| Year |
Citation |
Score |
| 2024 |
Schaeffer RD, Zhang J, Medvedev KE, Kinch LN, Cong Q, Grishin NV. ECOD domain classification of 48 whole proteomes from AlphaFold Structure Database using DPAM2. Plos Computational Biology. 20: e1011586. PMID 38416793 DOI: 10.1371/journal.pcbi.1011586 |
0.319 |
|
| 2023 |
Schaeffer RD, Zhang J, Kinch LN, Pei J, Cong Q, Grishin NV. Classification of domains in predicted structures of the human proteome. Proceedings of the National Academy of Sciences of the United States of America. 120: e2214069120. PMID 36917664 DOI: 10.1073/pnas.2214069120 |
0.315 |
|
| 2020 |
Medvedev KE, Kinch LN, Dustin Schaeffer R, Pei J, Grishin NV. A Fifth of the Protein World: Rossmann-like Proteins as an Evolutionarily Successful Structural unit. Journal of Molecular Biology. 433: 166788. PMID 33387532 DOI: 10.1016/j.jmb.2020.166788 |
0.34 |
|
| 2020 |
Bhat AS, Kinch LN, Grishin NV. β-Strand-mediated interactions of protein domains. Proteins. PMID 32543729 DOI: 10.1002/Prot.25970 |
0.36 |
|
| 2020 |
Baumhardt JM, Walker JS, Lee Y, Shakya B, Brautigam CA, Lapalombella R, Grishin N, Chook YM. Recognition of nuclear export signals by CRM1 carrying the oncogenic E571K mutation. Molecular Biology of the Cell. mbcE20040233. PMID 32520643 DOI: 10.1091/Mbc.E20-04-0233 |
0.308 |
|
| 2020 |
Pei J, Kinch LN, Otwinowski Z, Grishin NV. Mutation severity spectrum of rare alleles in the human genome is predictive of disease type. Plos Computational Biology. 16: e1007775. PMID 32413045 DOI: 10.1371/Journal.Pcbi.1007775 |
0.358 |
|
| 2020 |
Bhat AS, Dustin Schaeffer R, Kinch L, Medvedev KE, Grishin NV. Recent advances suggest increased influence of selective pressure in allostery. Current Opinion in Structural Biology. 62: 183-188. PMID 32302874 DOI: 10.1016/J.Sbi.2020.02.004 |
0.387 |
|
| 2020 |
Zhang J, Brockmann E, Cong Q, Shen J, Grishin NV. A genomic perspective on the taxonomy of the subtribe Carcharodina (Lepidoptera: Hesperiidae: Carcharodini). Zootaxa. 4748: zootaxa.4748.1.10. PMID 32230093 DOI: 10.11646/Zootaxa.4748.1.10 |
0.309 |
|
| 2020 |
Zhang J, Lees DC, Shen J, Cong Q, Huertas B, Martin G, Grishin NV. The mitogenome of a Malagasy butterfly (Mabille, 1884) recovered from the holotype collected over 140 years ago adds support for a new subfamily of Hesperiidae (Lepidoptera). Genome. 195-202. PMID 32142382 DOI: 10.1139/Gen-2019-0189 |
0.331 |
|
| 2020 |
Medvedev KE, Kinch LN, Grishin NV. Rossmann-Like Proteins Function and Evolution Analysis of a Fifth of the Protein World Biophysical Journal. 118. DOI: 10.1016/J.Bpj.2019.11.1182 |
0.386 |
|
| 2019 |
Medvedev KE, Kinch LN, Schaeffer RD, Grishin NV. Functional analysis of Rossmann-like domains reveals convergent evolution of topology and reaction pathways. Plos Computational Biology. 15. PMID 31869345 DOI: 10.1371/Journal.Pcbi.1007569 |
0.388 |
|
| 2019 |
Bhat AS, Grishin NV. Predicting Sequence Features, Function, and Structure of Proteins Using MESSA. Current Protocols in Bioinformatics. 67: e84. PMID 31524991 DOI: 10.1002/Cpbi.84 |
0.44 |
|
| 2019 |
Lee Y, Baumhardt JM, Pei J, Chook YM, Grishin NV. pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes. Bioinformatics (Oxford, England). PMID 31504173 DOI: 10.1093/Bioinformatics/Btz657 |
0.357 |
|
| 2019 |
Zhang J, Cong Q, Shen J, Brockmann E, Grishin NV. Three new subfamilies of skipper butterflies (Lepidoptera, Hesperiidae). Zookeys. 861: 91-105. PMID 31333327 DOI: 10.3897/Zookeys.861.34686 |
0.341 |
|
| 2019 |
Kinch LN, Kryshtafovych A, Monastyrskyy B, Grishin NV. CASP13 target classification into tertiary structure prediction categories. Proteins. 87: 1021-1036. PMID 31294862 DOI: 10.1002/Prot.25775 |
0.368 |
|
| 2019 |
Zhang J, Kinch LN, Cong Q, Katsonis P, Lichtarge O, Savojardo C, Babbi G, Martelli PL, Capriotti E, Casadio R, Garg A, Pal D, Weile J, Sun S, Verby M, ... ... Grishin NV, et al. Assessing predictions on fitness effects of missense variants in calmodulin. Human Mutation. PMID 31283071 DOI: 10.1002/Humu.23857 |
0.338 |
|
| 2019 |
Zhang J, Cong Q, Shen J, Brockmann E, Grishin NV. Genomes reveal drastic and recurrent phenotypic divergence in firetip skipper butterflies (Hesperiidae: Pyrrhopyginae). Proceedings. Biological Sciences. 286: 20190609. PMID 31113329 DOI: 10.1098/Rspb.2019.0609 |
0.345 |
|
| 2019 |
Lee Y, Pei J, Baumhardt JM, Chook YM, Grishin NV. Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site. Scientific Reports. 9: 6627. PMID 31036839 DOI: 10.1038/S41598-019-43004-0 |
0.458 |
|
| 2019 |
Nelson ED, Grishin NV. How Often Do Protein Genes Navigate Valleys of Low Fitness? Genes. 10. PMID 30965625 DOI: 10.3390/Genes10040283 |
0.306 |
|
| 2019 |
Li W, Cong Q, Shen J, Zhang J, Hallwachs W, Janzen DH, Grishin NV. Genomes of skipper butterflies reveal extensive convergence of wing patterns. Proceedings of the National Academy of Sciences of the United States of America. PMID 30877254 DOI: 10.1073/Pnas.1821304116 |
0.309 |
|
| 2019 |
Wang J, Kinch LN, Denard B, Lee CE, Esmaeilzadeh Gharehdaghi E, Grishin N, Ye J. Identification of residues critical for topology inversion of the transmembrane protein TM4SF20 through regulated alternative translocation. The Journal of Biological Chemistry. PMID 30808712 DOI: 10.1074/Jbc.Ra119.007681 |
0.353 |
|
| 2019 |
Zhang J, Cong Q, Rex EA, Hallwachs W, Janzen DH, Grishin NV, Gammon DB. Gypsy moth genome provides insights into flight capability and virus-host interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 30642971 DOI: 10.1073/Pnas.1818283116 |
0.312 |
|
| 2019 |
Schaeffer D, Grishin NV. Identification of Protein Homologs and Domain Boundaries by Iterative Sequence Alignment. Methods of Molecular Biology. 1851: 277-286. PMID 30298403 DOI: 10.1007/978-1-4939-8736-8_15 |
0.397 |
|
| 2019 |
Tomchick DR, Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, et al. Protein AMPylation by an evolutionarily conserved pseudokinase Acta Crystallographica Section A. 75. DOI: 10.1107/S0108767319096922 |
0.397 |
|
| 2018 |
Cong Q, Li W, Borek D, Otwinowski Z, Grishin NV. The Bear Giant-Skipper genome suggests genetic adaptations to living inside yucca roots. Molecular Genetics and Genomics : Mgg. PMID 30293092 DOI: 10.1007/S00438-018-1494-6 |
0.341 |
|
| 2018 |
Sreelatha A, Yee SS, Lopez VA, Park BC, Kinch LN, Pilch S, Servage KA, Zhang J, Jiou J, Karasiewicz-Urbańska M, Łobocka M, Grishin NV, Orth K, Kucharczyk R, Pawłowski K, et al. Protein AMPylation by an Evolutionarily Conserved Pseudokinase. Cell. PMID 30270044 DOI: 10.1016/J.Cell.2018.08.046 |
0.409 |
|
| 2018 |
Schaeffer RD, Liao Y, Grishin NV. Searching ECOD for Homologous Domains by Sequence and Structure. Current Protocols in Bioinformatics. 61: e45. PMID 30040199 DOI: 10.1002/Cpbi.45 |
