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Publications

rotating 4D cylinder
our 'supercomputer'
Cold Shock OB-fold
periodic 2D distribution
structure models
are protein folds simple?
CASP predictor evolution
SasA and KaiB fold change
amino-acid similarity
active site of kinase-ATP grasp
EGIG PDF
ferredoxin-like domains with a swap
SH3 domain in a box
MH1 motif alignment
Treble-Clef proteins
transitive links between proteins
protein contact map
Ramachandran on torus
2 types of KH domain
structurally similar or not?
FMN adenylyltransferase
this can happen to you
internal duplication in TIM-barrel
pEVD parameter fit
3 topologies of P-loop kinases
Eigenvectors
α-helix
PII-like trimer
lattice model
covariance matrix of contacts
power EVD distribution
Thioredoxin fold 3dex
Grishin Lab members and alumni are shown in bold, PI-collaborators are underlined.
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252. E.D.Nelson and N.V.Grishin (2016) "Evolution of off-lattice model proteins under ligand binding constraints." Phys Rev E Stat Nonlin Soft Matter Phys 94(6): 022410; PMID: 27627338

251. B.Chitturi, S.Shi, L.N.Kinch, N.V.Grishin (2016) "Compact Structure Patterns in Proteins." Journal of Molecular Biology Aug 4(doi:10.1016/j.jmb.2016.07.022): Epub ahead of print; PMID: 27498165

250. E.D.Nelson and N.V.Grishin (2015) "Anomalous diffusion in neutral evolution of model proteins." Phys Rev E Stat Nonlin Soft Matter Phys 91(6): 060701; PMID: 26172648

249. H.Cheng, Y.Liao, R.D.Schaeffer, N.V.Grishin (2015) "Manual classification strategies in the ECOD database." Proteins Apr 27(doi: 10.1002/prot.24818): Epub ahead of print; PMID: 25917548

248. Q.Cong, D.Borek, Z.Otwinowski and N.V.Grishin (2015) "Tiger Swallowtail genome reveals speciation hotspots and caterpillar chemical defense mechanisms." Cell Reports 10(6): 910-919; PMID: 25683714

247. Y.Liu, J.Pei, N.V.Grishin and W.J.Snell (2015) "The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site and regulates the fusion reaction." Development 142(5): 962-971; PMID: 25655701

246. S.Liu, X.Cai, J.Wu, Q.Cong, X.Chen, T.Li, F.Du, J.Ren, Y.Wu, N.V.Grishin and Z.J.Chen (2015) "Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation." Science 347(6227): aaa2630; PMID: 25636800

245. M.Keane, J.Semeiks, A.E.Webb, Y.I.Li, V.Quesada, T.Craig, L.B.Madsen, S.van Dam, D.Brawand, P.I.Marques, P.Michalak, L.Kang, J.Bhak, H.S.Yim, N.V.Grishin, N.H.Nielsen, M.P.Heide-Jorgensen, E.M.Oziolor, C.W.Matson, G.M.Church, G.W.Stuart, J.C.Patton, J.C.George, R.Suydam, K.Larsen, C.Lopez-Otin, M.J.O'Connell, J.W.Bickham, B.Thomsen and J.P.de Magalhaes (2014) "Insights into the evolution of longevity from the bowhead whale genome." Cell Reports 10(1): 112-122; PMID: 25565328

244. J.Tong, J.Pei, Z.Otwinowski and N.V.Grishin (2014) "Refinement by shifting secondary structure elements improves sequence alignments." Proteins 83(3): 411-427; PMID: 25546158

243. E.D.Nelson and N.V.Grishin (2014) "Structural evolution of proteinlike heteropolymers." Phys Rev E Stat Nonlin Soft Matter Phys 90(6): 062715; PMID: 25615137

242. K.Shiraiwa, Q.Cong and N.V.Grishin (2014) "A new Heraclides swallowtail (Lepidoptera, Papilionidae) from North America is recognized by the pattern on its neck." Zookeys 468: 85-135; PMID: 25610342

241. D.Xu, K.Marquis, J.Pei, S.C.Fu, T.Cagatay, N.V.Grishin, and Y.M.Chook (2014) "LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins." Bioinformatics pii: btu826; PMID: 25515756

240. H.Cheng, R.D.Schaeffer, Y.Liao, L.N.Kinch, J.Pei, S-Y.Shi, B-H.Kim and N.V.Grishin (2014) "ECOD: An evolutionary classification of protein domains." PLoS Comput Biol. 10(12): e1003926; PMID: 25474468

239. Y.Liao, J.Pei, H.Cheng and N.V.Grishin (2014) "An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98." J Mol Biol 426(24): 3935-3945; PMID: 25451782

238. S.Durinck, E.W.Stawiski, A.Pavia-Jimenez, Z.Modrusan, P.Kapur, B.S.Jaiswal, N.Zhang, V.Toffessi-Tcheuyap, T.T.Nguyen, K.B.Pahuja, Y.J.Chen, S.Saleem, S.Chaudhuri, S.Heldens, M.Jackson, S.Pena-Llopis, J.Guillory, K.Toy, C.Ha, C.J.Harris, E.Holloman, H.M.Hill, J.Stinson, C.S.Rivers, V.Janakiraman, W.Wang, L.N.Kinch, N.V.Grishin, P.M.Haverty, B.Chow, J.S.Gehring, J.Reeder, G.Pau, T.D.Wu, V.Margulis, Y.Lotan, A.Sagalowsky, I.Pedrosa, F.J.de Sauvage, J.Brugarolas and S.Seshagiri (2014) "Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes." Nat. Genet. 47(1): 13-21; PMID: 25401301

237. T.Calder, L.M.Kinch, J.Fernandez, D.Salomon, N.V.Grishin and K.Orth (2014) "Vibrio Type III Effector VPA1380 Is Related to the Cysteine Protease Domain of Large Bacterial Toxins." PLoS One 9(8): e104387; PMID: 25099122

236. P.Ayaz, S.Munyoki, E.A.Geyer, F.A.Piedra, E.S.Vu, R.Bromberg, Z.Otwinowski, N.V.Grishin, C.A.Brautigam and L.M.Rice (2014) "A tethered delivery mechanism explains the catalytic action of a microtubule polymerase." Elife 3: e03069; PMID: 25097237

235. J.Semeiks, D.Borek, Z.Otwinowski & N.V.Grishin (2014) "Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys." BMC Genomics 15: 590; PMID: 25015739

234. J.Pei, W.Li, L.N.Kinch and N.V.Grishin (2014) "Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families." Protein Sci. 23(9): 1220-1234; PMID: 24931479

233. D.Salomon, L.N.Kinch, D.C.Trudgian, X.Guo, J.A.Klimko, N.V.Grishin, H.Mirzaei, K.Orth (2014) "Marker for type VI secretion system effectors." Proc Natl Acad Sci U S A 111(25): 9271-9276; PMID: 24927539

232. K.S.Makarova, V.Anantharaman, N.V.Grishin, E.V.Koonin and L.Aravind (2014) "CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems." Front. Genet. 5: 102; PMID: 24817877

231. Q.Cong and N.V.Grishin (2014) "A new Hermeuptychia (Lepidoptera, Nymphalidae, Satyrinae) is sympatric and synchronic with H. sosybius in southeast US coastal plains, while another new Hermeuptychia species - not hermes - inhabits south Texas and northeast Mexico." Zookeys 379: 43-91; PMID: 24574857

230. B.Chen, K.Brinkmann, Z.Chen, C.W.Pak, Y.Liao, S.Shi, L.Henry, N.V.Grishin, S.Bogdan, and M.K.Rosen (2014) "The WAVE Regulatory Complex Links Diverse Receptors to the Actin Cytoskeleton." Cell 156(1-2): 195-207; PMID: 24439376

229. D.Salomon, Y.Guo, L.N.Kinch, N.V.Grishin, K.H.Gardner, and K.Orth (2013) "Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides." Nat Commun. 4: 2973; PMID: 24346350

