006526 · Cited by 30 · see citing works

Toward high-resolution computational design of the structure and function of helical membrane proteins

Barth, P., & Senes, A. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3231 · Cited by 30 · see citing works

DeepCDpred: Inter-residue distance and contact prediction for improved prediction of protein structure

Ji, S., Oruç, T., Mead, L., Rehman, M. F. U., Thomas, C. M., Butterworth, S., & Winn, P. J. (2019) · PLoS ONE · doi:10.1371/journal.pone.0205214 · Cited by 29 · see citing works

The ghrelin O-acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation

Campaña, M. B., Irudayanathan, F. J., Davis, T. R., McGovern-Gooch, K. R., Loftus, R., Ashkar, M., Escoffery, N., Navarro, M., Sieburg, M. A., Nangia, S., et al. (2019) · Journal of Biological Chemistry · doi:10.1074/jbc.ac119.009749 · Cited by 30 · see citing works

Structural model of human PORCN illuminates disease-associated variants and drug-binding sites

Yu, J., Liao, P.-J., Xu, W., Jones, J. R., Everman, D. B., Flanagan‐Steet, H. R., Keller, T. H., & Virshup, D. M. (2021) · Journal of Cell Science · doi:10.1242/jcs.259383 · Cited by 29 · see citing works

Comparing co-evolution methods and their application to template-free protein structure prediction

de Oliveira, S. H. P., Shi, J., & Deane, C. M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw618 · Cited by 28 · see citing works

A large-scale comparative assessment of methods for residue–residue contact prediction

Wuyun, Q., Zheng, W. H., Peng, Z., & Yang, J. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw106 · Cited by 28 · see citing works

Functional expression and characterization of the envelope glycoprotein E1E2 heterodimer of hepatitis C virus

Cao, L., Yu, B., Kong, D., Cong, Q., Tao, Y., Chen, Z., Hu, Z., Chang, H., Zhong, J., Baker, D. A., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1007759 · Cited by 28 · see citing works

Tools and Approaches for Dissecting Protein Bacteriocin Import in Gram-Negative Bacteria

Atanasković, I., & Kleanthous, C. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00646 · Cited by 28 · see citing works

Co-evolution techniques are reshaping the way we do structural bioinformatics

de Oliveira, S. H. P., & Deane, C. M. (2017) · F1000Research · doi:10.12688/f1000research.11543.1 · Cited by 27 · see citing works

Protein structure prediction: making AWSEM AWSEM‐ER by adding evolutionary restraints

Sirovetz, B. J., Schafer, N. P., & Wolynes, P. G. (2017) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.25367 · Cited by 27 · see citing works

Chemical tools to characterize peptidoglycan synthases

Taguchi, A., Kahne, D. E., & Walker, S. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.07.009 · Cited by 25 · see citing works

Observation selection bias in contact prediction and its implications for structural bioinformatics

Orlando, G., Raimondi, D., & Vranken, W. (2016) · Scientific Reports · doi:10.1038/srep36679 · Cited by 25 · see citing works

SARS-CoV2 billion-compound docking

Rogers, D. O. W., Agarwal, R., Vermaas, J. V., Smith, M. D., Tatikonda, R. R., Cooper, C. J., Sedova, A., Boehm, S., Baker, M. B., Gläser, J., et al. (2023) · Scientific Data · doi:10.1038/s41597-023-01984-9 · Cited by 25 · see citing works

The carboxy-terminal insert in the Q-loop is needed for functionality of Escherichia coli cytochrome bd-I

Goojani, H. G., Konings, J., Hakvoort, H. W. J., Hong, S., Gennis, R. B., Sakamoto, J., Lill, H., & Bald, D. (2020) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2020.148175 · Cited by 24 · see citing works

Structurally Mapping Endogenous Heme in the CcmCDE Membrane Complex for Cytochrome c Biogenesis

Sutherland, M. C., Jarodsky, J. M., Ovchinnikov, S., Baker, D., & Kranz, R. G. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.01.022 · Cited by 23 · see citing works

Roles of the DedD Protein in Escherichia coli Cell Constriction

Liu, B., Hale, C. A., Persons, L., Phillips‐Mason, P. J., & de Boer, P. A. J. (2019) · Journal of Bacteriology · doi:10.1128/jb.00698-18 · Cited by 24 · see citing works

Targeting Lipoprotein Biogenesis: Considerations towards Antimicrobials

Arnaout, T. E., & Soulimane, T. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.03.007 · Cited by 23 · see citing works

Using molecular simulation to explore the nanoscale dynamics of the plant kinome

Moffett, A. S., & Shukla, D. (2018) · Biochemical Journal · doi:10.1042/bcj20170299 · Cited by 24 · see citing works

Co-Evolution of Intrinsically Disordered Proteins with Folded Partners Witnessed by Evolutionary Couplings

Pancsa, R., Zsolyomi, F., & Tompa, P. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19113315 · Cited by 22 · see citing works

Data from: Large scale determination of previously unsolved protein structures using evolutionary information

Ovchinnikov, S., Kinch, L. N., Park, H., Liao, Y., Pei, J., Kim, D. E., Kamisetty, H., Grishin, N. V., & Baker, D. A. (2015) · Data Archiving and Networked Services (DANS) · doi:10.5061/dryad.987j0 · Cited by 1 · see citing works

Improved de novo structure prediction in CASP 11 by incorporating coevolution information into Rosetta

Ovchinnikov, S., Kim, D. E., Wang, R. Y., Liu, Y., DiMaio, F., & Baker, D. A. (2015) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.24974 · Cited by 111 · see citing works

3D Protein Structure Predicted from SequencePreprint

Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · arXiv (Cornell University) · doi:10.48550/arxiv.1110.5091 · Cited by 4 · see citing works

Protein structure determination using metagenome sequence data

Ovchinnikov, S., Park, H., Varghese, N., Huang, P.-S., Pavlopoulos, G. A., Kim, D. E., Kamisetty, H., Kyrpides, N. C., & Baker, D. (2017) · Science · doi:10.1126/science.aah4043 · Cited by 520 · see citing works

State-of-the-art web services for de novo protein structure prediction

Abriata, L. A., & Peraro, M. D. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa139 · Cited by 21 · see citing works