0.465 |
|
| 2018 |
Nelson ED, Grishin NV. Inference of epistatic effects in a key mitochondrial protein. Physical Review. E. 97: 062404. PMID 30011480 DOI: 10.1103/Physreve.97.062404 |
0.34 |
|
| 2018 |
Pei J, Kinch LN, Grishin NV. FlyXCDB - a resource for Drosophila cell surface and secreted proteins and their extracellular domains. Journal of Molecular Biology. PMID 29890119 DOI: 10.1016/J.Jmb.2018.06.002 |
0.41 |
|
| 2018 |
Medvedev KE, Kinch LN, Grishin NV. Functional and evolutionary analysis of viral proteins containing a Rossmann‐like fold Protein Science. 27: 1450-1463. PMID 29722076 DOI: 10.1002/Pro.3438 |
0.447 |
|
| 2018 |
Liao Y, Schaeffer RD, Pei J, Grishin NV. A Sequence Family Database Built on ECOD Structural Domains. Bioinformatics (Oxford, England). PMID 29659718 DOI: 10.1093/Bioinformatics/Bty214 |
0.414 |
|
| 2018 |
Wendt GR, Collins JN, Pei J, Pearson MS, Bennett HM, Loukas A, Berriman M, Grishin NV, Collins JJ. Flatworm-specific transcriptional regulators promote the specification of tegumental progenitors in. Elife. 7. PMID 29557781 DOI: 10.7554/Elife.33221 |
0.307 |
|
| 2017 |
Zhang J, Cong Q, Shen J, Fan XL, Wang M, Grishin NV. The complete mitogenome of (Lepidoptera: Hesperiidae). Mitochondrial Dna. Part B, Resources. 2: 136-138. PMID 30931394 DOI: 10.1080/23802359.2017.1292478 |
0.313 |
|
| 2017 |
Zhang J, Cong Q, Shen J, Grishin NV. Mitogenomes of the four holotypes collected 55 years ago. Mitochondrial Dna. Part B, Resources. 2: 598-600. PMID 30740526 DOI: 10.1080/23802359.2017.1372701 |
0.334 |
|
| 2017 |
Zhang J, Cong Q, Shen J, Wang R, Grishin NV. The complete mitochondrial genome of a skipper Burara striata (Lepidoptera: Hesperiidae). Mitochondrial Dna. Part B, Resources. 2: 145-147. PMID 29376128 DOI: 10.1080/23802359.2017.1298416 |
0.316 |
|
| 2017 |
Angrisano F, Sala KA, Da DF, Liu Y, Pei J, Grishin NV, Snell WJ, Blagborough AM. Targeting the Conserved Fusion Loop of HAP2 Inhibits the Transmission of Plasmodium berghei and falciparum. Cell Reports. 21: 2868-2878. PMID 29212032 DOI: 10.1016/J.Celrep.2017.11.024 |
0.3 |
|
| 2017 |
Shi J, Bi P, Pei J, Li H, Grishin NV, Bassel-Duby R, Chen EH, Olson EN. Requirement of the fusogenic micropeptide myomixer for muscle formation in zebrafish. Proceedings of the National Academy of Sciences of the United States of America. PMID 29078404 DOI: 10.1073/Pnas.1715229114 |
0.336 |
|
| 2017 |
Zhang J, Kinch LN, Cong Q, Weile J, Sun S, Cote AG, Roth FP, Grishin NV. Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I. Human Mutation. 38: 1051-1063. PMID 28817247 DOI: 10.1002/Humu.23293 |
0.323 |
|
| 2017 |
Gao Q, Binns DD, Kinch LN, Grishin NV, Ortiz N, Chen X, Goodman JM. Pet10p is a yeast perilipin that stabilizes lipid droplets and promotes their assembly. The Journal of Cell Biology. PMID 28801319 DOI: 10.1083/Jcb.201610013 |
0.329 |
|
| 2017 |
Cong Q, Shen J, Li W, Borek D, Otwinowski Z, Grishin NV. The first complete genomes of Metalmarks and the classification of butterfly families. Genomics. PMID 28757157 DOI: 10.1016/J.Ygeno.2017.07.006 |
0.353 |
|
| 2017 |
Hou Z, Su L, Pei J, Grishin NV, Zhang H. Crystal Structure of the CLOCK Transactivation Domain Exon19 in Complex with a Repressor. Structure (London, England : 1993). PMID 28669630 DOI: 10.1016/J.Str.2017.05.023 |
0.373 |
|
| 2017 |
Zhang J, Cong Q, Fan XL, Wang R, Wang M, Grishin NV. Mitogenomes of Giant-Skipper Butterflies reveal an ancient split between deep and shallow root feeders. F1000research. 6: 222. PMID 28408977 DOI: 10.12688/F1000Research.10970.1 |
0.31 |
|
| 2017 |
Fédry J, Liu Y, Péhau-Arnaudet G, Pei J, Li W, Tortorici MA, Traincard F, Meola A, Bricogne G, Grishin NV, Snell WJ, Rey FA, Krey T. The Ancient Gamete Fusogen HAP2 Is a Eukaryotic Class II Fusion Protein. Cell. 168: 904-915.e10. PMID 28235200 DOI: 10.1016/J.Cell.2017.01.024 |
0.329 |
|
| 2016 |
Shen J, Cong Q, Grishin NV. The complete mitogenome of Achalarus lyciades (Lepidoptera: Hesperiidae). Mitochondrial Dna. Part B, Resources. 1: 581-583. PMID 28367503 DOI: 10.1080/23802359.2016.1197070 |
0.31 |
|
| 2016 |
Shen J, Cong Q, Kinch LN, Borek D, Otwinowski Z, Grishin NV. Complete genome of Pieris rapae, a resilient alien, a cabbage pest, and a source of anti-cancer proteins. F1000research. 5: 2631. PMID 28163896 DOI: 10.12688/F1000Research.9765.1 |
0.364 |
|
| 2016 |
Pei J, Grishin NV. Expansion of Divergent SEA Domains in Cell Surface Proteins and Nucleoporin 54. Protein Science : a Publication of the Protein Society. PMID 27977898 DOI: 10.1002/Pro.3096 |
0.431 |
|
| 2016 |
Volkov OA, Kinch LN, Ariagno C, Deng X, Zhong S, Grishin NV, Tomchick DR, Chen Z, Phillips MA. Relief of autoinhibition by conformational switch explains enzyme activation by a catalytically dead paralog. Elife. 5. PMID 27977001 DOI: 10.7554/Elife.20198 |
0.351 |
|
| 2016 |
Schaeffer RD, Liao Y, Cheng H, Grishin NV. ECOD: new developments in the evolutionary classification of domains. Nucleic Acids Research. PMID 27899594 DOI: 10.1093/Nar/Gkw1137 |
0.422 |
|
| 2016 |
Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. Structure of protein O-mannose kinase reveals a unique active site architecture. Elife. 5. PMID 27879205 DOI: 10.7554/Elife.22238 |
0.326 |
|
| 2016 |
Nelson ED, Grishin NV. Long-Range Epistasis Mediated by Structural Change in a Model of Ligand Binding Proteins. Plos One. 11: e0166739. PMID 27870911 DOI: 10.1371/Journal.Pone.0166739 |
0.374 |
|
| 2016 |
Leija C, Rijo-Ferreira F, Kinch LN, Grishin NV, Nischan N, Kohler JJ, Hu Z, Phillips MA. Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. Plos Pathogens. 12: e1006010. PMID 27820863 DOI: 10.1371/Journal.Ppat.1006010 |
0.332 |
|
| 2016 |
Nelson ED, Grishin NV. Evolution of off-lattice model proteins under ligand binding constraints. Physical Review. E. 94: 022410. PMID 27627338 DOI: 10.1103/Physreve.94.022410 |
0.408 |
|
| 2016 |
Chitturi B, Shi S, Kinch LN, Grishin NV. Compact Structure Patterns in Proteins. Journal of Molecular Biology. PMID 27498165 DOI: 10.1016/J.Jmb.2016.07.022 |
0.374 |
|
| 2016 |
Ray A, Kinch LN, de Souza Santos M, Grishin NV, Orth K, Salomon D. Proteomics Analysis Reveals Previously Uncharacterized Virulence Factors in Vibrio proteolyticus. Mbio. 7. PMID 27460800 DOI: 10.1128/Mbio.01077-16 |
0.308 |
|
| 2016 |
Li P, Rivera-Cancel G, Kinch LN, Salomon D, Tomchick DR, Grishin NV, Orth K. Bile salt receptor complex activates a pathogenic type III secretion system. Elife. 5. PMID 27377244 DOI: 10.7554/Elife.15718 |
0.334 |
|
| 2016 |
Bromberg R, Grishin NV, Otwinowski Z. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. Plos Computational Biology. 12. PMID 27336403 DOI: 10.1371/Journal.Pcbi.1004985 |
