Pfam: clans, web tools and services

Pfam: The protein families database in 2021

Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G. A., Sonnhammer, E. L. L., Tosatto, S. C. E., Paladin, L., Raj, S., Richardson, L. J., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkaa913 · Cited by 7,452

Pfam: the protein families database

Finn, R. D., Bateman, A., Clements, J., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Heger, A., Hetherington, K., Holm, L., Mistry, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1223 · Cited by 6,148

The Pfam protein families database: towards a more sustainable future

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1344 · Cited by 5,975

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

Price, M. N., Dehal, P. S., & Arkin, A. P. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp077 · Cited by 5,602

HMMER web server: interactive sequence similarity searching

Finn, R. D., Clements, J., & Eddy, S. R. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr367 · Cited by 5,952

The Pfam protein families database in 2019

El-Gebali, S., Mistry, J., Bateman, A., Eddy, S. R., Luciani, A., Potter, S. C., Qureshi, M., Richardson, L. J., Salazar, G. A., Smart, A., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gky995 · Cited by 4,602

The Pfam protein families database

Punta, M., Coggill, P. C., Eberhardt, R. Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G., Clements, J., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr1065 · Cited by 3,719

The Pfam protein families database

Finn, R. D., Mistry, J., Tate, J., Coggill, P., Heger, A., Pollington, J. E., Gavin, O. L., Gunasekaran, P., Ceric, G., Forslund, K., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp985 · Cited by 2,694

Phylogenomics resolves the timing and pattern of insect evolution

Misof, B., Liu, S., Meusemann, K., Peters, R. S., Donath, A., Mayer, C., Frandsen, P. B., Ware, J., Flouri, T., Beutel, R. G., et al. (2014) · Science · doi:10.1126/science.1257570 · Cited by 2,694

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

Holt, C., & Yandell, M. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-491 · Cited by 2,118

Some remarks on protein attribute prediction and pseudo amino acid composition

Chou, K.-C. (2011) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.12.024 · Cited by 1,225

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans

King, N., Westbrook, M. J., Young, S. L., Kuo, A., Abedin, M., Chapman, J., Fairclough, S., Hellsten, U., Isogai, Y., Letunic, I., et al. (2008) · Nature · doi:10.1038/nature06617 · Cited by 1,139

LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana

Hundertmark, M., & Hincha, D. K. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-118 · Cited by 1,044

Database resources of the National Center for Biotechnology Information

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm1000 · Cited by 1,007

Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes

Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V. K., Srivastava, T. P., et al. (2007) · DNA Research · doi:10.1093/dnares/dsm018 · Cited by 869

Database resources of the National Center for Biotechnology Information

Wheeler, D. L., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl1031 · Cited by 734

A human functional protein interaction network and its application to cancer data analysis

Wu, G., Feng, X., & Stein, L. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r53 · Cited by 692

Distinguishing protein-coding and noncoding genes in the human genome

Clamp, M., Fry, B., Kamal, M., Xie, X., Cuff, J., Lin, M. F., Kellis, M., Lindblad-Toh, K., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0709013104 · Cited by 624

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

Hogan, D. J., Riordan, D. P., Gerber, A. P., Herschlag, D., & Brown, P. O. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060255 · Cited by 609

eggNOG: automated construction and annotation of orthologous groups of genes

Jensen, L. J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T., & Bork, P. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm796 · Cited by 547

RTX proteins: a highly diverse family secreted by a common mechanism

Linhartová, I., Bumba, L., Mašín, J., Basler, M., Osička, R., Kamanová, J., Procházková, K., Adkins, I., Hejnová-Holubová, J., Sadílková, L., et al. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00231.x · Cited by 530

A genome-wide association study identifies KIAA0350 as a type 1 diabetes gene

Hakonarson, H., Grant, S. F. A., Bradfield, J. P., Marchand, L., Kim, C. E., Glessner, J. T., Grabs, R., Casalunovo, T., Taback, S. P., Frackelton, E. C., et al. (2007) · Nature · doi:10.1038/nature06010 · Cited by 542

Structure and function of plant photoreceptors

Möglich, A., Yang, X., Ayers, R. A., & Moffat, K. (2010) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-042809-112259 · Cited by 499

A Specificity Map for the PDZ Domain Family

Tonikian, R., Zhang, Y., Sazinsky, S. L., Currell, B., Yeh, J.-H., Reva, B., Held, H. A., Appleton, B. A., Evangelista, M., Wu, Y., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060239 · Cited by 476

The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life.

Atkinson, G. C., Tenson, T., & Hauryliuk, V. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023479 · Cited by 447

Allergens are distributed into few protein families and possess a restricted number of biochemical functions.