228. V.M.Zacharia, P.S.Manzanillo, V.R.Nair, D.K.Marciano, L.N.Kinch, N.V.Grishin, J.C.Cox, and M.U.Shiloh (2013) "cor, a novel carbon monoxide resistance gene, is essential for Mycobacterium tuberculosis pathogenesis." MBio 4(6): e00721-13; PMID: 24255121

227. J.Pei and N.V.Grishin (2013) "A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals." PLoS One 8(11): e81109; PMID: 24244731

226. J.Pei and N.V.Grishin (2013) "PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information." Methods Mol Biol, 1079: 263-271; PMID: 24170408

225. Y.Wei, Z.Zou, N.Becker, M.Anderson, R.Sumpter, G.Xiao, L.N.Kinch, P.Koduru, C.S.Christudass, R.W.Veltri, N.V.Grishin, M.Peyton, J.Minna, G.Bhagat, and B. Levine (2013) "EGFR-mediated Beclin 1 phosphorylation in autophagy suppression, tumor progression, and tumor chemoresistance." Cell 154(6): 1269-1284; PMID: 24034250

224. R.Ji, Q.Cong, W.Li, and N.V.Grishin (2013) "M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci." Bioinformatics 29(22): 2953-2954; PMID: 24002112

223. C.He, Y.Wei, K.Sun, B.Li, X.Dong, Z.Zou, Y.Liu, L.N.Kinch, S.Khan, S.Sinha, R.J.Xavier, N.V.Grishin, G.Xiao, E.L.Eskelinen, P.E.Scherer, J.L.Whistler, and B.Levine (2013) "Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism." Cell 154(5): 1085-1099; PMID: 23954414

222. W.Li, L.N.Kinch, and N.V.Grishin (2013) "Pclust: protein network visualization highlighting experimental data." Bioinformatics 29(20): 2647-2648; PMID: 23918248

221. T.A.Tran, L.N.Kinch, S.Peña-Llopis, L.Kockel, N.V.Grishin, H.Jiang, and J.Brugarolas (2013) "Platelet-derived growth factor/vascular endothelial growth factor receptor inactivation by sunitinib results in Tsc1/Tsc2-dependent inhibition of TORC1." Mol Cell Biol. 33(19): 3762-3779; PMID: 23878397

220. L.N.Kinch and N.V.Grishin (2013) "Bioinformatics perspective on rhomboid intramembrane protease evolution and function." Biochim Biophys Acta 1828(12): 2937-2943; PMID: 23845876

219. M.N.Farley, L.S.Schmidt, J.L.Mester, S.Peña-Llopis, A.Pavia-Jimenez, A.Christie, C.D.Vocke, C.J.Ricketts, J.Peterson, L.Middelton, L.N.Kinch, N.V.Grishin, M.J.Merino, A.R.Metwalli, C.Xing, X.J.Xie, P.L.Dahia, C.Eng, W.M.Linehan, and J.Brugarolas (2013) "A novel germline mutation in BAP1 predisposes to familial clear-cell renal cell carcinoma." Mol Cancer Res. 11(9): 1061-1071; PMID: 23709298

218. J.Ning, T.D.Otto, C.Pfander, F.Schwach, M.Brochet, E.Bushell, D.Goulding, M.Sanders, P.A.Lefebvre, J.Pei, N.V.Grishin, G.Vanderlaan, O.Billker, and W.J.Snell (2013) "Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates." Genes Dev. 27(10): 1198-1215; PMID: 23699412

217. C.Huerta, N.V.Grishin, H.Zhang (2013) "The 'super mutant' of yeast FMN adenylyltransferase enhances the enzyme turnover rate by attenuating product inhibition." Biochemistry 52(21): 3615-3617; PMID: 23663086

216. S.Shoji-Kawata, R.Sumpter, M.Leveno, C.R.Campbell, Z.Zou, L.N.Kinch, A.D.Wilkins, Q.Sun, K.Pallauf, D.MacDuff, C.Huerta, H.W.Virgin, J.B.Helms, R.Eerland, S.A.Tooze, R.Xavier, D.J.Lenschow, A.Yamamoto, D.King, O.Lichtarge, N.V.Grishin, S.A.Spector, D.V.Kaloyanova, and B.Levine (2013) "Identification of a candidate therapeutic autophagy-inducing peptide." Nature 494(7436): 201-206; PMID: 23364696

215. W.Li, Q.Cong, L.N.Kinch, and N.V.Grishin (2013) "Seq2Ref: a web server to facilitate functional interpretation." BMC Bioinformatics 14: 30; PMID: 23356573

214. J.K.Huang, J.Pei, and N.V.Grishin (2013) "Defining and predicting structurally conserved regions in protein superfamilies." Bioinformatics 29(2): 175-181; PMID: 23193223

213. B-H.Kim, B.Chitturi, and N.V.Grishin (2012) "Self consistency grouping: a stringent clustering method." BMC Bioinformatics 13: S3; PMID: 23320864

212. F.Quagliarini, Y.Wang, J.Kozlitina, N.V.Grishin, R.Hyde, E.Boerwinkle, D.M.Valenzuela, A.J.Murphy, J.C.Cohen, and H.H.Hobbs (2012) "Atypical angiopoietin-like protein that regulates ANGPTL3." Proc Natl Acad Sci U S A 109(48): 19751-19756; PMID: 23150577

211. Q.Cong and N.V.Grishin (2012) "MESSA: MEta-Server for protein Sequence Analysis." BMC Biol. 10: 82; PMID: 23031578

210. I.A.Rodionova, D.A.Scott, N.V.Grishin, A.L.Osterman, and D.A.Rodionov (2012) "Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima." Environ Microbiol. 14(11): 2920-2934; PMID: 22925190

209. D.Xu, A.Farmer, G.Collett, N.V.Grishin, and Y-M.Chook (2012) "Sequence and structural analyses of nuclear export signals in the NESdb database." Mol Biol Cell. 23(18): 3677-3693; PMID: 22833565

208. D.Xu, N.V.Grishin, and Y-M.Chook (2012) "NESdb: a database of NES-containing CRM1 cargoes." Mol Biol Cell. 23(18): 3673-2676; PMID: 22833564

207. Q.Cong, L.N.Kinch, B-H.Kim, and N.V.Grishin (2012) "Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome." PLoS One 7(7): e41071; PMID: 22815919

206. W.Li, Q.Cong, J.Pei, L.N.Kinch, and N.V.Grishin (2012) "The ABC transporters in Candidatus Liberibacter asiaticus." Proteins 80(11): 2614-2628; PMID: 22807026

205. N.V.Grishin (2012) "Membrane protein structure predictions for exploration." 149(7): 1424-1425; PMID: 22726429

204. X.Jiang, L.N.Kinch, C.A.Brautigam, X.Chen, F.Du, N.V.Grishin, and Z.J.Chen (2012) "Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response." Immunity 36(6): 959-973; PMID: 22705106

203. J.Semeiks and N.V.Grishin (2012) "A method to find longevity-selected positions in the mammalian proteome." PLoS One 7(6): e38595; PMID: 22701678

202. J.Pei and N.V.Grishin (2012) "Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins." Protein Sci. 21(8): 1172-1184; PMID: 22693159

201. S.Peña-Llopis, S.Vega-Rubin-de-Celis, A.Liao, N.Leng, A.Pavia-Jimenez, S.Wang, T.Yamasaki, L.Zhrebker, S.Sivanand, P.Spence, L.N.Kinch, T.Hambuch, S.Jain, Y.Lotan, V.Margulis, A.I.Sagalowsky, P.B.Summerour, W.Kabbani, S.W.Wong, N.V.Grishin, M.Laurent, X.J.Xie, C.D.Haudenschild, M.T.Ross, D.R.Bentley, P.Kapur, and J.Brugarolas (2012) "BAP1 loss defines a new class of renal cell carcinoma." Nat Genet. 44(7): 751-759; PMID: 22683710