0.362 |
|
| 2016 |
Li W, Schaeffer RD, Otwinowski Z, Grishin NV. Estimation of Uncertainties in the Global Distance Test (GDT_TS) for CASP Models. Plos One. 11: e0154786. PMID 27149620 DOI: 10.1371/Journal.Pone.0154786 |
0.318 |
|
| 2016 |
Cong Q, Shen J, Borek D, Robbins RK, Otwinowski Z, Grishin NV. Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence. Scientific Reports. 6: 24863. PMID 27120974 DOI: 10.1038/Srep24863 |
0.31 |
|
| 2016 |
Zhang Y, Lee KM, Kinch LN, Clark L, Grishin NV, Rosenbaum DM, Brown MS, Goldstein JL, Radhakrishnan A. Direct Demonstration that Loop1 of Scap Binds to Loop7, a crucial event in cholesterol homeostasis. The Journal of Biological Chemistry. PMID 27068746 DOI: 10.1074/Jbc.M116.729798 |
0.324 |
|
| 2016 |
Cong Q, Shen J, Warren AD, Borek D, Otwinowski Z, Grishin NV. Speciation in Cloudless Sulphurs gleaned from complete genomes. Genome Biology and Evolution. PMID 26951782 DOI: 10.1093/Gbe/Evw045 |
0.344 |
|
| 2016 |
Schaeffer RD, Kinch LN, Liao Y, Grishin NV. Classification of proteins with shared motifs and internal repeats in the ECOD database. Protein Science : a Publication of the Protein Society. PMID 26833690 DOI: 10.1002/Pro.2893 |
0.452 |
|
| 2016 |
Cong Q, Grishin NV. The complete mitochondrial genome of Lerema accius and its phylogenetic implications. Peerj. 4: e1546. PMID 26788426 DOI: 10.7717/Peerj.1546 |
0.362 |
|
| 2016 |
Kinch LN, Li W, Schaeffer RD, Dunbrack RL, Monastyrskyy B, Kryshtafovych A, Grishin NV. CASP 11 Target Classification. Proteins. PMID 26756794 DOI: 10.1002/Prot.24982 |
0.381 |
|
| 2016 |
Zhu Q, Venzke D, Walimbe AS, Anderson ME, Fu Q, Kinch LN, Wang W, Chen X, Grishin NV, Huang N, Yu L, Dixon JE, Campbell KP, Xiao J. Author response: Structure of protein O-mannose kinase reveals a unique active site architecture Elife. DOI: 10.7554/Elife.22238.021 |
0.319 |
|
| 2015 |
Kinch LN, Li W, Monastyrskyy B, Kryshtafovych A, Grishin NV. Evaluation of free modeling targets in CASP11 and ROLL. Proteins. PMID 26677002 DOI: 10.1002/Prot.24973 |
0.385 |
|
| 2015 |
Yang X, Pei J, Kaeser-Woo YJ, Bacaj T, Grishin NV, Südhof TC. Evolutionary conservation of complexins: from choanoflagellates to mice. Embo Reports. 16: 1308-17. PMID 26338476 DOI: 10.15252/Embr.201540305 |
0.3 |
|
| 2015 |
Tong J, Pei J, Grishin NV. SFESA: a web server for pairwise alignment refinement by secondary structure shifts. Bmc Bioinformatics. 16: 282. PMID 26335387 DOI: 10.1186/S12859-015-0711-0 |
0.407 |
|
| 2015 |
Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Large scale determination of previously unsolved protein structures using evolutionary information. Elife. 4. PMID 26335199 DOI: 10.7554/Elife.09248 |
0.442 |
|
| 2015 |
Cong Q, Borek D, Otwinowski Z, Grishin NV. Skipper genome sheds light on unique phenotypic traits and phylogeny. Bmc Genomics. 16: 639. PMID 26311350 DOI: 10.1186/S12864-015-1846-0 |
0.312 |
|
| 2015 |
Salomon D, Klimko JA, Trudgian DC, Kinch LN, Grishin NV, Mirzaei H, Orth K. Type VI Secretion System Toxins Horizontally Shared between Marine Bacteria. Plos Pathogens. 11: e1005128. PMID 26305100 DOI: 10.1371/Journal.Ppat.1005128 |
0.324 |
|
| 2015 |
Cong Q, Pei J, Grishin NV. Predictive and comparative analysis of Ebolavirus proteins. Cell Cycle (Georgetown, Tex.). 14: 2785-97. PMID 26158395 DOI: 10.1080/15384101.2015.1068472 |
0.449 |
|
| 2015 |
Shen J, Cong Q, Grishin NV. The complete mitochondrial genome of Papilio glaucus and its phylogenetic implications. Meta Gene. 5: 68-83. PMID 26106582 DOI: 10.1016/J.Mgene.2015.05.002 |
0.336 |
|
| 2015 |
Tagliabracci VS, Wiley SE, Guo X, Kinch LN, Durrant E, Wen J, Xiao J, Cui J, Nguyen KB, Engel JL, Coon JJ, Grishin N, Pinna LA, Pagliarini DJ, Dixon JE. A Single Kinase Generates the Majority of the Secreted Phosphoproteome. Cell. 161: 1619-32. PMID 26091039 DOI: 10.1016/J.Cell.2015.05.028 |
0.314 |
|
| 2015 |
Nguyen S, Leija C, Kinch L, Regmi S, Li Q, Grishin NV, Phillips MA. Deoxyhypusine modification of eIF5A is essential for Trypanosoma brucei growth and for expression of polyprolyl-containing proteins. The Journal of Biological Chemistry. PMID 26082486 DOI: 10.1074/Jbc.M115.656785 |
0.349 |
|
| 2015 |
Tong J, Sadreyev RI, Pei J, Kinch LN, Grishin NV. Using homology relations within a database markedly boosts protein sequence similarity search. Proceedings of the National Academy of Sciences of the United States of America. 112: 7003-8. PMID 26038555 DOI: 10.1073/Pnas.1424324112 |
0.441 |
|
| 2015 |
Li W, Kinch LN, Karplus PA, Grishin NV. ChSeq: A database of chameleon sequences. Protein Science : a Publication of the Protein Society. 24: 1075-86. PMID 25970262 DOI: 10.1002/Pro.2689 |
0.455 |
|
| 2015 |
Cheng H, Liao Y, Schaeffer RD, Grishin NV. Manual classification strategies in the ECOD database. Proteins. PMID 25917548 DOI: 10.1002/Prot.24818 |
0.455 |
|
| 2015 |
Cong Q, Borek D, Otwinowski Z, Grishin NV. Tiger Swallowtail Genome Reveals Mechanisms for Speciation and Caterpillar Chemical Defense. Cell Reports. PMID 25683714 DOI: 10.1016/J.Celrep.2015.01.026 |
0.347 |
|
| 2015 |
Liu Y, Pei J, Grishin N, Snell WJ. The cytoplasmic domain of the gamete membrane fusion protein HAP2 targets the protein to the fusion site in Chlamydomonas and regulates the fusion reaction. Development (Cambridge, England). 142: 962-71. PMID 25655701 DOI: 10.1242/Dev.118844 |
0.356 |
|
| 2015 |
Liu S, Cai X, Wu J, Cong Q, Chen X, Li T, Du F, Ren J, Wu YT, Grishin NV, Chen ZJ. Phosphorylation of innate immune adaptor proteins MAVS, STING, and TRIF induces IRF3 activation. Science (New York, N.Y.). 347: aaa2630. PMID 25636800 DOI: 10.1126/Science.Aaa2630 |
0.306 |
|
| 2015 |
Tong J, Pei J, Otwinowski Z, Grishin NV. Refinement by shifting secondary structure elements improves sequence alignments. Proteins. 83: 411-27. PMID 25546158 DOI: 10.1002/Prot.24746 |
0.391 |
|
| 2015 |
Xu D, Marquis K, Pei J, Fu SC, Ca?atay T, Grishin NV, Chook YM. LocNES: a computational tool for locating classical NESs in CRM1 cargo proteins. Bioinformatics (Oxford, England). 31: 1357-65. PMID 25515756 DOI: 10.1093/Bioinformatics/Btu826 |
0.327 |
|
| 2015 |
Ovchinnikov S, Kinch L, Park H, Liao Y, Pei J, Kim DE, Kamisetty H, Grishin NV, Baker D. Author response: Large-scale determination of previously unsolved protein structures using evolutionary information Elife. DOI: 10.7554/Elife.09248.031 |
0.336 |
|
| 2015 |
Nelson ED, Grishin NV. Anomalous diffusion in neutral evolution of model proteins Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 91. DOI: 10.1103/Physreve.91.060701 |
0.368 |
|
| 2014 |
