The Pfam Protein Families Database

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302

<tt>BLAT</tt> —The <tt>BLAST</tt> -Like Alignment Tool

Kent, W. J. (2002) · Genome Research · doi:10.1101/gr.229202 · Cited by 8,480

Predicting coiled coils from protein sequences.

Lupas, A., Van Dyke, M., & Stock, J. (1991) · Science · doi:10.1126/science.252.5009.1162 · Cited by 3,953

TreeFam: 2008 update

Ruan, J., Li, H., Chen, Z., Coghlan, A., Coin, L. J. M., Guo, Y., Heriche, J.-K., Hu, Y., Kristiansen, K., Li, R., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1005 · Cited by 332

The ABC Transporter HrtAB Confers Resistance to Hemin Toxicity and Is Regulated in a Hemin-Dependent Manner by the ChrAS Two-Component System in Corynebacterium diphtheriae

Bibb, L. A., & Schmitt, M. P. (2010) · Journal of Bacteriology · doi:10.1128/jb.00525-10 · Cited by 59

The hmuQ and hmuD Genes from Bradyrhizobium japonicum Encode Heme-Degrading Enzymes

Puri, S., & O'Brian, M. R. (2006) · Journal of Bacteriology · doi:10.1128/jb.00737-06 · Cited by 59

Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer

Narayan, S., Bader, G. D., & Reimand, J. (2016) · Genome Medicine · doi:10.1186/s13073-016-0311-2 · Cited by 54

DIALIGN at GOBICS—Multiple sequence alignment using various sources of external information

Al Ait, L., Yamak, Z., & Morgenstern, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt283 · Cited by 58

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

Leyn, S. A., Kazanov, M. D., Sernova, N. V., Ermakova, E. O., Novichkov, P. S., & Rodionov, D. A. (2013) · Journal of Bacteriology · doi:10.1128/jb.00140-13 · Cited by 58

Evolutionary insights into premetazoan functions of the neuronal protein homer

Burkhardt, P., Grønborg, M., McDonald, K., Sulur, T., Wang, Q., & King, N. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu178 · Cited by 56

Mutation screening of SCN2A in schizophrenia and identification of a novel loss-of-function mutation

Carroll, L. S., Woolf, R., Ibrahim, Y., Williams, H. J., Dwyer, S., Walters, J., Kirov, G., O’Donovan, M. C., & Owen, M. J. (2016) · Psychiatric Genetics · doi:10.1097/ypg.0000000000000110 · Cited by 54

Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

Jacquemin, J., Ammiraju, J. S. S., Haberer, G., Billheimer, D. D., Yu, Y., Liu, L. C., Rivera, L. F., Mayer, K., Chen, M., & Wing, R. A. (2014) · Molecular Plant · doi:10.1093/mp/sst149 · Cited by 54

Yeast PPR proteins, watchdogs of mitochondrial gene expression

Herbert, C. J., Golik, P., & Bonnefoy, N. (2013) · RNA Biology · doi:10.4161/rna.25392 · Cited by 54

AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae

Zheng, H.-Q., Chiang-Hsieh, Y.-F., Chien, C.-H., Hsu, B.-K. J., Liu, T.-L., Chen, C.-N. N., & Chang, W.-C. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-196 · Cited by 53

Small protein modules dictate prophage fates during polylysogeny

Silpe, J. E., Duddy, O. P., Johnson, G. E., Beggs, G. A., Hussain, F. A., Forsberg, K. J., & Bassler, B. L. (2023) · Nature · doi:10.1038/s41586-023-06376-y · Cited by 52

The rise and fall of TRP-N, an ancient family of mechanogated ion channels, in Metazoa

Schüler, A., Schmitz, G., Reft, A., Özbek, S., Thurm, U., & Bornberg-Bauer, E. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv091 · Cited by 51

New Insights into Histidine Triad Proteins: Solution Structure of a Streptococcus pneumoniae PhtD Domain and Zinc Transfer to AdcAII

Bersch, B., Bougault, C., Roux, L., Favier, A., Vernet, T., & Durmort, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0081168 · Cited by 49

Two surfaces on the histone chaperone Rtt106 mediate histone binding, replication, and silencing