Radauer, C., Bublin, M., Wagner, S., Mari, A., & Breiteneder, H. (2008) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2008.01.025 · Cited by 429

Rfam: Wikipedia, clans and the “decimal” release

Gardner, P. P., Daub, J., Tate, J., Moore, B. L., Osuch, I. H., Griffiths-Jones, S., Finn, R. D., Nawrocki, E. P., Kolbe, D. L., Eddy, S. R., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1129 · Cited by 390

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H., & Breaker, R. R. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r31 · Cited by 354

Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA

Perrin, R. M., Fedorova, N. D., Bok, J. W., Cramer, R. A., Wortman, J. R., Kim, H. S., Nierman, W. C., & Keller, N. P. (2007) · PLoS Pathogens · doi:10.1371/journal.ppat.0030050 · Cited by 352

Using deep learning to annotate the protein universe

Bileschi, M. L., Belanger, D., Bryant, D. H., Sanderson, T., Carter, B., Sculley, D., Bateman, A., DePristo, M. A., & Colwell, L. J. (2022) · Nature Biotechnology · doi:10.1038/s41587-021-01179-w · Cited by 332

A korarchaeal genome reveals insights into the evolution of the Archaea

Elkins, J. G., Podar, M., Graham, D. E., Makarova, K. S., Wolf, Y., Randau, L., Hedlund, B. P., Brochier-Armanet, C., Kunin, V., Anderson, I., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0801980105 · Cited by 296

Improved human disease candidate gene prioritization using mouse phenotype

Chen, J., Xu, H., Aronow, B. J., & Jegga, A. G. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-392 · Cited by 284

A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

Peña-Castillo, L., Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. K., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-s1-s2 · Cited by 248

Examination of Triacylglycerol Biosynthetic Pathways via De Novo Transcriptomic and Proteomic Analyses in an Unsequenced Microalga

Guarnieri, M. T., Nag, A., Smolinski, S. L., Darzins, A., Seibert, M., & Pienkos, P. T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0025851 · Cited by 234

Protein Family Expansions and Biological Complexity

Vogel, C., & Chothia, C. (2006) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0020048 · Cited by 227

“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

Gillis, J., & Pavlidis, P. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002444 · Cited by 214

Docking interactions in protein kinase and phosphatase networks

Reményi, A., Good, M. C., & Lim, W. A. (2006) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2006.10.008 · Cited by 188

The echinoderm adhesome

Whittaker, C. A., Bergeron, K.-F., Whittle, J., Brandhorst, B. P., Burke, R. D., & Hynes, R. O. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.07.044 · Cited by 183

Alternative binding proteins: Anticalins – harnessing the structural plasticity of the lipocalin ligand pocket to engineer novel binding activities

Skerra, A. (2008) · The FEBS Journal · doi:10.1111/j.1742-4658.2008.06439.x · Cited by 176

Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome

Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D., & Arnone, M. I. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.070 · Cited by 170

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination

Mukherjee, S., & Zhang, Y. (2011) · Structure · doi:10.1016/j.str.2011.04.006 · Cited by 174

Why Are There Still Over 1000 Uncharacterized Yeast Genes?

Peña-Castillo, L., & Hughes, T. R. (2007) · Genetics · doi:10.1534/genetics.107.074468 · Cited by 161

Genome-Wide Survey and Developmental Expression Mapping of Zebrafish SET Domain-Containing Genes

Sun, X.-J., Xu, P.-F., Zhou, T., Hu, M., Fu, C.-T., Zhang, Y., Jin, Y., Chen, Y., Chen, S.-J., Huang, Q.-H., et al. (2008) · PLoS ONE · doi:10.1371/journal.pone.0001499 · Cited by 127

Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system

Belov, K., Sanderson, C. E., Deakin, J. E., Wong, E. S. W., Assange, D., McColl, K. A., Gout, A., de Bono, B., Barrow, A. D., Speed, T. P., et al. (2007) · Genome Research · doi:10.1101/gr.6121807 · Cited by 116

structureViz: linking cytoscape and UCSF Chimera

Morris, J. H., Huang, C. C., Babbitt, P. C., & Ferrin, T. E. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm329 · Cited by 82

Identification and Characterization of PWWP Domain Residues Critical for LEDGF/p75 Chromatin Binding and Human Immunodeficiency Virus Type 1 Infectivity

Shun, M.-C., Botbol, Y., Li, X., Di Nunzio, F., Daigle, J. E., Yan, N., Lieberman, J., Lavigne, M., & Engelman, A. (2008) · Journal of Virology · doi:10.1128/jvi.01561-08 · Cited by 78