Nelson ED, Grishin NV. Structural evolution of proteinlike heteropolymers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 90: 062715. PMID 25615137 DOI: 10.1103/Physreve.90.062715 |
0.408 |
|
| 2014 |
Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, Shi S, Kim BH, Grishin NV. ECOD: an evolutionary classification of protein domains. Plos Computational Biology. 10: e1003926. PMID 25474468 DOI: 10.1371/Journal.Pcbi.1003926 |
0.489 |
|
| 2014 |
Liao Y, Pei J, Cheng H, Grishin NV. An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98. Journal of Molecular Biology. 426: 3935-45. PMID 25451782 DOI: 10.1016/J.Jmb.2014.10.011 |
0.395 |
|
| 2014 |
Calder T, Kinch LN, Fernandez J, Salomon D, Grishin NV, Orth K. Vibrio type III effector VPA1380 is related to the cysteine protease domain of large bacterial toxins. Plos One. 9: e104387. PMID 25099122 DOI: 10.1371/Journal.Pone.0104387 |
0.4 |
|
| 2014 |
Ayaz P, Munyoki S, Geyer EA, Piedra FA, Vu ES, Bromberg R, Otwinowski Z, Grishin NV, Brautigam CA, Rice LM. A tethered delivery mechanism explains the catalytic action of a microtubule polymerase. Elife. 3: e03069. PMID 25097237 DOI: 10.7554/Elife.03069 |
0.315 |
|
| 2014 |
Semeiks J, Borek D, Otwinowski Z, Grishin NV. Comparative genome sequencing reveals chemotype-specific gene clusters in the toxigenic black mold Stachybotrys. Bmc Genomics. 15: 590. PMID 25015739 DOI: 10.1186/1471-2164-15-590 |
0.313 |
|
| 2014 |
Pei J, Li W, Kinch LN, Grishin NV. Conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families. Protein Science : a Publication of the Protein Society. 23: 1220-34. PMID 24931479 DOI: 10.1002/Pro.2503 |
0.467 |
|
| 2014 |
Salomon D, Kinch LN, Trudgian DC, Guo X, Klimko JA, Grishin NV, Mirzaei H, Orth K. Marker for type VI secretion system effectors. Proceedings of the National Academy of Sciences of the United States of America. 111: 9271-6. PMID 24927539 DOI: 10.1073/Pnas.1406110111 |
0.404 |
|
| 2014 |
Makarova KS, Anantharaman V, Grishin NV, Koonin EV, Aravind L. CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. Frontiers in Genetics. 5: 102. PMID 24817877 DOI: 10.3389/Fgene.2014.00102 |
0.412 |
|
| 2014 |
Chen B, Brinkmann K, Chen Z, Pak CW, Liao Y, Shi S, Henry L, Grishin NV, Bogdan S, Rosen MK. The WAVE regulatory complex links diverse receptors to the actin cytoskeleton. Cell. 156: 195-207. PMID 24439376 DOI: 10.1016/J.Cell.2013.11.048 |
0.337 |
|
| 2014 |
Pei J, Grishin NV. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. Methods in Molecular Biology (Clifton, N.J.). 1079: 263-71. PMID 24170408 DOI: 10.1007/978-1-62703-646-7_17 |
0.432 |
|
| 2013 |
Salomon D, Guo Y, Kinch LN, Grishin NV, Gardner KH, Orth K. Effectors of animal and plant pathogens use a common domain to bind host phosphoinositides. Nature Communications. 4: 2973. PMID 24346350 DOI: 10.1038/Ncomms3973 |
0.324 |
|
| 2013 |
Pei J, Grishin NV. A new family of predicted Krüppel-like factor genes and pseudogenes in placental mammals. Plos One. 8: e81109. PMID 24244731 DOI: 10.1371/Journal.Pone.0081109 |
0.382 |
|
| 2013 |
Ji R, Cong Q, Li W, Grishin NV. M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci. Bioinformatics (Oxford, England). 29: 2953-4. PMID 24002112 DOI: 10.1093/Bioinformatics/Btt507 |
0.381 |
|
| 2013 |
He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, et al. Beclin 2 functions in autophagy, degradation of G protein-coupled receptors, and metabolism. Cell. 154: 1085-99. PMID 23954414 DOI: 10.1016/J.Cell.2013.07.035 |
0.308 |
|
| 2013 |
Li W, Kinch LN, Grishin NV. Pclust: protein network visualization highlighting experimental data. Bioinformatics (Oxford, England). 29: 2647-8. PMID 23918248 DOI: 10.1093/Bioinformatics/Btt451 |
0.378 |
|
| 2013 |
Kinch LN, Grishin NV. Bioinformatics perspective on rhomboid intramembrane protease evolution and function. Biochimica Et Biophysica Acta. 1828: 2937-43. PMID 23845876 DOI: 10.1016/J.Bbamem.2013.06.031 |
0.402 |
|
| 2013 |
Ning J, Otto TD, Pfander C, Schwach F, Brochet M, Bushell E, Goulding D, Sanders M, Lefebvre PA, Pei J, Grishin NV, Vanderlaan G, Billker O, Snell WJ. Comparative genomics in Chlamydomonas and Plasmodium identifies an ancient nuclear envelope protein family essential for sexual reproduction in protists, fungi, plants, and vertebrates. Genes & Development. 27: 1198-215. PMID 23699412 DOI: 10.1101/Gad.212746.112 |
0.34 |
|
| 2013 |
Li W, Cong Q, Kinch LN, Grishin NV. Seq2Ref: a web server to facilitate functional interpretation. Bmc Bioinformatics. 14: 30. PMID 23356573 DOI: 10.1186/1471-2105-14-30 |
0.388 |
|
| 2013 |
Huang IK, Pei J, Grishin NV. Defining and predicting structurally conserved regions in protein superfamilies. Bioinformatics (Oxford, England). 29: 175-81. PMID 23193223 DOI: 10.1093/Bioinformatics/Bts682 |
0.449 |
|
| 2012 |
Cong Q, Grishin NV. MESSA: MEta-Server for protein Sequence Analysis. Bmc Biology. 10: 82. PMID 23031578 DOI: 10.1186/1741-7007-10-82 |
0.419 |
|
| 2012 |
Rodionova IA, Scott DA, Grishin NV, Osterman AL, Rodionov DA. Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima. Environmental Microbiology. 14: 2920-34. PMID 22925190 DOI: 10.1111/J.1462-2920.2012.02856.X |
0.323 |
|
| 2012 |
Xu D, Farmer A, Collett G, Grishin NV, Chook YM. Sequence and structural analyses of nuclear export signals in the NESdb database. Molecular Biology of the Cell. 23: 3677-93. PMID 22833565 DOI: 10.1091/Mbc.E12-01-0046 |
0.422 |
|
| 2012 |
Xu D, Grishin NV, Chook YM. NESdb: a database of NES-containing CRM1 cargoes. Molecular Biology of the Cell. 23: 3673-6. PMID 22833564 DOI: 10.1091/Mbc.E12-01-0045 |
0.374 |
|
| 2012 |
Li W, Cong Q, Pei J, Kinch LN, Grishin NV. The ABC transporters in Candidatus Liberibacter asiaticus. Proteins. 80: 2614-28. PMID 22807026 DOI: 10.1002/Prot.24147 |
0.321 |
|
| 2012 |
Grishin NV. Membrane protein structure predictions for exploration. Cell. 149: 1424-5. PMID 22726429 DOI: 10.1016/J.Cell.2012.06.004 |
0.409 |
|
| 2012 |
Semeiks J, Grishin NV. A method to find longevity-selected positions in the mammalian proteome. Plos One. 7: e38595. PMID 22701678 DOI: 10.1371/Journal.Pone.0038595 |
0.407 |
|
| 2012 |
Pei J, Grishin NV. Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins. Protein Science : a Publication of the Protein Society. 21: 1172-84. PMID 22693159 DOI: 10.1002/Pro.2105 |
0.464 |
|
| 2012 |
Tagliabracci VS, Engel JL, Wen J, Wiley SE, Worby CA, Kinch LN, Xiao J, Grishin NV, Dixon JE. Secreted kinase phosphorylates extracellular proteins that regulate biomineralization. Science (New York, N.Y.). 336: 1150-3. PMID 22582013 DOI: 10.1126/Science.1217817 |
0.328 |
|
| 2012 |
Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, et al. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell. 149: 753-67. PMID 22579281 DOI: 10.1016/J.Cell.2012.04.017 |
