A computational interactome and functional annotation for the human proteome

eLife

Volumn 5, Issue OCTOBER2016, 2016, Pages

  Garzón, José Ignacio ^a   Deng, Lei ^a,b   Murray, Diana ^a   Shapira, Sagi ^a   Petrey, Donald ^a   Honig, Barry ^a  

^a Columbia University ^*  (United States)

^b CENTRAL SOUTH UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ALGORITHM; ARTICLE; GENE EXPRESSION PROFILING; GENE ONTOLOGY; HUMAN; MOLECULAR GENETICS; ORTHOLOGY; PHENOTYPE; PHYLOGENY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RECEIVER OPERATING CHARACTERISTIC; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGY; PROCEDURES; PROTEIN DATABASE; VALIDATION STUDY;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPS; PROTEOME;

EID: 84996565370     PISSN: None     EISSN: 2050084X     Source Type: Journal    
DOI: 10.7554/eLife.18715     Document Type: Article

References (78)

1. Altenhoff AM, Škunca N, Glover N, Train CM, Sueki A, Piližota I, Gori K, Tomiczek B, Müller S, Redestig H, Gonnet GH, Dessimoz C. 2015. The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research 43:D240–D249. doi:10.1093/nar/gku1158, PMID:25399418
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25:25–29. doi:10.1038/75556, PMID:10802651
3. Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR, The Genomes Project C, 1000
4. Genomes Project Consortium. 2015. A global reference for human genetic variation. Nature 526:68–74. doi:10.1038/nature15393, PMID:26432245
5. Beigi F, Schmeckpeper J, Pow-Anpongkul P, Payne JA, Zhang L, Zhang Z, Huang J, Mirotsou M, Dzau VJ. 2013. C3orf58, a novel paracrine protein, stimulates cardiomyocyte cell-cycle progression through the PI3K-AKT- CDK7 pathway. Circulation Research 113:372–380. doi:10.1161/CIRCRESAHA.113.301075, PMID:23784961
6. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The protein data bank. Nucleic Acids Research 28:235–242. doi:10.1093/nar/28.1.235, PMID:10592235
7. Bhardwaj N, Lu H. 2005. Correlation between gene expression profiles and protein-protein interactions within and across genomes. Bioinformatics 21:2730–2738. doi:10.1093/bioinformatics/bti398, PMID:15797912
8. Brown KR, Jurisica I. 2007. Unequal evolutionary conservation of human protein interactions in interologous networks. Genome Biology 8:R95. doi:10.1186/gb-2007-8-5-r95, PMID:17535438
9. Chatr-aryamontri A, Ceol A, Palazzi LM, Nardelli G, Schneider MV, Castagnoli L, Cesareni G. 2007. MINT: the Molecular INTeraction database. Nucleic Acids Research 35:D572–574. doi:10.1093/nar/gkl950, PMID:17135203
10. Chen TS, Petrey D, Garzon JI, Honig B. 2015. Predicting peptide-mediated interactions on a genome-wide scale. PLoS Computational Biology 11:e1004248. doi:10.1371/journal.pcbi.1004248
11. de Chassey B, Navratil V, Tafforeau L, Hiet MS, Aublin-Gex A, Agaugué S, Meiffren G, Pradezynski F, Faria BF, Chantier T, Le Breton M, Pellet J, Davoust N, Mangeot PE, Chaboud A, Penin F, Jacob Y, Vidalain PO, Vidal M, André P, et al. 2008. Hepatitis C virus infection protein network. Molecular Systems Biology 4:230. doi:10.1038/msb.2008.66, PMID:18985028
12. de Juan D, Pazos F, Valencia A. 2013. Emerging methods in protein co-evolution. Nature Reviews Genetics 14: 249–261. doi:10.1038/nrg3414, PMID:23458856
13. Dey F, Cliff Zhang Q, Petrey D, Honig B. 2013. Toward a "structural BLAST": using structural relationships to infer function. Protein Science 22:359–366. doi:10.1002/pro.2225, PMID:23349097
14. Dudkiewicz M, Lenart A, Pawłowski K. 2013. A novel predicted calcium-regulated kinase family implicated in neurological disorders. PLoS One 8:e66427. doi:10.1371/journal.pone.0066427, PMID:23840464
15. Edwards R. 2006. GOPHER: Generation of Orthologous proteins from high -throughput estimations of relationships. http://www.southampton.ac.uk/~re1u06/software/packages/slimsuite/docs/manuals/GOPHER% 20Manual.pdf.
16. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. 2003. Tools for comparative protein structure modeling and analysis. Nucleic Acids Research 31:3375–3380. doi:10.1093/nar/gkg543, PMID:12824331
17. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, et al. 2014. Ensembl 2014. Nucleic Acids Research 42:D749–D755. doi:10.1093/nar/gkt1196, PMID:24316576
