Skip to main content
SpringerLink
Log in

Harvesting the information from a family of proteins

  • Chapter
Modern Genome Annotation

  • 872 Accesses

Abstract

The need for information about the functional roles of the elements comprising the human genome became larger than ever with the completion of its sequencing in 2003 (Lander et al. 2001; Venter et al. 2001; Consortium 2004b). BioSapiens (Excellence 2005) is contributing to the ENCODE (Consortium 2004a) program, which is providing a biologically informative representation of the human genome using high-throughput methods to identify and catalogue all functional elements. The ENCODE pilot project consisted of annotating 1% of the genome (Consortium et al. 2007). The presently ongoing functional annotation of the other 99% will be a crucial next step for many, diverse fields of science.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Aloy P, Querol E, Aviles FX, Sternberg MJ (2001) Automated structure-based prediction of functional sités in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J Mol Biol 311: 395–408

    Article  PubMed  CAS  Google Scholar 

  • Armon A, Graur D, Ben-Tal N (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 307: 447–463

    Article  PubMed  CAS  Google Scholar 

  • Bairoch A, Apweiler R (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res 28: 45–48

    Article  PubMed  CAS  Google Scholar 

  • Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The Protein Data Bank. Nucleic Acids Res 28: 235–242

    Article  PubMed  CAS  Google Scholar 

  • Beukers MW, Kristiansen I, AP IJ, Edvardsen I (1999) TinyGRAP database: a bioinformatics tool to mine G-protein-coupled receptor mutant data. Trends Pharmacol Sci 20: 475–477

    Article  PubMed  CAS  Google Scholar 

  • Campagne F, Jestin R, Reversat JL, Bernassau JM, Maigret B (1999) Visualisation and integration of G protein-coupled receptor related information help the modelling: description and applications of the Viseur program. J Comput Aided Mol Des 13: 625–643

    Article  PubMed  CAS  Google Scholar 

  • Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM (2006) TreeDet: a web server to explore sequence space. Nucleic Acids Res 34: W110–W115

    Article  PubMed  CAS  Google Scholar 

  • Casari G, Sander C, Valencia A (1995) A method to predict functional residues in proteins. Nat Struct Biol 2: 171–178

    Article  PubMed  CAS  Google Scholar 

  • Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5: 823–826

    PubMed  CAS  Google Scholar 

  • Consortium EP (2004a) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636–640

    Article  CAS  Google Scholar 

  • Consortium EP, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799–816

    Article  CAS  Google Scholar 

  • Consortium IHGS (2004b) Finishing the euchromatic sequence of the human genome. Nature 431: 931–945

    Article  CAS  Google Scholar 

  • Dean MK, Higgs C, Smith RE, Bywater RP, Snell CR, Scott PD, Upton GJ, Howe TJ, Reynolds CA (2001) Dimerization of G-protein-coupled receptors. J Med Chem 44: 4595–4614

    Article  PubMed  CAS  Google Scholar 

  • DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R (1988) Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known threedimensional structure. J Med Chem 31: 722–729

    Article  PubMed  CAS  Google Scholar 

  • Edvardsen O, Reiersen AL, Beukers MW, Kristiansen K (2002) tGRAP, the G-protein coupled receptors mutant database. Nucleic Acids Res 30: 361–363

    Article  PubMed  CAS  Google Scholar 

  • Excellence TBNo (2005) Research networks: BioSapiens: a European network for integrated genome annotation. Eur J Hum Genet 13: 994–997

    Article  Google Scholar 

  • Feenstra KA, Pirovano W, Krab K, Heringa J (2007) Sequence harmony: detecting functional specificity from alignments. Nucleic Acids Res 35: W495–W498

    Article  PubMed  Google Scholar 

  • Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R (2005) Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins 58: 134–143

    Article  PubMed  CAS  Google Scholar 

  • Filizola M, Olmea O, Weinstein H (2002) Prediction of heterodimerization interfaces of G-protein coupled receptors with a new subtractive correlated mutation method. Protein Eng 15: 881–885

    Article  PubMed  CAS  Google Scholar 

  • Filizola M, Weinstein H (2002) Structural models for dimerization of G-protein coupled receptors: the opioid receptor homodimers. Biopolymers 66: 317–325

    Article  PubMed  CAS  Google Scholar 

  • Folkertsma S, Van Noort P, Van Durme J, Joosten HJ, Bettler E, Fleuren W, Oliveira L, Horn F, de Vlieg J, Vriend G (2004) A family-based approach reveals the function of residues in the nuclear receptor ligand-binding domain. J Mol Biol 341: 321–335