200. V.S.Tagliabracci, J.L.Engel, J.Wen, S.E.Wiley, C.A.Worby, L.N.Kinch, J.Xiao, N.V.Grishin, and J.E.Dixon (2012) "Secreted kinase phosphorylates extracellular proteins that regulate biomineralization." Science 336(6085): 1150-1153; PMID: 22582013

199. M.Kato, T.W.Han, S.Xie, K.Shi, X.Du, L.C.Wu, H.Mirzaei, E.J.Goldsmith, J.Longgood, J.Pei, N.V.Grishin, D.E.Frantz, J.W.Schneider, S.Chen, L.Li, M.R.Sawaya, D.Eisenberg, R.Tycko R, and S.L.McKnight (2012) "Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels." Cell 149(4): 753-767; PMID: 22579281

198. S.Han, S.Bahmanyar, P.Zhang, N.V.Grishin, K.Oegema, R.Crooke, M.Graham, K.Reue, J.E.Dixon, and J.M.Goodman (2012) "Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway." J Biol Chem. 287(5): 3123-3137; PMID: 22134922

197. J.Pei and N.V.Grishin (2012) "Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors." Cell Signal. 24(3): 758-769; PMID: 22120523

196. L.N.Kinch, N.V.Grishin, and J.Brugarolas (2011) "Succination of Keap1 and activation of Nrf2-dependent antioxidant pathways in FH-deficient papillary renal cell carcinoma type 2." Cancer Cell. 20(4): 418-420; PMID: 22014567

195. L.N.Kinch, S-Y.Shi, H.Cheng, Q.Cong, J.Pei, W.Mariani, T.Schwede, and N.V.Grishin (2011) "CASP9 target classification." Proteins 79(Suppl 10): 21-36; PMID: 21997778

194. L.N.Kinch, S-Y.Shi, Q.Cong, H.Cheng, Y.Liao, and N.V.Grishin (2011) "CASP9 assessment of free modeling target predictions." Proteins 79(Suppl 10): 59-73; PMID: 21997521

193. Q.Cong, L.N.Kinch, J.Pei, S-Y.Shi, V.N.Grishin, W.Li, and N.V.Grishin (2011) "An automatic method for CASP9 free modeling structure prediction assessment." Bioinformatics 27(24): 3371-3378; PMID: 21994223

192. J.Pei, D.P.Millay, E.N.Olson, and N.V.Grishin (2011) "CREST--a large and diverse superfamily of putative transmembrane hydrolases." Biol Direct 6: 37; PMID: 21733186

191. D.Quiat, K.A.Voelker, J.Pei, N.V.Grishin, R.W.Grange, R.Bassel-Duby, and E.N.Olson (2011) "Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6." Proc Natl Acad Sci U S A 108(25): 10196-10201; PMID: 21633012

190. J.Pei, D.A.Mitchell, J.E.Dixon, and N.V.Grishin (2011) "Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1." J Mol Biol. 410(1): 18-26; PMID: 21570408

189. S.Liang, Y.Zhou, N.V.Grishin, and D.M.Standley (2011) "Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions." J Comput Chem 32(8): 1680-1686; PMID: 21374632

188. J.Wang, N.V.Grishin, L.N.Kinch, J.C.Cohen, H.H.Hobbs, and X-S.Xie (2011) "Sequences in the nonconsensus nucleotide-binding domain of ABCG5/ABCG8 required for sterol transport." J Biol Chem 286(9): 7308-7314; PMID: 21209088

187. D.Das, N.V.Grishin, A.Kumar, D.Carlton, C.Bakolitsa, M.D.Miller, P.Abdubek, T.Astakhova, H.L.Axelrod, P.Burra, C.Chen, H.J.Chiu, M.Chiu, T.Clayton, M.C.Deller, L.Duan, K.Ellrott, D.Ernst, C.L.Farr, J.Feuerhelm, A.Grzechnik, S.K.Grzechnik, J.C.Grant, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.S.Krishna, D.Marciano, D.McMullan, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, T.Wooten, Q.Xu, K.O.Hodgson, J.Wooley, M.A.Elsliger, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010) "The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation." Acta Crystallogr Sect F Struct Biol Cryst Commun. 66(Pt 10): 1174-1181; PMID: 20944208

186. S.A.Teichmann and N.V.Grishin (2010) "Sequences and topology: evolution of proteins and evolution of computational approaches." Curr Opin Struct Biol. 20(3): 333-334; PMID: 20483587

185. Q.Cong, B-H. Kim, L.N.Kinch, and N.V.Grishin (2010) "Structural Differences Between Proteins With Similar Sequences" IEEE Proc. Bioinformatics and Bioengineering: 250-257

184. B.Chitturi, D.Bein, and N.V.Grishin (2010) "Complete Enumeration of Compact Structural Motifs in Proteins" ISB '10 Proceedings of the International Symposium on Biocomputing: 1-8.

183. B-H.Kim, Q.Cong, and N.V.Grishin (2010) "HangOut: generating clean PSI-BLAST profiles for domains with long insertions." Bioinformatics 26(12): 1564-1565; PMID: 20413635

182. P.Luong, L.N.Kinch, C.A.Brautigam, N.V.Grishin, D.R.Tomchick, and K.Orth (2010) "Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain." J Biol Chem. 285(26): 20155-20163; PMID: 20410310

181. S.Vega-Rubin-de-Celis, Z.Abdallah, L.N.Kinch, N.V.Grishin, J.Brugarolas, X.Zhang (2010) "Structural analysis and functional implications of the negative mTORC1 regulator REDD1." Biochemistry 49(11): 2491-2501; PMID: 20166753

180. S.He, C.McPhaul, J.Z.Li, R.Garuti, L.N.Kinch, N.V.Grishin, J.C.Cohen, H.H.Hobbs (2010) "A sequence variation (I148M) in PNPlA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis." J Biol Chem 285(9): 6706-6715; PMID: 20034933

179. S.Shi, J.Pei, R.I.Sadreyev, L.N.Kinch, I.Majumdar, J.Tong, H.Cheng, B.H.Kim, N.V.Grishin (2009) "Analysis of CASP8 targets, predictions and assessment methods." Database (Oxford) 2009: bap003; PMID: 20157476

178. R.I.Sadreyev, Y.Wang, and N.V.Grishin (2009) "Considering scores between unrelated proteins in the search database improves profile comparison." BMC Bioinformatics 10: 399; PMID: 19961610

177. A.A.Salahudeen, J.W.Thompson, J.C.Ruiz, H.W.Ma, L.N.Kinch, Q.Li, N.V.Grishin, and R.K.Bruick (2009) "An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis." Science 326(5953): 722-726; PMID: 19762597

176. R.I.Sadreyev, J.D.Feramisco, H.Tsao, and N.V.Grishin (2009) "Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways." Bioinformatics 25(22): 2891-2896; PMID: 19744994

175. S.Raman, R.Vernon, J.Thompson, M.Tyka, R.I.Sadreyev, J.Pei, D.Kim, E.Kellogg, F.DiMaio, O.Lange, L.N.Kinch, W.Sheffler, B.H.Kim, R.Das, N.V.Grishin, and D.Baker (2009) "Structure prediction for CASP8 with all-atom refinement using Rosetta." Proteins 77 Suppl 9: 89-99; PMID: 19701941

174. Y.Liu, X.Ye, F.Jiang, C.Liang, D.Chen, J.Peng, L.N.Kinch, N.V.Grishin, and Q.Liu (2009) "C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation." Science 325(5941): 750-753; PMID: 19661431

173. L.Zhao, H.Dong, C.C.Zhang, L.N.Kinch, M.Osawa, M.Iacovino, N.V.Grishin, M.Kyba, and L.J.Huang (2009) "A JAK2 interdomain linker relays Epo receptor engagement signals to kinase activation." J Biol Chem 284(39): 26988-26998; PMID: 19638629