A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants

de la Grange, P., Dutertre, M., Correa, M., & Auboeuf, D. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-180 · Cited by 78

Identification of mammalian orthologs using local synteny

Jun, J., Mandoiu, I. I., & Nelson, C. E. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-630 · Cited by 78

Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus

Cramer, R. A., Stajich, J. E., Yamanaka, Y., Dietrich, F. S., Steinbach, W. J., & Perfect, J. R. (2006) · Gene · doi:10.1016/j.gene.2006.07.008 · Cited by 66

The use of Gene Ontology terms for predicting highly-connected 'hub' nodes in protein-protein interaction networks

Hsing, M., Byler, K. G., & Cherkasov, A. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-80 · Cited by 66

Calcareous sponge genomes reveal complex evolution of α-carbonic anhydrases and two key biomineralization enzymes

Voigt, O., Adamski, M., Sluzek, K., & Adamska, M. (2014) · BMC Evolutionary Biology · doi:10.1186/s12862-014-0230-z · Cited by 63

Revisiting the yeast PPR proteins–application of an iterative hidden Markov model algorithm reveals new members of the rapidly evolving family

Lipinski, K. A., Puchta, O., Surendranath, V., Kudla, M., & Golik, P. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr120 · Cited by 62

Congenital syndactyly in cattle: four novel mutations in the low density lipoprotein receptor-related protein 4 gene (LRP4)

Drögemüller, C., Leeb, T., Harlizius, B., Tammen, I., Distl, O., Höltershinken, M., Gentile, A., Duchesne, A., & Eggen, A. (2007) · BMC Genetics · doi:10.1186/1471-2156-8-5 · Cited by 60

The spindle protein CHICA mediates localization of the chromokinesin Kid to the mitotic spindle

Santamaria, A., Nagel, S., Sillje, H. H. W., & Nigg, E. A. (2008) · Current Biology · doi:10.1016/j.cub.2008.04.041 · Cited by 58

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors

Liu, J., & Stormo, G. D. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn331 · Cited by 48

High Molecular Weight Kininogen: A Review of the Structural Literature

Ponczek, M. B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222413370 · Cited by 45

The mouth, the anus, and the blastopore—open questions about questionable openings

Hejnol, A., & Martindale, M. Q. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0004 · Cited by 37

Ancient divergence of animal protein tyrosine kinase genes demonstrated by a gene family tree including choanoflagellate genes

Suga, H., Sasaki, G., Kuma, K.-I., Nishiyori, H., Hirose, N., Su, Z.-H., Iwabe, N., & Miyata, T. (2008) · FEBS Letters · doi:10.1016/j.febslet.2008.02.002 · Cited by 29

DENN domain-containing protein FAM45A regulates the homeostasis of late/multivesicular endosomes

Zhang, J., Zhang, K., Qi, L., Hu, Q., Shen, Z., Liu, B., Deng, J., Zhang, C., & Zhang, Y. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2019.02.006 · Cited by 29

Identification of neuroglycan C and interacting partners as potential susceptibility genes for schizophrenia in a Southern Chinese population

So, H., Fong, P. Y., Chen, R. Y. L., Hui, T. C. K., Ng, M. Y. M., Cherny, S. S., Mak, W. W. M., Cheung, E. F. C., Chan, R. C. K., Chen, E. Y. H., et al. (2010) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30961 · Cited by 28

Genomic, phylogenetic, and cell biological insights into metazoan origins

Nichols, S. A., Dayel, M. J., & King, N. (2009) · Animal Evolution · doi:10.1093/acprof:oso/9780199549429.003.0003 · Cited by 24

Two Zinc-Cluster Transcription Factors Control Induction of Alternative Oxidase in Neurospora crassa

Chae, M. S., Nargang, C. E., Cleary, I. A., Lin, C. C., Todd, A. T., & Nargang, F. E. (2007) · Genetics · doi:10.1534/genetics.107.078212 · Cited by 22

Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family

Wang, Z., & Zhang, Q. (2009) · Evolutionary Bioinformatics · doi:10.4137/ebo.s2948 · Cited by 16

Large language models transform biological research: from architecture to utilization

Wang, T., & Luo, Z. (2025) · Science China Information Sciences · doi:10.1007/s11432-024-4466-3 · Cited by 14

Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Shin, D. H., Hou, J., Chandonia, J.-M., Das, D., Choi, I.-G., Kim, R., & Kim, S.-H. (2007) · Journal of Structural and Functional Genomics · doi:10.1007/s10969-007-9025-4