0.362 |
|
| 2012 |
Pei J, Grishin NV. Unexpected diversity in Shisa-like proteins suggests the importance of their roles as transmembrane adaptors. Cellular Signalling. 24: 758-69. PMID 22120523 DOI: 10.1016/J.Cellsig.2011.11.011 |
0.469 |
|
| 2011 |
Kinch LN, Shi S, Cheng H, Cong Q, Pei J, Mariani V, Schwede T, Grishin NV. CASP9 target classification. Proteins. 79: 21-36. PMID 21997778 DOI: 10.1002/Prot.23190 |
0.394 |
|
| 2011 |
Kinch L, Yong Shi S, Cong Q, Cheng H, Liao Y, Grishin NV. CASP9 assessment of free modeling target predictions. Proteins. 79: 59-73. PMID 21997521 DOI: 10.1002/Prot.23181 |
0.373 |
|
| 2011 |
Cong Q, Kinch LN, Pei J, Shi S, Grishin VN, Li W, Grishin NV. An automatic method for CASP9 free modeling structure prediction assessment. Bioinformatics (Oxford, England). 27: 3371-8. PMID 21994223 DOI: 10.1093/Bioinformatics/Btr572 |
0.305 |
|
| 2011 |
Pei J, Millay DP, Olson EN, Grishin NV. CREST--a large and diverse superfamily of putative transmembrane hydrolases. Biology Direct. 6: 37. PMID 21733186 DOI: 10.1186/1745-6150-6-37 |
0.407 |
|
| 2011 |
Pei J, Mitchell DA, Dixon JE, Grishin NV. Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1. Journal of Molecular Biology. 410: 18-26. PMID 21570408 DOI: 10.1016/J.Jmb.2011.04.066 |
0.418 |
|
| 2011 |
Liang S, Zhou Y, Grishin N, Standley DM. Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions. Journal of Computational Chemistry. 32: 1680-6. PMID 21374632 DOI: 10.1002/Jcc.21747 |
0.311 |
|
| 2010 |
Das D, Grishin NV, Kumar A, Carlton D, Bakolitsa C, Miller MD, Abdubek P, Astakhova T, Axelrod HL, Burra P, Chen C, Chiu HJ, Chiu M, Clayton T, Deller MC, et al. The structure of the first representative of Pfam family PF09836 reveals a two-domain organization and suggests involvement in transcriptional regulation. Acta Crystallographica. Section F, Structural Biology and Crystallization Communications. 66: 1174-81. PMID 20944208 DOI: 10.1107/S1744309109022672 |
0.45 |
|
| 2010 |
Teichmann SA, Grishin N. Sequences and topology: evolution of proteins and evolution of computational approaches. Current Opinion in Structural Biology. 20: 333-4. PMID 20483587 DOI: 10.1016/J.Sbi.2010.04.004 |
0.477 |
|
| 2010 |
Kim BH, Cong Q, Grishin NV. HangOut: generating clean PSI-BLAST profiles for domains with long insertions. Bioinformatics (Oxford, England). 26: 1564-5. PMID 20413635 DOI: 10.1093/Bioinformatics/Btq208 |
0.401 |
|
| 2010 |
Luong P, Kinch LN, Brautigam CA, Grishin NV, Tomchick DR, Orth K. Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain. The Journal of Biological Chemistry. 285: 20155-63. PMID 20410310 DOI: 10.1074/Jbc.M110.114884 |
0.389 |
|
| 2010 |
Vega-Rubin-de-Celis S, Abdallah Z, Kinch L, Grishin NV, Brugarolas J, Zhang X. Structural analysis and functional implications of the negative mTORC1 regulator REDD1. Biochemistry. 49: 2491-501. PMID 20166753 DOI: 10.1021/Bi902135E |
0.424 |
|
| 2010 |
He S, McPhaul C, Li JZ, Garuti R, Kinch L, Grishin NV, Cohen JC, Hobbs HH. A sequence variation (I148M) in PNPLA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis. The Journal of Biological Chemistry. 285: 6706-15. PMID 20034933 DOI: 10.1074/Jbc.M109.064501 |
0.34 |
|
| 2010 |
Chitturi B, Bein D, Grishin NV. Complete enumeration of compact structural motifs in proteins Isb 2010 Proceedings - International Symposium On Biocomputing. DOI: 10.1145/1722024.1722047 |
0.31 |
|
| 2009 |
Shi S, Pei J, Sadreyev RI, Kinch LN, Majumdar I, Tong J, Cheng H, Kim BH, Grishin NV. Analysis of CASP8 targets, predictions and assessment methods. Database : the Journal of Biological Databases and Curation. 2009: bap003. PMID 20157476 DOI: 10.1093/Database/Bap003 |
0.354 |
|
| 2009 |
Sadreyev RI, Wang Y, Grishin NV. Considering scores between unrelated proteins in the search database improves profile comparison. Bmc Bioinformatics. 10: 399. PMID 19961610 DOI: 10.1186/1471-2105-10-399 |
0.372 |
|
| 2009 |
Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, et al. Structure prediction for CASP8 with all-atom refinement using Rosetta. Proteins. 77: 89-99. PMID 19701941 DOI: 10.1002/Prot.22540 |
0.349 |
|
| 2009 |
Pei J, Ma C, Rizo J, Grishin NV. Remote homology between Munc13 MUN domain and vesicle tethering complexes. Journal of Molecular Biology. 391: 509-17. PMID 19563813 DOI: 10.1016/J.Jmb.2009.06.054 |
0.402 |
|
| 2009 |
Kinch LN, Yarbrough ML, Orth K, Grishin NV. Fido, a novel AMPylation domain common to fic, doc, and AvrB. Plos One. 4: e5818. PMID 19503829 DOI: 10.1371/Journal.Pone.0005818 |
0.353 |
|
| 2009 |
Wang Y, Sadreyev RI, Grishin NV. PROCAIN server for remote protein sequence similarity search. Bioinformatics (Oxford, England). 25: 2076-7. PMID 19497935 DOI: 10.1093/Bioinformatics/Btp346 |
0.418 |
|
| 2009 |
Sadreyev RI, Kim BH, Grishin NV. Discrete-continuous duality of protein structure space. Current Opinion in Structural Biology. 19: 321-8. PMID 19482467 DOI: 10.1016/J.Sbi.2009.04.009 |
0.373 |
|
| 2009 |
Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for homology detection: improved statistical accuracy, speed and functionality. Nucleic Acids Research. 37: W90-4. PMID 19435884 DOI: 10.1093/Nar/Gkp360 |
0.405 |
|
| 2009 |
Pei J, Grishin NV. The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold. Proteins. 77: 413-9. PMID 19434753 DOI: 10.1002/Prot.22447 |
0.433 |
|
| 2009 |
Shi S, Chitturi B, Grishin NV. ProSMoS server: a pattern-based search using interaction matrix representation of protein structures. Nucleic Acids Research. 37: W526-31. PMID 19420061 DOI: 10.1093/Nar/Gkp316 |
0.389 |
|
| 2009 |
Kim BH, Cheng H, Grishin NV. HorA web server to infer homology between proteins using sequence and structural similarity. Nucleic Acids Research. 37: W532-8. PMID 19417074 DOI: 10.1093/Nar/Gkp328 |
0.437 |
|
| 2009 |
Huerta C, Borek D, Machius M, Grishin NV, Zhang H. Structure and mechanism of a eukaryotic FMN adenylyltransferase. Journal of Molecular Biology. 389: 388-400. PMID 19375431 DOI: 10.1016/J.Jmb.2009.04.022 |
0.411 |
|
| 2009 |
Wang Y, Sadreyev RI, Grishin NV. PROCAIN: protein profile comparison with assisting information. Nucleic Acids Research. 37: 3522-30. PMID 19357092 DOI: 10.1093/Nar/Gkp212 |
0.446 |
|
| 2009 |
Majumdar I, Kinch LN, Grishin NV. A database of domain definitions for proteins with complex interdomain geometry. Plos One. 4: e5084. PMID 19352501 DOI: 10.1371/Journal.Pone.0005084 |
0.407 |
|
| 2009 |
Sadreyev RI, Shi S, Baker D, Grishin NV. Structure similarity measure with penalty for close non-equivalent residues. Bioinformatics (Oxford, England). 25: 1259-63. PMID 19321733 DOI: 10.1093/Bioinformatics/Btp148 |
0.328 |
|
| 2009 |