172. J.Pei, C.Ma, J.Rizo, and N.V.Grishin (2009) "Remote homology between Munc13 MUN domain and vesicle tethering complexes." J Mol Biol 391(3): 509-517; PMID: 19563813

171. J.D.Feramisco, R.I.Sadreyev, M.L.Murray, N.V.Grishin, and H.Tsao (2009) "Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database." J Invest Dermatol 129(11): 2628-2636; PMID: 19536140

170. L.N.Kinch, M.L.Yarbrough, K.Orth, and N.V.Grishin (2009) "Fido, a novel AMPylation domain common to fic, doc, and AvrB." PLoS One 4(6): e5818; PMID: 19503829

169. Y.Wang, R.I.Sadreyev, and N.V.Grishin (2009) "PROCAIN server for remote protein sequence similarity search." Bioinformatics 25(16): 2076-2077; PMID: 19497935

168. R.I.Sadreyev, B.H.Kim, and N.V.Grishin (2009) "Discrete-continuous duality of protein structure space." Curr Opin Struct Biol. 19(3): 321-328; PMID: 19482467

167. R.I.Sadreyev, M.Tang, B.H.Kim, and N.V.Grishin (2009) "COMPASS server for homology detection: improved statistical accuracy, speed and functionality." Nucleic Acids Res. 37(WSi): W90-W94; PMID: 19435884

166. J.Pei and N.V.Grishin (2009) "The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold." Proteins 77(2): 413-419; PMID: 19434753

165. S-Y.Shi, B.Chitturi, and N.V.Grishin (2009) "ProSMoS server: a pattern-based search using interaction matrix representation of protein structures." Nucleic Acids Res. 37(WSi): W526-W531; PMID: 19420061

164. B.H.Kim, H.Cheng, and N.V.Grishin (2009) "HorA web server to infer homology between proteins using sequence and structural similarity." Nucleic Acids Res. 37(WSi): W532-W538; PMID: 19417074

163. C.Huerta, D.Borek, M.Machius, N.V.Grishin, and H.Zhang (2009) "Structure and mechanism of a eukaryotic FMN adenylyltransferase." J Mol. Biol. 389(2): 388-400 Jun 5; PMID: 19375431

162. Y.Wang, R.I.Sadreyev, and N.V.Grishin (2009) "PROCAIN: protein profile comparison with assisting information." Nucleic Acids Res. 37(11): 3522-3530; PMID: 19357092

161. I.Majumdar, L.N.Kinch, and N.V.Grishin (2009) "A database of domain definitions for proteins with complex interdomain geometry." PLoS ONE 4(4): e5084 Apr 8; PMID: 19352501

160. R.I.Sadreyev, S-Y.Shi, D.Baker and N.V.Grishin (2009) "Structure similarity measure with penalty for close non-equivalent residues." Bioinformatics 25(10): 1259-1263; PMID: 19321733

159. J.Pei, P.J.Lupardus, K.C.Garcia and N.V.Grishin (2009) "CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins." Protein Science 18(4): 856-862 Feb 10; PMID: 19309740

158. J.Pei and N.V.Grishin (2009) "Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH." Cell Cycle 8(9): [Epub] May 19; PMID: 19305154

157. W.Yin, S.Romeo, S.Chang, N.V.Grishin, H.H.Hobbs, and J.C.Cohen (2009) "Genetic Variation in ANGPTL4 Provides Insights into Protein Processing and Function." J.Biol.Chem. 284(19): 13213-13222 Mar 7; PMID: 19270337

156. L.N.Kinch and N.V.Grishin (2009) "The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif." Biol Direct 4: 2 Jan 21; PMID: 19159466

155. Y.Wang, P.J.Kuan, C.Xing, J.T.Cronkhite, F.Torres, R.L.Rosenblatt, J.M.DiMaio, L.N.Kinch, N.V.Grishin, and C.K.Garcia (2009) "Genetic Defects in Surfactant Protein A2 Are Associated with Pulmonary Fibrosis and Lung Cancer." The American Journal of Human Genetics 84(1): 52-59 Jan 9; PMID: 19100526

154. M.L.Yarbrough, Y.Li, L.N.Kinch, N.V.Grishin, H.L.Ball and K.Orth (2009) "AMPylation of Rho GTPases by Vibrio VopS Disrupts Effector Binding and Downstream Signaling." Science 323(5911): 269-272 Nov 27 2008; PMID: 19039103

153. J.Zhang, R.Sprung, J.Pei, X.Tan, S.Kim, H.Zhu, C.F. Liu, N.V.Grishin and Y.Zhao (2008) "Lysine acetylation is a highly abundant and evolutionarily conserved modification in E. coli." Mol Cell Proteomics 8(2): 215-225 Aug 23; PMID: 18723842

152. S.A.Teichmann and N.V.Grishin (2008) "Sequences and topology: from genome structure to protein structure." Curr Opin Struct Biol. 18(3): 340-341 Jun 6; PMID: 18539451

151. J.Pei, M.Tang and N.V.Grishin (2008) "PROMALS3D: a web server for accurate multiple protein sequence and structure alignment". Nucleic Acids Research 36(Web Server issue): W30-34 Jul 1; PMID: 18503087

150. Y.Liu, R.Tewari, J.Ning, A.M.Blagborough, S.Garbom, J.Pei, N.V.Grishin, R.E.Steele, R.E.Sinden, W.J.Snell and O.Billker (2008) "The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes". Genes & Development 22(8): 1051-1068 Apr 15; PMID: 18367645

149. M.F.Bolliger, J.Pei, S.Maxeiner, A.Boucard, N.V.Grishin and T.C.Südhof (2008) "Unusually rapid evolution of neuroligin-4 in mice." PNAS 105(17): 6421-6426 PMID: 18434543

148. J.Pei, B.H.Kim and N.V.Grishin (2008) "PROMALS3D: a tool for multiple protein sequence and structure alignments." Nucleic Acids Res. 36(7): 2295-2300 PMID: 18287115

147. J.O.Wrabl and N.V.Grishin (2008) "Statistical Modeling of Random Protein Superpositions: p-Values for Pairwise Structure Alignment." J.Comp.Biol. 15(3): 317-355 PMID: 18333756

146. R.I.Sadreyev and N.V.Grishin (2008) "Accurate statistical model of comparison between multiple sequence alignments." Nucleic Acids Res. 36(7): 2240-2248 PMID: 18285364

145. H.Cheng, B.H.Kim and N.V.Grishin (2008) "Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable datasets." J.Mol.Biol. 377(4): 1265-1278 PMID: 18313074

144. N.Huang, L.Sorci, X.Zhang, C.A.Brautigam, X.Li, N.Raffaelli, G.Magni, N.V.Grishin, A.L.Osterman and H.Zhang (2008) "Bifunctional NMN Adenylyltransferase/ADP-Ribose Pyrophosphatase: Structure and Function in Bacterial NAD Metabolism" Structure 16(2): 196-209 PMID: 18275811

143. J.Yang. M.S.Brown, G.Liang, N.V.Grishin and J.L.Goldstein (2008) "Identification of the acyltransferase that octanoylates and activates ghrelin, an appetite-stimulating peptide hormone". Cell 132(3): 387-396 PMID: 18267071

142. E.D.Nelson and N.V.Grishin (2008) "Folding domain B of protein A on a dynamically partitioned free energy landscape". PNAS 105(5): 1489-1493 PMID: 18503087

141. R.E.Infante, A.Radhakrishnan, L.Abi-Mosleh, L.N.Kinch, M.L.Wang, N.V.Grishin, J.L.Goldstein, M.S.Brown (2008) "Purified NPC1 Protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loop". J Biol Chem. 283(2): 1064-1075 Jan 11; PMID: 17989072

140. H.Cheng, B.H.Kim and N.V.Grishin (2007) "MALISAM: a database of structurally analogous motifs". Nucleic Acids 36(Database Issue): D211-217 PMID: 17855399