    Article  PubMed  CAS  Google Scholar 

  • Glaser F, Morris RJ, Najmanovich RJ, Laskowski RA, Thornton JM (2006) A method for localizing ligand binding pockets in protein structures. Proteins 62: 479–488

    Article  PubMed  CAS  Google Scholar 

  • Glaser F, Pupko T, Paz I, Bell RE, Bechor-Shental D, Martz E, Ben-Tal N (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163–164

    Article  PubMed  CAS  Google Scholar 

  • Göbel U, Sander C, Schneider R, Valencia A (1994) Correlated mutations and residue contacts in proteins. Proteins 18: 309–317

    Article  PubMed  Google Scholar 

  • Gouldson PR, Dean MK, Snell CR, Bywater RP, Gkoutos G, Reynolds CA (2001) Lipid-facing correlated mutations and dimerization in G-protein coupled receptors. Protein Eng 14: 759–767

    Article  PubMed  CAS  Google Scholar 

  • Gouldson PR, Higgs C, Smith RE, Dean MK, Gkoutos GV, Reynolds CA (2000) Dimerization and domain swapping in G-protein-coupled receptors: a computational study. Neuropsychopharmacology 23: S60–S77

    Article  PubMed  CAS  Google Scholar 

  • Gouldson PR, Snell CR, Bywater RP, Higgs C, Reynolds CA (1998) Domain swapping in G-protein coupled receptor dimers. Protein Eng 11: 1181–1193

    Article  PubMed  CAS  Google Scholar 

  • Hamosh A, Scott AF, Amberger JS, Bocchini CA, McKusick VA (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 33: D514–D517

    Article  PubMed  CAS  Google Scholar 

  • Hernanz-Falcón P, Rodríguez-Frade JM, Serrano A, Juan D, del Sol A, Soriano SF, Roncal F, Gómez L, Valencia A, Martínez-A C, Mellado M (2004) Identification of amino acid residues crucial for chemokine receptor dimerization. Nat Immunol 5: 216–223

    Article  PubMed  CAS  Google Scholar 

  • Honig B, Nicholls A (1995) Classical electrostatics in biology and chemistry. Science 268: 1144–1149

    Article  PubMed  CAS  Google Scholar 

  • Horn F, Bettler E, Oliveira L, Campagne F, Cohen FE, Vriend G (2003) GPCRDB information system for G-protein-coupled receptors. Nucleic Acids Res 31: 294–297

    Article  PubMed  CAS  Google Scholar 

  • Horn F, Bywater R, Krause G, Kuipers W, Oliveira L, Paiva AC, Sander C, Vriend G (1998a) The interaction of class B G-protein-coupled receptors with their hormones. Recept Channels 5: 305–314

    PubMed  CAS  Google Scholar 

  • Horn F, Lau AL, Cohen FE (2004) Automated extraction of mutation data from the literature: application of MuteXt to G-protein-coupled receptors and nuclear hormone receptors. Bioinformatics 20: 557–568

    Article  PubMed  CAS  Google Scholar 

  • Horn F, Van der Wenden EM, Oliveira L, IJzerman AP, Vriend G (2000) Receptors coupling to G proteins: is there a signal behind the sequence? Proteins 41: 448–459

    Article  PubMed  CAS  Google Scholar 

  • Horn F, Vriend G, Cohen FE (2001) Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res 29: 346–349

    Article  PubMed  CAS  Google Scholar 

  • Horn F, Weare J, Beukers MW, Hörsch S, Bairoch A, Chen W, Edvardsen O, Campagne F, Vriend G (1998b) GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res 26: 275–279

    Article  PubMed  CAS  Google Scholar 

  • Howard AD, McAllister G, Feighner SD, Liu Q, Nargund RP, Van der Ploeg LH, Patchett AA (2001) Orphan G-protein-coupled receptors and natural ligand discovery. Trends Pharmacol Sci 22: 132–140

    Article  PubMed  CAS  Google Scholar 

  • Lutje Hulsik D (2002) Public-domain database of GPCR interaction parameters. Trends Pharmacol Sci 23: 258–259

    Article  Google Scholar 

  • Jones S, Thornton JM (1997) Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 272: 133–143

    Article  PubMed  CAS  Google Scholar 

  • Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB (2004) SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res 32: W424–W428