Zunder, R. M., Antczak, A. J., Berger, J. M., & Rine, J. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1119095109 · Cited by 48

A no X cel : an Anopheles gambiae protein database

Ribeiro, J. M. C., Topalis, P., & Louis, C. (2004) · Insect Molecular Biology · doi:10.1111/j.0962-1075.2004.00503.x · Cited by 45

Discovery of archaeal fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

(2022) · doi:10.1038/s41467-022-31564-1 · Cited by 45

Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium

Yang, C., Lin, F., Li, Q., Li, T., & Zhao, J. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00394 · Cited by 44

Studies on the regulation of the human E1 subunit of the 2-oxoglutarate dehydrogenase complex, including the identification of a novel calcium-binding site

Armstrong, C. T., Anderson, J. L. R., & Denton, R. M. (2014) · Biochemical Journal · doi:10.1042/bj20131664 · Cited by 44

Recognition models to predict DNA-binding specificities of homeodomain proteins

Christensen, R. G., Enuameh, M. S., Noyes, M. B., Brodsky, M. H., Wolfe, S. A., & Stormo, G. D. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts202 · Cited by 42

The identification of response regulator‐specific binding sites reveals new roles of two‐component systems in Bacillus cereus and closely related low‐GC Gram‐positives

de Been, M., Bart, M. J., Abee, T., Siezen, R. J., & Francke, C. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01700.x · Cited by 42

PTMScout, a Web Resource for Analysis of High Throughput Post-translational Proteomics Studies

Naegle, K. M., Gymrek, M., Joughin, B. A., Wagner, J. P., Welsch, R. E., Yaffe, M. B., Lauffenburger, D. A., & White, F. M. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001206 · Cited by 41

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.

Vance, T. D. R., Olijve, L. L. C., Campbell, R. L., Voets, I. K., Davies, P. L., & Guo, S. (2014) · Bioscience Reports · doi:10.1042/bsr20140083 · Cited by 40

Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins

DeBartolo, J., Taipale, M., & Keating, A. E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003693 · Cited by 39

FINDSITEcomb2.0: A New Approach for Virtual Ligand Screening of Proteins and Virtual Target Screening of Biomolecules

Zhou, H., Cao, H., & Skolnick, J. (2018) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.8b00309 · Cited by 39

Putative Monofunctional Type I Polyketide Synthase Units: A Dinoflagellate-Specific Feature?

Eichholz, K., Beszteri, B., & John, U. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048624 · Cited by 37

Discovery of a novel insecticidal protein from Chromobacterium piscinae, with activity against Western Corn Rootworm, Diabrotica virgifera virgifera

Sampson, K., Zaitseva, J., Stauffer, M., Vande Berg, B., Guo, R., Tomso, D., McNulty, B., Desai, N., & Balasubramanian, D. (2017) · Journal of Invertebrate Pathology · doi:10.1016/j.jip.2016.10.004 · Cited by 30

Identification of a covert evolutionary pathway between two protein folds

Chakravarty, D., Sreenivasan, S., Swint-Kruse, L., & Porter, L. L. (2023) · Nature Communications · doi:10.1038/s41467-023-38519-0 · Cited by 29

Sister Dehalobacter Genomes Reveal Specialization in Organohalide Respiration and Recent Strain Differentiation Likely Driven by Chlorinated Substrates

Tang, S., Wang, P. H., Higgins, S. A., Löffler, F. E., & Edwards, E. A. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00100 · Cited by 27

Expression of the Pupal Determinant broad during Metamorphic and Neotenic Development of the Strepsipteran Xenos vesparum Rossi

Erezyilmaz, D. F., Hayward, A., Huang, Y., Paps, J., Acs, Z., Delgado, J. A., Collantes, F., & Kathirithamby, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093614 · Cited by 23

Discovery of archaeal Fusexins homologous to eukaryotic HAP2/GCS1 gamete fusion proteins

Moi, D., Nishio, S., Li, X., Valansi, C., Langleib, M., Brukman, N. G., Flyak, K., Dessimoz, C., de Sanctis, D., Tunyasuvunakool, K., et al. (2021) · doi:10.1101/2021.10.13.464100 · Cited by 23