139. K.M.Szymanski, D.Binns, R.Bartz, N.V.Grishin, W.P.Li, A.K.Agarwal, A.Garg, R.G.Anderson, J.M.Goodman (2007) "The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology". PNAS 104(52): 20890-20895 Dec 26; PMID: 18093937

138. H.Cheng, B.H.Kim and N.V.Grishin (2007) "MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs". Proteins 70(4): 1162-1166 PMID: 17932926

137. N.B.Holladay, L.N.Kinch and N.V.Grishin (2007) "Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity". Protein Science 16(10): 2140-2152 PMID: 17893360

136. Y.Qi, R.I.Sadreyev, Y.Wang, B.H.Kim and N.V.Grishin (2007) "A comprehensive system for evaluation of remote sequence similarity detection". BMC Bioinformatics 8: 314 PMID: 17725841

135. L.Knizewski, L.N.Kinch, N.V.Grishin, L.Rychlewski and K.Ginalski (2007) "Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches". BMC Structural Biology 7: 40 PMID: 17584917

134. R.I.Sadreyev, M.Tang, B.H.Kim and N.V.Grishin (2007) "COMPASS server for remote homology inference". Nucleic Acids Res. 35(Web Server issue): W653-658 PMID: 17517780

133. A.Dikiy, S.V.Novoselov, D.E.Fomenko, A.Sengupta, B.A.Carlson, R.L.Cerny, K.Ginalski, N.V.Grishin, D.L.Hatfield, V.N.Gladyshev (2007) "SelT, SelW, SelH, and Rdx12: Genomics and Molecular Insights into the Functions of Selenoproteins of a Novel Thioredoxin-like Family". Biochemistry 46(23): 6871-6882 Jun 12; PMID: 17503775

132. J.Pei, B.H.Kim, M.Tang and N.V.Grishin (2007) "PROMALS web server for accurate multiple protein sequence alignments". Nucleic Acids Res. 35(Web Server issue): W649-652 PMID: 17452345

131. G.A.Belogurov, M.N.Vassylyeva, V.Svetlov, S.Klyuyev, N.V.Grishin, D.G.Vassylyev and I.Artsimovitch (2007) "Structural basis for converting a general transcription factor into an operon-specific virulence regulator". Mol Cell 26(1): 117-129 PMID: 17434131

130. S.Shi, Y.Zhong, I.Majumdar, S.S.Krishna and N.V.Grishin (2007) "Searching for three dimensional secondary structural patterns in proteins with ProSMoS". Bioinformatics 23(11): 1331-1338 PMID: 17384423

129. J.Pei and N.V.Grishin (2007) "PROMALS: towards accurate multiple sequence alignments of distantly related proteins". Bioinformatics. 23(7): 802-808 PMID: 17267437

128. K.S.Saikatendu, X.Zhang, L.N.Kinch, M.Leybourne, N.V.Grishin and H.Zhang (2006) "Structure of a conserved hypothetical protein SA1388 from S. aureus reveals a capped hexameric toroid with two PII domain lids and a dinuclear metal center". BMC Struct Biol. 6: 27 PMID: 17187687

127. K.Steczkiewicz, L.N. Kinch, N.V.Grishin, L.Rychlewski and K.Ginalski (2006) "Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily". Cell Cycle. 5(24): 2927-2930 PMID: 17172875

126. L.N.Kinch and N.V.Grishin (2006) "Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution". Protein Sci. 15(11): 2669-2674 PMID: 17075139

125. J. Pei and N.V.Grishin (2006) "MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information". Nucleic Acids Res 34(16): 4364-4374 PMID: 16936316

124. S.Kim, R.Sprung, Y.Chen, Y.Xu, H.Ball, J.Pei, T.Cheng, Y.Kho, L.Xiao, H.Xiao, N.V.Grishin, M.White, X-J.Yang, Y.Zhao (2006) "Substrate and Functional Diversity of Lysine Acetylation Revealed by a Proteomics Survey". Molecular Cell 23(4): 607-618 PMID: 16916647

123. KS.Makarova, N.V.Grishin and E.V. Koonin (2006) "The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria". Bioinformatics 22(21): 2581-2584 PMID: 16895922

122. Z.Zhao, Y.Tuakli-Wosornu, T.A.Lagace, L.N.Kinch, N.V.Grishin, J.D.Horton, J.C.Cohen, H.H.Hobbs (2006) "Loss-of-function mutations in PCSK9 - Genetic absence of PCSK9 in humans results in very low LDL." Am J Hum Genet. 79(3): 514-523 PMID: 16909389

121. S.A.Teichmann and N.V.Grishin (2006) "Sequences and topology: from methods to meaning". Curr Opin Struct Biol. 16(3): 359-361 PMID: 18539451

120. S.Cheek, S.S.Krishna and N.V.Grishin (2006) "Structural Classification of Small, Disulfide-rich Protein Domains". J Mol Biol. 359(1): 215-237 PMID: 16618491

119. S.S.Krishna, R.I.Sadreyev and N.V.Grishin (2006) "A tale of two ferredoxins: sequence similarity and structural differences". BMC Struct. Biol. 6: 8 PMID: 16603087

118. E.D.Nelson and N.V.Grishin (2006) "Alternate pathways for folding in the flavodoxin fold family revealed by a nucleation-growth model". J Mol Biol 358(3): 646-653 PMID: 16563435

117. R.I.Sadreyev and N.V.Grishin (2006) "Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds." BMC Struct Biol 6: 6 Mar 20; PMID: 16549009

116. K.S.Makarova, N.V.Grishin, S.A.Shabalina, Y.I.Wolf, E.V.Koonin (2006) "A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action". Biol Direct 1: 7 Mar 16; PMID: 16545108

115. E.D.Nelson and N.V.Grishin (2006) "Scaling approach to the folding kinetics of large proteins". Phys Rev E Stat Nonlin Soft Matter Phys 73(1 Pt 1):011904. PMID: 16486182

114. L.Knizewski, L.N.Kinch, N.V. Grishin, L.Rychlewski, K.Ginalski (2006) "Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease". J Virol. 80(5): 2575-2577 PMID: 16474163

113. L.N.Kinch, K.Ginalski and N.V.Grishin (2006) "Site-2 protease regulated intracellular proteolysis: sequence homologs define an ancient signaling cascade". Protein Sci. 15(1): 84-93 PMID: 16322567

112. J.Pei, W.Cai, L.N.Kinch and N.V.Grishin (2006) "Prediction of functional specificity determinants from protein sequences using log-likelihood ratios". Bioinformatics, 22(2): 164-171 PMID: 16278237

111. J.Basu, N.Shen, I.Dulubova, J.Lu, R.Guan, O.Guryev, N.V.Grishin, C.Rosenmund, J.Rizo (2005) "A minimal domain responsible for Munc13 activity". Nat Struct Mol Biol. 12(11): 1017-1018 PMID: 16228007

110. J.O.Wrabl and N.V.Grishin (2005) "Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization". Proteins, 61(3): 523-534 PMID: 16184599

109. J.Pei and N.V.Grishin (2005) "COG3926 and COG5526: a tale of two new lysozyme-like protein families". Protein Sci. 14(10): 2574-2581 PMID: 16155206

108. I.Majumdar, S.S.Krishna and N.V.Grishin (2005) "PALSSE: A program to delineate linear secondary structural elements from protein structures". BMC Bioinformatics 6: 202 PMID: 16095538

107. L.N.Kinch, K.Ginalski, L.Rychlewski and N.V.Grishin (2005) 'Identification of novel restriction endonuclease-like families among hypothetical proteins". NAR 33(11): 3598-3605 PMID: 15972856

106. B.H.Kim, R.I.Sadreyev and N.V.Grishin (2005) "COG4849 belongs to nucleotidyltransferase superfamily". J. Mol. Recogn. 18(5): 422-425 PMID: 15983981

105. H.Cheng and N.V.Grishin (2005) "DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain". Protein Science, 14(7): 1902-10 PMID: 15937278