Pei J, Lupardus PJ, Garcia KC, Grishin NV. CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins. Protein Science : a Publication of the Protein Society. 18: 856-62. PMID 19309740 DOI: 10.1002/Pro.78 |
0.418 |
|
| 2009 |
Pei J, Grishin NV. Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH. Cell Cycle (Georgetown, Tex.). 8: 1453-5. PMID 19305154 DOI: 10.4161/Cc.8.9.8243 |
0.383 |
|
| 2009 |
Yin W, Romeo S, Chang S, Grishin NV, Hobbs HH, Cohen JC. Genetic variation in ANGPTL4 provides insights into protein processing and function. The Journal of Biological Chemistry. 284: 13213-22. PMID 19270337 DOI: 10.1074/Jbc.M900553200 |
0.408 |
|
| 2009 |
Kinch LN, Grishin NV. The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif. Biology Direct. 4: 2. PMID 19159466 DOI: 10.1186/1745-6150-4-2 |
0.367 |
|
| 2009 |
Wang Y, Kuan PJ, Xing C, Cronkhite JT, Torres F, Rosenblatt RL, DiMaio JM, Kinch LN, Grishin NV, Garcia CK. Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer. American Journal of Human Genetics. 84: 52-9. PMID 19100526 DOI: 10.1016/J.Ajhg.2008.11.010 |
0.322 |
|
| 2009 |
Yarbrough ML, Li Y, Kinch LN, Grishin NV, Ball HL, Orth K. AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling. Science (New York, N.Y.). 323: 269-72. PMID 19039103 DOI: 10.1126/Science.1166382 |
0.321 |
|
| 2009 |
Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Molecular & Cellular Proteomics : McP. 8: 215-25. PMID 18723842 DOI: 10.1074/Mcp.M800187-Mcp200 |
0.359 |
|
| 2009 |
Liang S, Grishin NV. Side-chain modeling with an optimized scoring function. Protein Science. 11: 322-331. PMID 11790842 DOI: 10.1110/Ps.24902 |
0.337 |
|
| 2008 |
Teichmann SA, Grishin NV. Sequences and topology: from genome structure to protein structure. Current Opinion in Structural Biology. 18: 340-1. PMID 18539451 DOI: 10.1016/J.Sbi.2008.05.006 |
0.417 |
|
| 2008 |
Pei J, Tang M, Grishin NV. PROMALS3D web server for accurate multiple protein sequence and structure alignments. Nucleic Acids Research. 36: W30-4. PMID 18503087 DOI: 10.1093/Nar/Gkn322 |
0.427 |
|
| 2008 |
Bolliger MF, Pei J, Maxeiner S, Boucard AA, Grishin NV, Südhof TC. Unusually rapid evolution of Neuroligin-4 in mice. Proceedings of the National Academy of Sciences of the United States of America. 105: 6421-6. PMID 18434543 DOI: 10.1073/Pnas.0801383105 |
0.312 |
|
| 2008 |
Liu Y, Tewari R, Ning J, Blagborough AM, Garbom S, Pei J, Grishin NV, Steele RE, Sinden RE, Snell WJ, Billker O. The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes. Genes & Development. 22: 1051-68. PMID 18367645 DOI: 10.1101/Gad.1656508 |
0.327 |
|
| 2008 |
Wrabl JO, Grishin NV. Statistics of random protein superpositions: p-values for pairwise structure alignment. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 317-55. PMID 18333756 DOI: 10.1089/Cmb.2007.0161 |
0.33 |
|
| 2008 |
Cheng H, Kim BH, Grishin NV. Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. Journal of Molecular Biology. 377: 1265-78. PMID 18313074 DOI: 10.1016/J.Jmb.2007.12.076 |
0.443 |
|
| 2008 |
Pei J, Kim BH, Grishin NV. PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Research. 36: 2295-300. PMID 18287115 DOI: 10.1093/Nar/Gkn072 |
0.421 |
|
| 2008 |
Sadreyev RI, Grishin NV. Accurate statistical model of comparison between multiple sequence alignments. Nucleic Acids Research. 36: 2240-8. PMID 18285364 DOI: 10.1093/Nar/Gkn065 |
0.437 |
|
| 2008 |
Huang N, Sorci L, Zhang X, Brautigam CA, Li X, Raffaelli N, Magni G, Grishin NV, Osterman AL, Zhang H. Bifunctional NMN Adenylyltransferase/ADP-Ribose Pyrophosphatase: Structure and Function in Bacterial NAD Metabolism Structure. 16: 196-209. PMID 18275811 DOI: 10.1016/J.Str.2007.11.017 |
0.381 |
|
| 2008 |
Yang J, Brown MS, Liang G, Grishin NV, Goldstein JL. Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone. Cell. 132: 387-96. PMID 18267071 DOI: 10.1016/J.Cell.2008.01.017 |
0.303 |
|
| 2008 |
Nelson ED, Grishin NV. Folding domain B of protein A on a dynamically partitioned free energy landscape Proceedings of the National Academy of Sciences of the United States of America. 105: 1489-1493. PMID 18230738 DOI: 10.1073/Pnas.0705707105 |
0.347 |
|
| 2008 |
Cheng H, Kim BH, Grishin NV. MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs Proteins: Structure, Function and Genetics. 70: 1162-1166. PMID 17932926 DOI: 10.1002/Prot.21783 |
0.453 |
|
| 2008 |
Cheng H, Kim BH, Grishin NV. MALISAM: A database of structurally analogous motifs in proteins Nucleic Acids Research. 36: D211-D217. PMID 17855399 DOI: 10.1093/Nar/Gkm698 |
0.482 |
|
| 2008 |
Makarova KS, Grishin NV. Thermolysin and mitochondrial processing peptidase: How far structure—functional convergence goes Protein Science. 8: 2537-2540. PMID 10595562 DOI: 10.1110/Ps.8.11.2537 |
0.341 |
|
| 2007 |
Qi Y, Sadreyev RI, Wang Y, Kim BH, Grishin NV. A comprehensive system for evaluation of remote sequence similarity detection. Bmc Bioinformatics. 8: 314. PMID 17725841 DOI: 10.1186/1471-2105-8-314 |
0.385 |
|
| 2007 |
Sadreyev RI, Tang M, Kim BH, Grishin NV. COMPASS server for remote homology inference. Nucleic Acids Research. 35: W653-8. PMID 17517780 DOI: 10.1093/Nar/Gkm293 |
0.385 |
|
| 2007 |
Dikiy A, Novoselov SV, Fomenko DE, Sengupta A, Carlson BA, Cerny RL, Ginalski K, Grishin NV, Hatfield DL, Gladyshev VN. SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family. Biochemistry. 46: 6871-82. PMID 17503775 DOI: 10.1021/Bi602462Q |
0.449 |
|
| 2007 |
Pei J, Kim BH, Tang M, Grishin NV. PROMALS web server for accurate multiple protein sequence alignments Nucleic Acids Research. 35: W649-W652. PMID 17452345 DOI: 10.1093/Nar/Gkm227 |
0.424 |
|
| 2007 |
Belogurov GA, Vassylyeva MN, Svetlov V, Klyuyev S, Grishin NV, Vassylyev D, Artsimovitch I. Structural Basis for Converting a General Transcription Factor into an Operon-Specific Virulence Regulator Molecular Cell. 26: 117-129. PMID 17434131 DOI: 10.1016/J.Molcel.2007.02.021 |
0.368 |
|
| 2007 |
Shi S, Zhong Y, Majumdar I, Sri Krishna S, Grishin NV. Searching for three-dimensional secondary structural patterns in proteins with ProSMoS. Bioinformatics (Oxford, England). 23: 1331-8. PMID 17384423 DOI: 10.1093/Bioinformatics/Btm121 |
0.384 |
|
| 2007 |
Pei J, Grishin NV. PROMALS: Towards accurate multiple sequence alignments of distantly related proteins Bioinformatics. 23: 802-808. PMID 17267437 DOI: 10.1093/Bioinformatics/Btm017 |
0.395 |
|
| 2006 |
Saikatendu KS, Zhang X, Kinch L, Leybourne M, Grishin NV, Zhang H. 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 Structural Biology. 6. PMID 17187687 DOI: 10.1186/1472-6807-6-27 |
0.458 |
|
| 2006 |
Steczkiewicz K, Kinch L, Grishin NV, Rychlewski L, Ginalski K. Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily Cell Cycle. 5: 2927-2930. PMID 17172875 DOI: 10.4161/Cc.5.24.3572 |