Identification of a broad family of lipid A late acyltransferases with non‐canonical substrate specificity

Rubin, E. J., O'Brien, J. P., Ivanov, P. L., Brodbelt, J. S., & Trent, M. S. (2014) · Molecular Microbiology · doi:10.1111/mmi.12501 · Cited by 21

Probiotic Potential and Safety Assessment of Lactiplantibacillus plantarum cqf-43 and Whole-Genome Sequence Analysis

Liu, B., Zhong, X., Liu, Z., Guan, X., Wang, Q., Qi, R., Zhou, X., & Huang, J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242417570 · Cited by 21

Sequencing effort dictates gene discovery in marine microbial metagenomes

Duarte, C. M., Ngugi, D. K., Alam, I., Pearman, J., Kamau, A., Eguiluz, V. M., Gojobori, T., Acinas, S. G., Gasol, J. M., Bajic, V., et al. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15182 · Cited by 22

Genome analysis of Hibiscus syriacus provides insights of polyploidization and indeterminate flowering in woody plants

Kim, Y.-M., Kim, S., Koo, N., Shin, A.-Y., Yeom, S.-I., Seo, E., Park, S.-J., Kang, W.-H., Kim, M.-S., Park, J., et al. (2016) · DNA Research · doi:10.1093/dnares/dsw049 · Cited by 21

Fluoxetine ameliorates depressive symptoms by regulating lncRNA expression in the mouse hippocampus

Zhang, C.-L., 昆明650201，中国, 中., State Key Laboratory of Phytochemistry and Plant Resources in West China, Y. K. L. O. N. M. C., Li, Y.-J., Lu, S., Zhang, T., Xiao, R., Luo, H.-R., 呼和浩特010110，中国, 内., 中国科学院大学，北京100049，中国, et al. (2021) · Zoological Research · doi:10.24272/j.issn.2095-8137.2020.294 · Cited by 20

Bioinformatics Analysis of Bacterial Annexins – Putative Ancestral Relatives of Eukaryotic Annexins

Kodavali, P. K., Dudkiewicz, M., Pikuła, S., & Pawłowski, K. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085428 · Cited by 18

Functional evaluation of the role of C-type lectin domain family 16A at the chromosome 16p13 locus

Zouk, H., D'Hennezel, E., Du, X., Ounissi-Benkalha, H., Piccirillo, C. A., & Polychronakos, C. (2014) · Clinical and Experimental Immunology · doi:10.1111/cei.12240 · Cited by 17

Viruses of sulfur oxidizing phototrophs encode genes for pigment, carbon, and sulfur metabolisms

Hesketh-Best, P. J., Bosco-Santos, A., Garcia, S. L., O’Beirne, M. D., Werne, J. P., Gilhooly, W. P., & Silveira, C. B. (2023) · Communications Earth & Environment · doi:10.1038/s43247-023-00796-4 · Cited by 16

Genome sequence and characterization of a new virus infecting Mikania micrantha H.B.K.

Wang, R.-L., Ding, L.-W., Sun, Q.-Y., Li, J., Xu, Z.-F., & Peng, S.-L. (2008) · Archives of Virology · doi:10.1007/s00705-008-0180-0 · Cited by 12

Glycoprotein gp130 of Dictyostelium discoideum Influences Macropinocytosis and Adhesion

Chia, C. P., Gomathinayagam, S., Schmaltz, R. J., & Smoyer, L. K. (2005) · Molecular Biology of the Cell · doi:10.1091/mbc.e04-06-0483 · Cited by 11

Lineage-specific expansions provide genomic complexity among sea urchin GTPases

Beane, W. S., Voronina, E., Wessel, G. M., & McClay, D. R. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.046 · Cited by 10

In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis

Franco, M. E., Bitencourt, T. A., Marins, M., & Fachin, A. L. (2017) · Database · doi:10.1093/database/bax035 · Cited by 4

Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection

Veldsman, W. P., Yang, C., Zhang, Z., Huang, Y., Chowdhury, D., & Zhang, L. (2024) · Viruses · doi:10.3390/v16010134 · Cited by 2