Publications
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