    Article  PubMed  CAS  Google Scholar 

  • Kanz C, Aldebert P, Althorpe N, Baker W, Baldwin A, Bates K, Browne P, van den Broek A, Castro M, Cochrane G, Duggan K, Eberhardt R, Faruque N, Gamble J, Diez FG, Harte N, Kulikova T, Lin Q, Lombard V, Lopez R, Mancuso R, McHale M, Nardone F, Silventoinen V, Sobhany S, Stoehr P, Tuli MA, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2005) The EMBL Nucleotide Sequence Database. Nucleic Acids Res 33: D29–D33

    Article  PubMed  CAS  Google Scholar 

  • Kazius J, Wurdinger K, van Iterson M, Kok J, Bäck T, IJzerman AP (2007) GPCR NaVa database: natural variants in human G-protein-coupled receptors. Hum Mutat

    Google Scholar 

  • Kufareva I, Budagyan L, Raush E, Totrov M, Abagyan R (2007) PIER: protein interface recognition for structural proteomics. Proteins 67: 400–417

    Article  PubMed  CAS  Google Scholar 

  • Kuipers W, Link R, Standaar PJ, Stoit AR, Van Wijngaarden I, Leurs R, IJzerman AP (1997a) Study of the interaction between aryloxypropanolamines and Asn386 in helix VII of the human 5-hydroxytryptaminel A receptor. Mol Pharmacol 51: 889–896

    PubMed  CAS  Google Scholar 

  • Kuipers W, Oliveira L, Vriend G, IJzerman AP (1997b) Identification of class-determining residues in G protein-coupled receptors by sequence analysis. Receptors Channels 5: 159–174

    PubMed  CAS  Google Scholar 

  • Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol 161: 269–288

    Article  PubMed  CAS  Google Scholar 

  • Lamb ML, Jorgensen WL (1997) Computational approaches to molecular recognition. Curr Opi Chem Biol 1: 449–457

    Article  CAS  Google Scholar 

  • Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921

    Article  PubMed  CAS  Google Scholar 

  • Lichtarge O, Bourne HR, Cohen FE (1996a) Evolutionarily conserved Galphabetagamma binding surfaces support a model of the G protein-receptor complex. Proc Natl Acad Sci USA 93: 7507–7511

    Article  PubMed  CAS  Google Scholar 

  • Lichtarge O, Bourne HR, Cohen FE (1996b) An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 257: 342–358

    Article  PubMed  CAS  Google Scholar 

  • Lichtarge O, Yamamoto KR, Cohen FE (1997) Identification of functional surfaces of the zinc binding domains of intracellular receptors. J Mol Biol 274: 325–337

    Article  PubMed  CAS  Google Scholar 

  • Madabushi S, Gross AK, Philippi A, Meng EC, Wensel TG, Lichtarge O (2004) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J Biol Chem 279: 8126–8132

    Article  PubMed  CAS  Google Scholar 

  • Madabushi S, Yao H, Marsh M, Kristensen DM, Philippi A, Sowa ME, Lichtarge O (2002) Structural clusters of evolutionary trace residues are statistically significant and common in proteins. J Mol Biol 316: 139–154

    Article  PubMed  CAS  Google Scholar 

  • Miranker A, Karplus M (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11: 29–34

    Article  PubMed  CAS  Google Scholar 

  • Mirny L, Shakhnovich E (2001) Evolutionary conservation of the folding nucleus. J Mol Biol 308: 123–129

    Article  PubMed  CAS  Google Scholar 

  • Mirny LA, Shakhnovich EI (1999) Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J Mol Biol 291: 177–196

    Article  PubMed  CAS  Google Scholar 

  • Möller S, Vilo J, Croning MD (2001) Prediction of the coupling specificity of G protein coupled receptors to their G proteins. Bioinformatics 17(Suppl 1): S174–S181

    PubMed  Google Scholar 

  • Oliveira L, Paiva ACM, Vriend G (1993) A common motifin G protein-coupled seven transmembrane helix receptors. J Comp Aided Mol Des 7: 649–658

    Article  CAS  Google Scholar 

  • Oliveira L, Paiva ACM, Vriend G (1999) A low resolution model for the interaction of G-proteins with G-protein-coupled receptors. Protein Eng 12: 1087–1095

    Article  PubMed  CAS  Google Scholar 

  • Oliveira L, Paiva ACM, Vriend G (2002) Correlated mutation analyses on very large sequence families. Chembiochem 3: 1010–1017

    Article  PubMed  CAS  Google Scholar 

  • Oliveira L, Paiva PB, Paiva ACM, Vriend G (2003a) Identification of functionally conserved residues with the use of entropy-variability plots. Proteins 52: 544–552