104. S.Cheek, K.Ginalski, H.Zhang and N.V.Grishin (2005) "A comprehensive update of the sequence and structure classification of kinases". BMC Structural Biology, 5(1): 6 PMID: 15771780

103. K.Ginalski, N.V.Grishin, A. Godzik, L. Rychlewski (2005) "Practical lessons from protein structure prediction". NAR 33(6): 1874-1891 PMID: 15805122

102. J.Pei and N.V.Grishin (2005) "The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases". Protein Science, 14(5): 1370-1374 PMID: 15802648

101. S.S.Krishna and N.V.Grishin (2005) "Structural drift: a possible path to protein fold change". Bioinformatics 21(8): 1308-1310 PMID: 15604105

100. M.Zheng, L.Rychlewski, K.Ginalski and N.V.Grishin (2005) "Protein domain of unknown function DUF1023 is an alpha/beta-hydrolase". Proteins 59(1): 1-6 PMID: 15688435

99. D.Araç, I.Dulubova, J.Pei, I.Huryeva, N.V.Grishin, T.C.Südhof and J.Rizo (2005) "Three-dimensional Structure of the rSly1 N-terminal Domain Reveals a Conformational Change Induced by Binding to Syntaxin 5". J. Mol. Biol. 346(2): 589-601 PMID: 15670607

98. L.N.Kinch, S.Cheek and N.V.Grishin (2005) "EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV". Protein Science 14(2): 360-367 PMID: 15632288

97. Y.Qi and N.V.Grishin (2005) "Structural Classification of Thioredoxin-like Fold Proteins". Proteins 58(2): 376-388 PMID: 15558583

96. E.D.Nelson and N.V.Grishin (2004) "Efficient expansion, folding, and unfolding of proteins". Phys Rev E Stat Nonlin Soft Matter Phys, 70(5 Pt 1): 051906 PMID: 15600655

95. S.Cheek, Y.Qi, S.S.Krishna, L.N.Kinch and N.V.Grishin (2004) "SCOPmap: automated assignment of protein structures to evolutionary superfamilies". BMC Bioinformatics 5(1): 197 PMID: 15598351

94. W.Cai, J.Pei and N.V.Grishin (2004) "Reconstruction of ancestral protein sequences and its applications". BMC Evolutionary Biology 4(1): 33 PMID: 15377393

93. Y.Qi and N.V.Grishin (2004) "PCOAT: positional correlation analysis using multiple methods". Bioinformatics 20(18): 3697-3699 PMID: 15271785

92. S.S.Krishna and N.V.Grishin (2004) "The finger domain of the human deubiquinating enzyme HAUSP is a zinc ribbon". Cellular Biology 3(8): 1046-1049 PMID: 15254399

91. T.A.Rand, K.Ginalski, N.V.Grishin and X.Wang (2004) "Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity". PNAS 101(40): 14385-14389 PMID: 15452342

90. K.Ginalski, H.Zhang and N.V.Grishin (2004) "Raptor Protein Contains Caspase-like Domain". TiBS 29(10): 522-524 PMID: 15450605

89. R.I.Sadreyev and N.V.Grishin (2004) "Estimates of statistical significance for comparison of individual positions of multiple sequence alignments". BMC Bioinformatics 5(1): 106 PMID: 15296518

88. R.Shah, C.Colemen, K.Mir, J.Baldwin, J.L.Van Etten, N.V.Grishin, A.E.Pegg, B.A.Stanley and M.A.Phillips (2004) "Chlorella virus encodes an unusual arginine decarboxylase that is a close homolog of eukaryotic ornithine decarboxylase". JBC 279(34): 35760-35767 PMID: 15190062

87. K.Ginalski, L.N.Kinch, L.Rychlewski and N.V.Grishin (2004) "BTLCP proteins: a novel family of bacterial cysteine proteinases". TiBS 29(8): 392-395 PMID: 15288868

86. H.Cheng, N.Shen, J.Pei and N.V.Grishin (2004) "Double-stranded DNA Bacteriophage Prohead Protease Is Homologous to Herpesvirus Protease". Protein Science 13(8): 2260-2269 PMID: 15273316

85. J.Pei and N.V.Grishin (2004) "Combining evolutionary and structural information for local protein structure prediction". Proteins 56(4): 782-794 PMID: 15281130

84. S.S.Krishna and N.V.Grishin (2004) "Structurally analogous proteins do exist!" Structure 12(7): 1125-1127 PMID: 1524287

83. K.Ginalski, L.N.Kinch, L.Rychlewski and N.V.Grishin (2004) “DCC proteins: a novel family of thiol-disulfide oxidoreductases.” TiBS 29(7): 339-342 PMID: 15236740

82. K. Ginalski, M.von Grotthuss, N.V.Grishin and L.Rychlewski (2004) "Detecting distant homology with Meta-BASIC". NAR 32: W576-581 PMID: 15215454

81. K.Ginalski, L.N.Kinch, L.Rychlewski and N.V.Grishin (2004) "BOF: a novel family of bacterial OB-fold proteins". FEMS Lett 567(2-3): 297-301 PMID: 15178340

80. K.Ginalski, L.Rychlewski, D.Baker and N.V.Grishin (2004) "Protein structure prediction for the male-specific region of the human Y chromosome". PNAS 101(8): 2305-2310 PMID: 14983005

79. R.I.Sadreyev and N.V.Grishin (2004) "Quality of alignment comparison by COMPASS improves with profile diversity". Bioinformatics 20(6): 818-828 PMID: 14751996

78. J.O.Wrabl and N.V.Grishin (2004) "Gaps in Structurally Similar Proteins: Towards Improvement of Multiple Sequence Alignment". Proteins 54(1): 71-87 PMID: 14705025

77. S.Liang and N.V.Grishin (2004) "Effective Scoring Function for Protein Sequence Design". Proteins 54(2): 271-281 PMID: 14696189

76. L.N.Kinch, J.O.Wrabl, S.S.Krishna, I.Majumdar, R.I.Sadreyev, Y.Qi, J.Pei, H.Cheng, and N.V. Grishin (2003) "CASP5 Assessment of Fold Recognition Target Predictions". Proteins 53(S6): 395-409 PMID: 14579328

75. L.N.Kinch, Y.Qi, T.Hubbard and N.V.Grishin (2003) "CASP5 Target Classification". Proteins, 53(S6): 340-351 PMID: 14579323

74. J.Pei, N.V.Dokholyan, E.I.Shakhnovich and N.V.Grishin (2003) "Using protein design for homology detection and active site searches". PNAS 100(20): 11361-11366 PMID: 12975528

73. R.Sadreyev, D.Baker and N.V.Grishin (2003) "Profile-profile comparisons by COMPASS predict intricate homologies between protein families". Protein Science. 12(10): 2262-2272 PMID: 14500884

72. D.Mittelman, R.I.Sadreyev and N.V.Grishin (2003) "Probablilistic scoring measures for profile-profile comparison yield more accurate seed alignments." Bioinformatics 19(12): 1531-1539 PMID: 12912834

71. L.N.Kinch, D.Baker and N.V.Grishin (2003) "Deciphering a Novel Thioredoxin - Like Fold Family." Proteins: Struct. Func. and Genetics 52(3): 323-331 PMID: 12866046

70. X.Zhang, O.V.Kurnasov, S.Karthikeyan, N.V.Grishin, A.L.Osterman and H.Zhang (2003) "Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis." J Biol Chem. 278(15): 13503-13511 PMID: 12574164

69. J.Pei and N.V.Grishin (2003) "Peptidase Family U34 is an Extension of the N-Terminal Nucleophile Hydrolases." Protein Science 12(5): 1131-1135 PMID: 12717035

68. S.Karthikeyan, Q.Zhou, F.Mseeh, N.V.Grishin, A.L.Osterman and H.Zhang (2003) "Crystal structure of human riboflavin kinase reveals a beta-barrel fold and a novel active site arch." Structure, 11(3): 265-273 PMID: 12623014