0.31 |
|
| 2006 |
Kinch LN, Grishin NV. Longin-like folds identified in CHiPS and DUF254 proteins: Vesicle trafficking complexes conserved in eukaryotic evolution Protein Science. 15: 2669-2674. PMID 17075139 DOI: 10.1110/Ps.062419006 |
0.426 |
|
| 2006 |
Pei J, Grishin NV. MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information Nucleic Acids Research. 34: 4364-4374. PMID 16936316 DOI: 10.1093/Nar/Gkl514 |
0.407 |
|
| 2006 |
Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L, Grishin NV, White M, Yang XJ, Zhao Y. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Molecular Cell. 23: 607-18. PMID 16916647 DOI: 10.1016/J.Molcel.2006.06.026 |
0.375 |
|
| 2006 |
Makarova KS, Grishin NV, Koonin EV. The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria Bioinformatics. 22: 2581-2584. PMID 16895922 DOI: 10.1093/Bioinformatics/Btl418 |
0.39 |
|
| 2006 |
Cheek S, Krishna SS, Grishin NV. Structural classification of small, disulfide-rich protein domains. Journal of Molecular Biology. 359: 215-37. PMID 16618491 DOI: 10.1016/J.Jmb.2006.03.017 |
0.397 |
|
| 2006 |
Krishna SS, Sadreyev RI, Grishin NV. A tale of two ferredoxins: sequence similarity and structural differences. Bmc Structural Biology. 6: 8. PMID 16603087 DOI: 10.1186/1472-6807-6-8 |
0.42 |
|
| 2006 |
Nelson ED, Grishin NV. Alternate Pathways for Folding in the Flavodoxin Fold Family Revealed by a Nucleation-growth Model Journal of Molecular Biology. 358: 646-653. PMID 16563435 DOI: 10.1016/J.Jmb.2006.02.026 |
0.368 |
|
| 2006 |
Sadreyev RI, Grishin NV. Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds. Bmc Structural Biology. 6: 6. PMID 16549009 DOI: 10.1186/1472-6807-6-6 |
0.469 |
|
| 2006 |
Makarova KS, Grishin NV, Shabalina SA, Wolf YI, Koonin EV. 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 Biology Direct. 1. PMID 16545108 DOI: 10.1186/1745-6150-1-7 |
0.341 |
|
| 2006 |
Kinch LN, Ginalski K, Grishin NV. Site-2 protease regulated intramembrane proteolysis: Sequence homologs suggest an ancient signaling cascade Protein Science. 15: 84-93. PMID 16322567 DOI: 10.1110/Ps.051766506 |
0.412 |
|
| 2006 |
Pei J, Cai W, Kinch LN, Grishin NV. Prediction of functional specificity determinants from protein sequences using log-likelihood ratios Bioinformatics. 22: 164-171. PMID 16278237 DOI: 10.1093/Bioinformatics/Bti766 |
0.421 |
|
| 2006 |
Nelson ED, Grishin NV. Scaling approach to the folding kinetics of large proteins Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 73. DOI: 10.1103/Physreve.73.011904 |
0.36 |
|
| 2006 |
Pei J, Grishin NV. Erratum: MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information (Nucleic Acids Research (2006) vol. 34 (4364)) Nucleic Acids Research. 34. DOI: 10.1093/Nar/Gkl918 |
0.316 |
|
| 2006 |
Teichmann SA, Grishin NV. Sequences and topology: from methods to meaning Current Opinion in Structural Biology. 16: 359-361. DOI: 10.1016/J.Sbi.2006.05.012 |
0.308 |
|
| 2005 |
Basu J, Shen N, Dulubova I, Lu J, Guan R, Guryev O, Grishin NV, Rosenmund C, Rizo J. A minimal domain responsible for Munc13 activity. Nature Structural & Molecular Biology. 12: 1017-8. PMID 16228007 DOI: 10.1038/Nsmb1001 |
0.311 |
|
| 2005 |
Pei J, Grishin NV. COG3926 and COG5526: A tale of two new lysozyme-like protein families Protein Science. 14: 2574-2581. PMID 16155206 DOI: 10.1110/Ps.051656805 |
0.468 |
|
| 2005 |
Majumdar I, Krishna SS, Grishin NV. PALSSE: a program to delineate linear secondary structural elements from protein structures. Bmc Bioinformatics. 6: 202. PMID 16095538 DOI: 10.1186/1471-2105-6-202 |
0.395 |
|
| 2005 |
Kim BH, Sadreyev R, Grishin NV. COG4849 is a novel family of nucleotidyltransferases Journal of Molecular Recognition. 18: 422-425. PMID 15983981 DOI: 10.1002/Jmr.746 |
0.454 |
|
| 2005 |
Kinch LN, Ginalski K, Rychlewski L, Grishin NV. Identification of novel restriction endonuclease-like fold families among hypothetical proteins Nucleic Acids Research. 33: 3598-3605. PMID 15972856 DOI: 10.1093/Nar/Gki676 |
0.477 |
|
| 2005 |
Cheng H, Grishin NV. DOM-fold: A structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain Protein Science. 14: 1902-1910. PMID 15937278 DOI: 10.1110/Ps.051364905 |
0.462 |
|
| 2005 |
Ginalski K, Grishin NV, Godzik A, Rychlewski L. Practical lessons from protein structure prediction Nucleic Acids Research. 33: 1874-1891. PMID 15805122 DOI: 10.1093/Nar/Gki327 |
0.405 |
|
| 2005 |
Pei J, Grishin NV. The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases Protein Science. 14: 1370-1374. PMID 15802648 DOI: 10.1110/Ps.041250005 |
0.442 |
|
| 2005 |
Cheek S, Ginalski K, Zhang H, Grishin NV. A comprehensive update of the sequence and structure classification of kinases Bmc Structural Biology. 5. PMID 15771780 DOI: 10.1186/1472-6807-5-6 |
0.315 |
|
| 2005 |
Zheng M, Ginalski K, Rychlewski L, Grishin NV. Protein Domain of Unknown Function DUF1023 is an α/β hydrolase Proteins: Structure, Function and Genetics. 59: 1-6. PMID 15688435 DOI: 10.1002/Prot.20388 |
0.379 |
|
| 2005 |
Araç D, Dulubova I, Pei J, Huryeva I, Grishin NV, Rizo J. Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5 Journal of Molecular Biology. 346: 589-601. PMID 15670607 DOI: 10.1016/J.Jmb.2004.12.004 |
0.435 |
|
| 2005 |
Kinch LN, Cheek S, Grishin NV. EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV Protein Science. 14: 360-367. PMID 15632288 DOI: 10.1110/Ps.041114805 |
0.47 |
|
| 2005 |
Krishna SS, Grishin NV. Structural drift: a possible path to protein fold change. Bioinformatics (Oxford, England). 21: 1308-10. PMID 15604105 DOI: 10.1093/Bioinformatics/Bti227 |
0.419 |
|
| 2005 |
Qi Y, Grishin NV. Structural classification of thioredoxin-like fold proteins Proteins: Structure, Function and Genetics. 58: 376-388. PMID 15558583 DOI: 10.1002/Prot.20329 |
0.487 |
|
| 2004 |
Nelson ED, Grishin NV. Efficient expansion, folding, and unfolding of proteins Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 70: 051906-1-051906-7. PMID 15600655 DOI: 10.1103/Physreve.70.051906 |
0.367 |
|
| 2004 |
Cheek S, Qi Y, Krishna SS, Kinch LN, Grishin NV. 4SCOPmap: automated assignment of protein structures to evolutionary superfamilies. Bmc Bioinformatics. 5: 197. PMID 15598351 DOI: 10.1186/1471-2105-5-197 |
0.416 |
|
| 2004 |
Rand TA, Ginalski K, Grishin NV, Wang X. Biochemical identification of Argonaute 2 as the sole protein required for RNA-induced silencing complex activity. Proceedings of the National Academy of Sciences of the United States of America. 101: 14385-9. PMID 15452342 DOI: 10.1073/Pnas.0405913101 |
0.379 |
|
| 2004 |