18. Forslund K, Sonnhammer EL. 2008. Predicting protein function from domain content. Bioinformatics 24:1681–1687. doi:10.1093/bioinformatics/btn312, PMID:18591194
19. Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ. 2013. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Research 41:D808–D815. doi:10.1093/nar/gks1094, PMID:23203871
20. Gavin AC, Bösche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick JM, Michon AM, Cruciat CM, Remor M, Höfert C, Schelder M, Brajenovic M, Ruffner H, Merino A, Klein K, Hudak M, Dickson D, Rudi T, et al. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147. doi:10.1038/415141a, PMID:11805826
21. Hart GT, Ramani AK, Marcotte EM. 2006. How complete are current yeast and human protein-interaction networks? Genome Biology 7:120. doi:10.1186/gb-2006-7-11-120, PMID:17147767
22. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, et al. 2012. A census of human soluble protein complexes. Cell 150:1068–1081. doi:10.1016/j.cell.2012.08.011, PMID:22939629
23. Hein MY, Hubner NC, Poser I, Cox J, Nagaraj N, Toyoda Y, Gak IA, Weisswange I, Mansfeld J, Buchholz F, Hyman AA, Mann M. 2015. A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 163:712–723. doi:10.1016/j.cell.2015.09.053, PMID:26496610
24. Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, Rattei T, Mende DR, Sunagawa S, Kuhn M, Jensen LJ, von Mering C, Bork P, Walter, T Rattei MC. 2016. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Research 44:D286–D293. doi:10.1093/nar/gkv1248, PMID:26582926
25. Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, et al. 2015. The BioPlex network: A systematic exploration of the human interactome. Cell 162:425–440. doi:10.1016/j.cell.2015.06.043, PMID:26186194
26. Ieker T, Krogan NJ. 2012. Differential network biology. Molecular Systems Biology 8:565. doi:10.1038/msb.2011.99, PMID:22252388
27. Jansen R, Greenbaum D, Gerstein M. 2002. Relating whole-genome expression data with protein-protein interactions. Genome Research 12:37–46. doi:10.1101/gr.205602, PMID:11779829
28. Jansen R, Yu H, Greenbaum D, Kluger Y, Krogan NJ, Chung S, Emili A, Snyder M, Greenblatt JF, Gerstein M. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449–453. doi:10.1126/science.1087361, PMID:14564010
29. Jessulat M, Pitre S, Gui Y, Hooshyar M, Omidi K, Samanfar B, Tan le H, Alamgir M, Green J, Dehne F, Golshani A, Tan LH. 2011. Recent advances in protein-protein interaction prediction: experimental and computational methods. Expert Opinion on Drug Discovery 6:921–935. doi:10.1517/17460441.2011.603722, PMID:22646215
30. Kamburov A, Lawrence MS, Polak P, Leshchiner I, Lage K, Golub TR, Lander ES, Getz G. 2015. Comprehensive assessment of cancer missense mutation clustering in protein structures. PNAS 112:E5486–E5495. doi:10.1073/pnas.1516373112
31. Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27–30. doi:10.1093/nar/28.1.27, PMID:10592173
32. Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, et al. 2007. IntAct–open source resource for molecular interaction data. Nucleic Acids Research 35: D561–565. doi:10.1093/nar/gkl958, PMID:17145710
33. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, et al. 2009. Human protein reference database–2009 update. Nucleic Acids Research 37:D767–D772. doi:10.1093/nar/gkn892, PMID:18988627
34. Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A. 2015. ArrayExpress update–simplifying data submissions. Nucleic Acids Research 43:D1113–1116. doi:10.1093/nar/gku1057, PMID:25361974
35. Krissinel E, Henrick K. 2007. Inference of macromolecular assemblies from crystalline state. Journal of Molecular Biology 372:774–797. doi:10.1016/j.jmb.2007.05.022, PMID:17681537
36. Kriventseva EV, Tegenfeldt F, Petty TJ, Waterhouse RM, Simão FA, Pozdnyakov IA, Ioannidis P, Zdobnov EM. 2015. OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Research 43:D250–D256. doi:10.1093/nar/gku1220, PMID:25428351
37. Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. 2014. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research 42:D980–D985. doi:10.1093/nar/gkt1113, PMID:24234437