67. E.D.Nelson and N.V.Grishin (2003) "Investigation of the folding profiles of evolutionarily selected model proteins". J.Chem.Phys 118 (7): 3342-3349

66. J.Pei, R.I.Sadreyev and N.V.Grishin (2003) "PCMA: Fast and Accurate Multiple Sequence Alignment Based on Profile Consistency". Bioinformatics 19(3): 427-428. PMID: 12584134

65. R.I.Sadreyev and N.V.Grishin (2003) "COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance.” J. Mol. Biol 326(1): 317-336 PMID: 12547212

64. S.S.Krishna, I.Majumdar and N.V.Grishin (2003) "Structural classification of zinc fingers". Nucleic Acid Research 31(2): 532-550 PMID: 12527760

63. V.N.Grishin and N.V.Grishin (2002) "Euclidean space and grouping of biological objects". Bioinformatics, 18(11): 1523-1534 PMID: 12424125

62. B.Barylko, P.Wlodarski, D.D.Binns, S.H.Gerber, S.Earnest, T.C.Sudhof, N.Grichine and J.P.Albanesi (2002) "Analysis of the catalytic domain of phosphatidylinositol 4-kinase type II." J Biol Chem. 277(46): 44366-44375 PMID: 12215430

61. Y.I.Wolf, I.B.Rogozin, N.V.Grishin and E.V.Koonin (2002) "Genome trees and the tree of life." Trends Genet. 18(9): 472-479 PMID: 12175808

60. S.K.Singh, O.V.Kurnasov, B.Chen, H.Robinson, N.V.Grishin, A.L.Osterman and H.Zhang (2002) "Crystal structure of Haemophilus influenzae NadR protein: a bifunctional enzyme endowed with NMN adenylyltransferase and ribosylnicotinamide kinase activities." J Biol Chem. 277(36): 33291-33299 PMID: 12068016

59. S.Cheek, H.Zhang and N.V.Grishin (2002) "Sequence and Structure Classification of Kinases." J.Mol.Biol. 320(4): 855-881 PMID: 12095261

58. L.N.Kinch and N.V.Grishin (2002) "Evolution of Protein Structures and Functions." Current Opinions in Struct. Biol. 12(3): 400-408 PMID: 12127461

57. L.N.Kinch and N.V.Grishin (2002) "Expanding the Nitrogen Regulatory Protein Superfamily: Homology Detection at Below Random Sequence Identity" Proteins: Struct. Func. and Genetics 48(1): 75-84 PMID: 12012339

56. Y.Qi, J.Pei, and N.V. Grishin (2002) "C-Terminal Domain of Gyrase A is Predicted to Have a β-Propeller Structure." Proteins: Struct. Func. and Genetics 47(3): 258-264 PMID: 11948780

55. L.N.Kinch, M.H.Saier, Jr. and N.V.Grishin (2002) "Sec61β – a component of the archaeal protein secretory system". TiBS 27(4): 170-171 PMID: 11943537

54. H.Zhang, T.Zhou, O.Kurnasov, S.Cheek, N.V. Grishin and A.L.Osterman (2002) "Crystal structure of E.coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD." Structure 10(1): 69-79 PMID: 11796112

53. J.Pei and N.V.Grishin (2002) "Breaking the Singleton of Germination Protease." Protein Science 11(3): 691-697 PMID: 11847292

52. D.A.Sierra, D.J.Gilbert, D.Householder, N.V.Grishin, K.Yu, P.Ukidwe, S.A.Barker, W.He, T.G.Wensel, G.Otero, G.Brown, N.G.Copeland, N.A.Jenkins and T.M.Wilkie (2002) "Evolution of the Regulators of G-Protein Signaling Multigene Family in Mouse and Human." Genomics 79(2): 177-185 PMID: 11829488

51. S.Liang and N.V.Grishin (2002) "Side-chain modeling with an optimized scoring function." Protein Science 11(2): 322-331 PMID: 11790842

50. K.S.Makarova, L.Aravind, N.V.Grishin, I.B.Rogozin and E.V.Koonin (2002) "A DNA repair system specific for thermophilic archaea and bacteria predicted by genomic context analysis." Nucleic Acid Research 30(2): 482-496 PMID: 11788711

49. T.Zhou, O.Kurnasov, D.R.Tomchick, D.D.Binns, N.V.Grishin, V.E.Marquez, A.L.Osterman and H.Zhang (2002) "Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin". J Biol Chem. 277(15): 13148-13154 PMID: 11488603

48. J.O.Wrabl and N.V.Grishin (2001) "Homology Between O-linked Glycosyl Transferases and the Glycogen Phosphorylase Superfamily." J.Mol.Biol. 314(3): 375-384 PMID: 11846551

47. Y.I.Wolf, I.B.Rogozin, N.V. Grishin, R.L.Tatusov and E.V.Koonin (2001) "Genome trees constructed using five different approaches suggest new major bacterial clades." BMC Evolutionary Biology 1(1): 8 PMID: 11734060

46. N.V.Grishin (2001) "Fold change in evolution of protein structures." J. Struct. Biol. 134: 167-185 PMID: 11551177

45. J.J.Abbott, J.Pei, J.L.Ford, Y.Qi, V.N.Grishin, L.A.Pitcher, M.A.Phillips and N.V.Grishin (2001) "Structure prediction and active site analysis of the metal binding determinants in g-glutamylcysteine synthetase." J Biol Chem 276(45): 42099-42107 PMID: 11527962

44. J.Pei and N.V.Grishin (2001) "AL2CO: Calculation of Positional Conservation in a Protein Sequence Alignment." Bioinformatics. 17(8): 700-712 PMID: 11524371

43. J.Pei and N.V.Grishin (2001) "Type II CAAX prenyl endopeptidases belong to a novel superfamily of putative membrane-bound metalloproteases." TiBS. 26(5): 275-277 PMID: 11343912

42. C.K.Garcia, K.Wilund, M.Arca, G.Zuliani, R.Fellin, M.Maioli, S.Calandra, S.Bertolini, F.Cossu, N.V.Grishin, R.Barnes, J.C.Cohen and H.H.Hobbs (2001) "Autosomal recessive hypercholesterolemia caused by mutations in a putative LDL receptor adaptor protein." Science. 292(5520): 1394-1398 PMID: 11326085

41. N.V.Grishin (2001) "Treble Clef Finger - a Functionally Diverse Zinc-Binding Structural Motif." Nucleic Acid Research. 29(8): 1703-1714 PMID: 11292843

40. N.V.Grishin (2001) "MH1 domain of Smad is a degraded homing endonuclease." J Mol Biol 307(1): 31-37 PMID: 11243801

39. B.Barylko, S.H.Gerber, D.D.Binns, N.Grichine, M.Khvotchev, T.C.Sudhof, J.P.Albanesi (2001) "A Novel Family of Phosphatidylinositol 4-Kinases Conserved from Yeast to Humans." J Biol Chem. 276(11): 7705-7708 PMID: 11244087

38. N.V.Grishin (2001) "KH domain: one motif, two folds." Nucleic Acid Research. 29(3): 638-643 PMID: 11160884

37. M.M.Horvath and N.V.Grishin (2001) "The C-terminal domain of E. coli HPII catalase is a member of the type I glutamine amidotransferase superfamily." Proteins: Struct. Func. and Genetics 42(2): 230-236 PMID: 11119647

36. J.Pei and N.V.Grishin (2001) "GGDEF domain is homologous to adenylate cyclase." Proteins: Struct. Func. and Genetics 42(2): 210-216 PMID: 11119645

35. K.E.Berge, H.Tian, G.A.Graf, L.Yu, N.V.Grishin, J.Schultz, P.Kwiterovich, B.Shan, R.Barnes and H.H.Hobbs (2000) "Accumulation of Dietary Cholesterol in Sitosterolemia Caused by Mutations in Adjacent ABC Transporters." Science 290(5497): 1771-1775 PMID: 11099417