    Article  PubMed  CAS  Google Scholar 

  • Oliveira L, Paiva PB, Paiva ACM, Vriend G (2003b) Sequence analysis reveals how G-protein-coupled receptors transduce the signal to the G-protein. Proteins 52: 553–560

    Article  PubMed  CAS  Google Scholar 

  • Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. J Mol Biol 271: 511–523

    Article  PubMed  CAS  Google Scholar 

  • Pei J, Grishin NV (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17: 700–712

    Article  PubMed  CAS  Google Scholar 

  • Pietrokovski S, Henikoff JG, Henikoff S (1996) The Blocks database — a system for protein classification. Nucleic Acids Res 24: 197–200

    Article  PubMed  CAS  Google Scholar 

  • Pirovano W, Feenstra KA, Heringa J (2006) Sequence comparison by sequence harmony identifies subtype-specific functional sites. Nucleic Acids Res 34: 6540–6548

    Article  PubMed  CAS  Google Scholar 

  • Russell RB, Sasieni PD, Sternberg MJ (1998) Supersites within superfolds. Binding site similarity in the absence of homology. J Mol Biol 282: 903–918

    Article  PubMed  CAS  Google Scholar 

  • Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9: 56–68

    Article  PubMed  CAS  Google Scholar 

  • Shatsky M, Nussinov R, Wolfson HJ (2002) Flexible protein alignment and hinge detection. Proteins 48: 242–256

    Article  PubMed  CAS  Google Scholar 

  • Shenkin PS, Erman B, Mastrandrea LD (1991) Information-theoretical entropy as a measure of sequence variability. Proteins 11: 297–313

    Article  PubMed  CAS  Google Scholar 

  • Shulman AI, Larson C, Mangelsdorf DJ, Ranganathan R (2004) Structural determinants of allosteric ligand activation in RXR heterodimers. Cell 116: 417–429

    Article  PubMed  CAS  Google Scholar 

  • Singer MS, Vriend G, Bywater RP (2002) Prediction of protein residue contacts with a PDB-derived likelihood matrix. Protein Eng 15: 721–725

    Article  PubMed  CAS  Google Scholar 

  • Slep KC, Kercher MA, He W, Cowan CW, Wensel TG, Sigler PB (2001) Structural determinants for regulation of phosphodiesterase by a G-protein at 2.0 A. Nature 409: 1071–1077

    Article  PubMed  CAS  Google Scholar 

  • Sowa ME, He W, Slep KC, Kercher MA, Lichtarge O, Wensel TG (2001) Prediction and confirmation of a site critical for effector regulation of RGS domain activity. Nat Struct Biol 8: 234–237

    Article  PubMed  CAS  Google Scholar 

  • Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12: 368–373

    Article  PubMed  CAS  Google Scholar 

  • Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al. (2001) The sequence of the human genome. Science 291: 1304–1351

    Article  PubMed  CAS  Google Scholar 

  • Wang W, Donini O, Reyes CM, Kollman PA (2001) Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu Rev Bioph Biom 30: 211–243

    Article  CAS  Google Scholar 

  • Ye K, Anton Feenstra K, Heringa J, Ijzerman AP, Marchiori E (2008) Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a machinelearning approach for feature weighting. Bioinformatics 24: 18–25

    Article  PubMed  CAS  Google Scholar 

  • Zuckerkandl E (1965) Evolutionary divergence and convergence in proteins. In: Zuckerkandl E, Pauling L (eds) Evolving genes and proteins. Academic Press

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. CMBI, NCMLS, Radboud University Nijmegen Medical Centre, Geert Grooteplein 26-28, 6525 GA, Nijmegen, The Netherlands

    B. Vroling & G. Vriend

Authors
  1. B. Vroling
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. G. Vriend
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. Vriend .

Editor information

Editors and Affiliations

  1. Wissenschaftszentrum Weihenstephan, TU München, Freising, Germany

    Dmitrij Frishman

  2. Structural and Computational Programme, Spanish National Cancer Research Centre, Madrid, Spain

    Alfonso Valencia

Rights and permissions

Reprints and permissions

Copyright information

© 2008 Springer-Verlag/Wien

About this chapter

Cite this chapter

Vroling, B., Vriend, G. (2008). Harvesting the information from a family of proteins. In: Frishman, D., Valencia, A. (eds) Modern Genome Annotation. Springer, Vienna. https://doi.org/10.1007/978-3-211-75123-7_13

Download citation

Publish with us

Policies and ethics

Search

Navigation