38. Lee I, Blom UM, Wang PI, Shim JE, Marcotte EM. 2011. Prioritizing candidate disease genes by network-based boosting of genome-wide association data. Genome Research 21:1109–1121. doi:10.1101/gr.118992.110, PMID:21536720
39. Lewis AC, Saeed R, Deane CM. 2010. Predicting protein-protein interactions in the context of protein evolution. Molecular BioSystems 6:55–64. doi:10.1039/B916371A, PMID:20024067
40. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E, Castagnoli L, Cesareni G. 2012. MINT, the molecular interaction database: 2012 update. Nucleic Acids Research 40:D857–D861. doi:10.1093/nar/gkr930, PMID:22096227
41. Lichtarge O, Sowa ME. 2002. Evolutionary predictions of binding surfaces and interactions. Current Opinion in Structural Biology 12:21–27. doi:10.1016/S0959-440X(02)00284-1, PMID:11839485
42. Lu L, Lu H, Skolnick J. 2002. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins: Structure, Function, and Genetics 49:350–364. doi:10.1002/prot.10222, PMID:12360525
43. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, et al. 2011. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Research 39:D225–D229. doi:10.1093/nar/gkq1189, PMID:21109532
44. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751–753. doi:10.1126/science.285.5428.751, PMID:10427000
45. Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. 2001. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Research 11:2120–2126. doi:10.1101/gr.205301, PMID:11731503
46. McDowall MD, Scott MS, Barton GJ. 2009. PIPs: human protein-protein interaction prediction database. Nucleic Acids Research 37:D651–D656. doi:10.1093/nar/gkn870, PMID:18988626
47. Mewes HW, Albermann K, Heumann K, Liebl S, Pfeiffer F. 1997. MIPS: a database for protein sequences, homology data and yeast genome information. Nucleic Acids Research 25:28–30. doi:10.1093/nar/25.1.28, PMID:9016498
48. Mosca R, Cé ol A, Aloy P. 2013. Interactome3D: adding structural details to protein networks. Nature Methods 10:47–53. doi:10.1038/nmeth.2289, PMID:23399932
49. Niwa T, Saito H, Imajoh-ohmi S, Kaminishi M, Seto Y, Miki Y, Nakanishi A. 2009. BRCA2 interacts with the cytoskeletal linker protein plectin to form a complex controlling centrosome localization. Cancer Science 100: 2115–2125. doi:10.1111/j.1349-7006.2009.01282.x, PMID:19709076
50. Okamura Y, Aoki Y, Obayashi T, Tadaka S, Ito S, Narise T, Kinoshita K 2015. COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems. Nucleic Acids Research 43:D82–D86. doi:10.1093/nar/gku1163, PMID:25392420
51. Pellegrini M. 2012. Using phylogenetic profiles to predict functional relationships. Methods in Molecular Biology 804:167–177. doi:10.1007/978-1-61779-361-5_9, PMID:22144153
52. Penel S, Arigon A-M, Dufayard J-F, Sertier A-S, Daubin V, Duret L, Gouy M, Perrière G. 2009. Databases of homologous gene families for comparative genomics. BMC Bioinformatics 10:S3–S13. doi:10.1186/1471-2105-10-S6-S3
53. Petrey D, Honig B. 2003. GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. Methods in Enzymology 374:492–509. doi:10.1016/S0076-6879(03)74021-X, PMID:14696386
54. Plewczyński D, Ginalski K. 2009. The interactome: predicting the protein-protein interactions in cells. Cellular and Molecular Biology Letters 14:1–22. doi:10.2478/s11658-008-0024-7, PMID:18839074
55. Porta-Pardo E, Garcia-Alonso L, Hrabe T, Dopazo J, Godzik A. 2015. A Pan-Cancer catalogue of cancer driver protein interaction interfaces. PLoS Computational Biology 11:e1004518. doi:10.1371/journal.pcbi.1004518, PMID:26485003
56. Remmert M, Biegert A, Hauser A, Söding J. 2012. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 9:173–175. doi:10.1038/nmeth.1818
57. Rolland T, Taşan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R, Kamburov A, Ghiassian SD, Yang X, Ghamsari L, Balcha D, Begg BE, Braun P, Brehme M, Broly MP, Carvunis AR, et al. 2014. A proteome-scale map of the human interactome network. Cell 159:1212–1226. doi:10.1016/j.cell.2014.10.050, PMID:25416956
58. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, Li N, Berriz GF, Gibbons FD, Dreze M, Ayivi- Guedehoussou N, Klitgord N, Simon C, Boxem M, Milstein S, Rosenberg J, Goldberg DS, Zhang LV, Wong SL, Franklin G, Li S, et al. 2005. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437:1173–1178. doi:10.1038/nature04209, PMID:16189514
59. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. 2010. CORUM: the comprehensive resource of mammalian protein complexes–2009. Nucleic Acids Research 38:D497–D501. doi:10.1093/nar/gkp914, PMID:19884131
60. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. 2004. The Database of Interacting Proteins: 2004 update. Nucleic Acids Research 32:D449–451. doi:10.1093/nar/gkh086, PMID:14681454
61. Shoemaker BA, Panchenko AR. 2007. Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners. PLoS Computational Biology 3:e43. doi:10.1371/journal.pcbi.0030043, PMID:17465672
62. Sonnhammer EL, Östlund G. 2015. InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic. Nucleic Acids Research 43:D234–D239. doi:10.1093/nar/gku1203, PMID:25429972
63. Sprinzak E, Margalit H. 2001. Correlated sequence-signatures as markers of protein-protein interaction. Journal of Molecular Biology 311:681–692. doi:10.1006/jmbi.2001.4920, PMID:11518523
64. Sprinzak E, Sattath S, Margalit H. 2003. How reliable are experimental protein-protein interaction data? Journal of Molecular Biology 327:919–923. doi:10.1016/S0022-2836(03)00239-0, PMID:12662919
65. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. 2011. The BioGRID interaction database: 2011 update. Nucleic Acids Research 39:D698–D704. doi:10.1093/nar/gkq1116, PMID:21071413
66. Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. 2014. The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine. Human Genetics 133:1–9. doi:10.1007/s00439-013-1358-4, PMID:24077912
67. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 102:15545–15550. doi:10.1073/pnas.0506580102, PMID:16199517
68. Tennant-Eyles AJ, Moffitt H, Whitehouse CA, Roberts RG. 2011. Characterisation of the FAM69 family of cysteine-rich endoplasmic reticulum proteins. Biochemical and Biophysical Research Communications 406:471–477. doi:10.1016/j.bbrc.2011.02.076, PMID:21334309
69. Tuncbag N, Gursoy A, Nussinov R, Keskin O. 2011. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nature Protocols 6:1341–1354. doi:10.1038/nprot.2011.367, PMID:21886100
70. Uetz P, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockshon D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623–627. doi:10.1038/35001009, PMID:10688190
71. UniProt Consortium. 2010. The universal protein resource (UniProt) in 2010. Nucleic Acids Research 38:D142–D148. doi:10.1093/nar/gkp846, PMID:19843607
72. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, Hirozane-Kishikawa T, Hao T, Zenkner M, Xin X, Goh KI, Yildirim MA, Simonis N, Heinzmann K, Gebreab F, Sahalie JM, Cevik S, Simon C, de Smet AS, Dann E, Smolyar A, et al. 2009. An empirical framework for binary interactome mapping. Nature Methods 6:83–90. doi:10.1038/nmeth.1280, PMID:19060904
73. Walhout AJ, Sordella R, Lu X, Hartley JL, Temple GF, Brasch MA, Thierry-Mieg N, Vidal M. 2000. Protein interaction mapping in C. elegans using proteins involved in vulval development. Science 287:116–122. doi:10.1126/science.287.5450.116, PMID:10615043
74. Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, et al. 2015. Panorama of ancient metazoan macromolecular complexes. Nature 525:339–344. doi:10.1038/nature14877, PMID:26344197
75. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, Yu H. 2012. Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nature Biotechnology 30:159–164. doi:10.1038/nbt.2106, PMID:22252508
76. Yang AS, Honig B. 2000. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. Journal of Molecular Biology 301:665–678. doi:10.1006/jmbi.2000.3973, PMID:10966776
77. Zhang QC, Petrey D, Deng L, Qiang L, Shi Y, Thu CA, Bisikirska B, Lefebvre C, Accili D, Hunter T, Maniatis T, Califano A, Honig B. 2012. Structure-based prediction of protein-protein interactions on a genome-wide scale. Nature 490:556–560. doi:10.1038/nature11503, PMID:23023127
78. Zhang QC, Petrey D, Garzón JI, Deng L, Honig B. 2013. PrePPI: a structure-informed database of protein-protein interactions. Nucleic Acids Research 41:D828–D833. doi:10.1093/nar/gks1231, PMID:23193263