34. T.Zhou, M.Daugherty, N.V.Grishin, A.L.Osterman and H.Zhang (2000) "Structure and Mechanism of Homoserine Kinase: prototype for GHMP kinase superfamily." Structure 8: 1247-1257 PMID: 11188689

33. M.Y.Galperin and N.V.Grishin (2000) "The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase." Proteins:Struct. Func. and Genetics 41(2): 238-247 PMID: 10966576

32. N.V.Grishin, Y.I.Wolf and E.V.Koonin (2000) "From complete genomes to measures of substitution rate variability within and between proteins." Genome Res. 10(7): 991-1000 PMID: 10899148

31. X.Shao and N.V.Grishin (2000) "Common fold in helix-hairpin-helix proteins" Nucleic Acid Research, 28(14): 2643-2650 PMID: 10908318

30. N.V.Grishin (2000) "C-terminal domains of Escherichia coli topoisomerase I belong to the zinc ribbon superfamily." J. Mol. Biol. 299(5): 1165-1177 PMID: 10873443

29. Y.I.Wolf, N.V.Grishin, and E.V.Koonin (2000) "Estimating the Number of Protein Folds and Families from Complete Genome Data." J. Mol. Biol 299(4): 897-905 PMID: 10843846

28. N.V.Grishin (2000) "Two tricks in one bundle: helix-turn-helix gains enzymatic activity." Nucleic Acid Research 28(11): 2229-2233 PMID: 10871343

27. H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein and O.Herzberg (2000) "Crystal structure of YBAK protein from Haemophilus influenzae at 1.8 resolution: functional implications". Proteins: Struct. Func. and Genetics 40(1): 86-97 PMID: 10813833

26. J.Ye, U.P.Dave, N.V.Grishin, J.L.Goldstein and M.S.Brown (2000) "Asparagine-proline sequence within membrane-spanning segment of SREBP triggers intramembrane cleavage by Site-2 protease." PNAS 97(10): 5123-5128 PMID: 10805775

25. DD.Leipe, L.Aravind, N.V.Grishin and E.V.Koonin (2000) "The Bacterial Replicative Helicase DnaB Evolved from a RecA Duplication" Genome Res 10(1):5-16 PMID: 10645945

24. J.J.Almrud, M.A.Oliveira, A.D.Kern, N.V.Grishin, M.A.Phillips, M.L.Hackert (2000) "Crystal structure of human ornithine decarboxylase at 2.1Å resolution: structural insights to antizyme binding." J Mol Biol 295(1): 7-16 PMID: 10623504

23. K.S.Makarova and N.V.Grishin (1999) "Thermolysin and Mitochondrial Processing Peptidase: How Far Structure-Functional Convergence Goes." Protein Science 8(11): 2537-2540 PMID: 10595562

22. N.V.Grishin, A.L.Osterman, H.B.Brooks, M.A.Phillips and E.J.Goldsmith (1999) "X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with α-difluoromethylornithine." Biochemistry 38(46): 15174-15184 PMID: 10563800

21. K.S.Makarova and N.V.Grishin (1999) "The Zn-peptidase Superfamily: Functional Convergence After Evolutionary Divergence." J. Mol. Biol. 292: 11-17 PMID: 10493853

20. H.Zhang and N.V.Grishin (1999) "The alpha subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family." Protein Science 8: 1658-1667 PMID: 10452610

19. Y.I.Wolf, L.Aravind, N.V.Grishin and E.V.Koonin (1999) "Evolution of aminoacyl-tRNA synthetases – analysis of synapomorphies and phylogenetic trees reveals a complex history of horizontal gene transfer events." Genome Research 9: 689-710 PMID: 10447505

18. N.V.Grishin (1999) "Phosphatidylinositol phosphate kinase - a link between protein kinase and glutathionesynthase folds." J. Mol. Biol. 291: 239-2047 PMID: 10438618

17. K.S.Makarova, L.Aravind, M.Y.Galperin, N.V.Grishin, R.L.Tatusov, Y.I.Wolf and E.V.Koonin (1999) "Comparative genomics of the archaea: evolution of conserved protein families, the stable core and the variable shell." Genome Research, 9: 608-628 PMID: 10413400

16. D.D.Binns, B.Barylko, N.V.Grishin, M.A.Atkinson, M.K.Helms, D.M.Jameson, J.F.Eccleston, J.P.Albanesi (1999) "Correlation between self-association modes and GTPase activation of dynamin". J Protein Chem 18(3): 277-290 PMID: 10395446

15. N.V.Grishin (1999) "A novel approach to phylogeny reconstruction from protein sequences". J. Mol. Evol 48: 264-273 PMID: 10093215

14. V.Kurvari, N.V.Grishin and W.J.Snell (1998) "A Gamete-specific, Sex-limited Homeodomain Protein in Chlamydomons." J. Cell. Biol. 143: 1971-1980 PMID: 9864368

13. N.V.Grishin (1998) “R3H: a putative single-stranded nucleic acid-binding domain.” TiBS 23: 329-330 PMID: 9787637

12. N.V.Grishin, A.L.Osterman, H.B. Brooks, M.A.Phillips and E.J.Goldsmith (1998) "The Structure of Trypanosoma brucei Ornithine Decarboxylase." Protein Science 7(S1): 144

11. N.V.Grishin (1997) "Estimation of Evolutionary Distances from Protein Spatial Structures". J. Mol. Evol. 45: 359-369 PMID: 9321415

10. N.V.Grishin, A.L.Osterman, E.J.Goldsmith and M.A.Phillips (1996) "Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei". Proteins: Structure, Function, and Genetics 24: 272-273 PMID: 8820496

9. N.V.Grishin, M.A.Phillips and E.J.Goldsmith (1995) "Modeling of spatial structure of eukaryotic ornithine decarboxylases." Protein Science 4: 1291-1304 PMID: 7670372

8. N.V.Grishin (1995) "Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites." J. Mol. Evol. 41:675-679 PMID: 18345592

7. A.L.Osterman, L.N.Kinch, N.V.Grishin, and M.A.Phillips (1995) "Acidic residues important for substrate binding and cofactor reactivity in eukaryotic decarboxylase identified by alanine scanning mutagenesis." J. Biol. Chem. 270: 11797-11802 PMID: 7744828

6. N.V.Grishin and M.A. Phillips (1994) "The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences." Protein Science 3: 2455-2458 PMID: 7757001

5. A.L.Osterman, N.V.Grishin, L.N.Kinch and M.A.Phillips (1994) "Formation of functional cross-species heterodimers of ornithine decarboxylase." Biochemistry 33: 13662-13667 PMID: 7947774

4. A.L.Osterman, L.N.Kinch, N.V.Grishin and M.A.Phillips (1994) "Active site mutants and cross-species heterodimers in a comparative study of host-parasite ornithine decarboxylases." Protein Science 3(S1): 130

3. A.Teplyakov, K.Polyakov, G.Obmolova, B.Strokopytov, I.Kuranova, A.L.Osterman, N.V.Grishin, S.V.Smulevitch, O.Zagnitko, O.Galperina, M.Matz and V.M.Stepanov (1992) "Crystal structure of Carboxypeptidase T from T.vulgaris." Eur. J. Biochem 208: 281-288 PMID: 1521526

2. A.L.Osterman, N.V.Grishin, S.V.Smulevitch, M.V.Matz, O.P.Zagnitko, L.P.Revina and V.M.Stepanov (1992) "Primary structure of Carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family." J. of Protein Chemistry 11(5): 561-570 PMID: 1449602

1. S.V.Smulevitch, A.L.Osterman, O.V.Galperina, M.V.Matz, O.P.Zagnitko, R.M.Kadyrov, I.A.Tsaplina, N.V.Grishin, G.G.Chestoukhina and V.M.Stepanov. (1991) "Molecular cloning and primary structure Thermoactino-myces vulgaris Carboxypeptidase T Endowed with Dual Substrate Specificity." FEBS Letts 291: 75-78 PMID: 1936254

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