Ginalski K, Zhang H, Grishin NV. Raptor protein contains a caspase-like domain Trends in Biochemical Sciences. 29: 522-524. PMID 15450605 DOI: 10.1016/J.Tibs.2004.08.006 |
0.429 |
|
| 2004 |
Cai W, Pei J, Grishin NV. Reconstruction of ancestral protein sequences and its applications Bmc Evolutionary Biology. 4. PMID 15377393 DOI: 10.1186/1471-2148-4-33 |
0.408 |
|
| 2004 |
Sadreyev RI, Grishin NV. Estimates of statistical significance for comparison of individual positions in multiple sequence alignments. Bmc Bioinformatics. 5: 106. PMID 15296518 DOI: 10.1186/1471-2105-5-106 |
0.407 |
|
| 2004 |
Ginalski K, Kinch L, Rychlewski L, Grishin NV. BTLCP proteins: A novel family of bacterial transglutaminase-like cysteine proteinases Trends in Biochemical Sciences. 29: 392-395. PMID 15288868 DOI: 10.1016/J.Tibs.2004.06.001 |
0.457 |
|
| 2004 |
Pei J, Grishin NV. Combining evolutionary and structural information for local protein structure prediction Proteins: Structure, Function and Genetics. 56: 782-794. PMID 15281130 DOI: 10.1002/Prot.20158 |
0.38 |
|
| 2004 |
Cheng H, Shen N, Pei J, Grishin NV. Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease Protein Science. 13: 2260-2269. PMID 15273316 DOI: 10.1110/Ps.04726004 |
0.388 |
|
| 2004 |
Qi Y, Grishin NV. PCOAT: Positional correlation analysis using multiple methods Bioinformatics. 20: 3697-3699. PMID 15271785 DOI: 10.1093/Bioinformatics/Bth431 |
0.354 |
|
| 2004 |
Krishna SS, Grishin NV. Structurally analogous proteins do exist! Structure (London, England : 1993). 12: 1125-7. PMID 15242587 DOI: 10.1016/J.Str.2004.06.004 |
0.413 |
|
| 2004 |
Ginalski K, Kinch L, Rychlewski L, Grishin NV. DCC proteins: a novel family of thiol-disulfide oxidoreductases Trends in Biochemical Sciences. 29: 339-342. PMID 15236740 DOI: 10.1016/J.Tibs.2004.04.003 |
0.431 |
|
| 2004 |
Ginalski K, von Grotthuss M, Grishin NV, Rychlewski L. Detecting distant homology with Meta-BASIC. Nucleic Acids Research. 32: W576-81. PMID 15215454 DOI: 10.1093/Nar/Gkh370 |
0.425 |
|
| 2004 |
Ginalski K, Kinch L, Rychlewski L, Grishin NV. BOF: a novel family of bacterial OB-fold proteins. Febs Letters. 567: 297-301. PMID 15178340 DOI: 10.1016/J.Febslet.2004.04.086 |
0.411 |
|
| 2004 |
Ginalski K, Rychlewski L, Baker D, Grishin NV. Protein structure prediction for the male-specific region of the human Y chromosome. Proceedings of the National Academy of Sciences of the United States of America. 101: 2305-10. PMID 14983005 DOI: 10.1073/Pnas.0306306101 |
0.427 |
|
| 2004 |
Sadreyev RI, Grishin NV. Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs. Bioinformatics (Oxford, England). 20: 818-28. PMID 14751996 DOI: 10.1093/Bioinformatics/Btg485 |
0.371 |
|
| 2004 |
Wrabl JO, Grishin NV. Gaps in structurally similar proteins: towards improvement of multiple sequence alignment. Proteins. 54: 71-87. PMID 14705025 DOI: 10.1002/Prot.10508 |
0.404 |
|
| 2004 |
Krishna SS, Grishin NV. The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon. Cell Cycle. 3: 1046-1049. DOI: 10.4161/Cc.3.8.1017 |
0.385 |
|
| 2003 |
Liang S, Grishin NV. Effective scoring function for protein sequence design. Proteins. 54: 271-281. PMID 14696189 DOI: 10.1002/Prot.10560 |
0.407 |
|
| 2003 |
Kinch LN, Wrabl JO, Krishna SS, Majumdar I, Sadreyev RI, Qi Y, Pei J, Cheng H, Grishin NV. CASP5 assessment of fold recognition target predictions. Proteins. 53: 395-409. PMID 14579328 DOI: 10.1002/Prot.10557 |
0.347 |
|
| 2003 |
Kinch LN, Qi Y, Hubbard TJP, Grishin NV. CASP5 target classification. Proteins. 53: 340-351. PMID 14579323 DOI: 10.1002/Prot.10555 |
0.341 |
|
| 2003 |
Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Science : a Publication of the Protein Society. 12: 2262-72. PMID 14500884 DOI: 10.1110/Ps.03197403 |
0.435 |
|
| 2003 |
Pei J, Dokholyan NV, Shakhnovich EI, Grishin NV. Using protein design for homology detection and active site searches. Proceedings of the National Academy of Sciences of the United States of America. 100: 11361-6. PMID 12975528 DOI: 10.1073/Pnas.2034878100 |
0.378 |
|
| 2003 |
Mittelman D, Sadreyev R, Grishin N. Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments Bioinformatics. 19: 1531-1539. PMID 12912834 DOI: 10.1093/Bioinformatics/Btg185 |
0.374 |
|
| 2003 |
Kinch LN, Baker D, Grishin NV. Deciphering a novel thioredoxin-like fold family. Proteins. 52: 323-31. PMID 12866046 DOI: 10.1002/Prot.10425 |
0.44 |
|
| 2003 |
Pei J, Grishin NV. Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases Protein Science. 12: 1131-1135. PMID 12717035 DOI: 10.1110/Ps.0240803 |
0.381 |
|
| 2003 |
Karthikeyan S, Zhou Q, Mseeh F, Grishin NV, Osterman AL, Zhang H. Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch. Structure (London, England : 1993). 11: 265-73. PMID 12623014 DOI: 10.1016/S0969-2126(03)00024-8 |
0.331 |
|
| 2003 |
Pei J, Sadreyev R, Grishin NV. PCMA: Fast and accurate multiple sequence alignment based on profile consistency Bioinformatics. 19: 427-428. PMID 12584134 DOI: 10.1093/Bioinformatics/Btg008 |
0.345 |
|
| 2003 |
Zhang X, Kurnasov OV, Karthikeyan S, Grishin NV, Osterman AL, Zhang H. Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis. The Journal of Biological Chemistry. 278: 13503-11. PMID 12574164 DOI: 10.1074/Jbc.M300073200 |
0.332 |
|
| 2003 |
Sadreyev R, Grishin N. COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance Journal of Molecular Biology. 326: 317-336. PMID 12547212 DOI: 10.1016/S0022-2836(02)01371-2 |
0.422 |
|
| 2003 |
Krishna SS, Majumdar I, Grishin NV. Structural classification of zinc fingers: survey and summary. Nucleic Acids Research. 31: 532-50. PMID 12527760 DOI: 10.1093/Nar/Gkg161 |
0.427 |
|
| 2003 |
Nelson E, Grishin N. Investigation of the folding profiles of evolutionarily selected model proteins Journal of Chemical Physics. 118: 3342-3349. DOI: 10.1063/1.1536621 |
0.388 |
|
| 2002 |
Grishin VN, Grishin NV. Euclidian space and grouping of biological objects. Bioinformatics. 18: 1523-1534. PMID 12424125 DOI: 10.1093/Bioinformatics/18.11.1523 |
0.344 |
|
| 2002 |
Wolf YI, Rogozin IB, Grishin NV, Koonin EV. Genome trees and the tree of life Trends in Genetics. 18: 472-479. PMID 12175808 DOI: 10.1016/S0168-9525(02)02744-0 |
0.324 |
|
| 2002 |
Kinch LN, Grishin NV. Evolution of protein structures and functions Current Opinion in Structural Biology. 12: 400-408. PMID 12127461 DOI: 10.1016/S0959-440X(02)00338-X |
0.445 |
|
| 2002 |
Cheek S, Zhang H, Grishin NV. Sequence and structure classification of kinases. Journal of Molecular Biology. 320: 855-881. PMID 12095261 DOI: 10.1016/S0022-2836(02)00538-7 |
0.38 |
|
| 2002 |
Singh SK, Kurnasov OV, Chen B, Robinson H, Grishin NV, Osterman AL, Zhang H. Crystal Structure of Haemophilus influenzae NadR Protein A BIFUNCTIONAL ENZYME ENDOWED WITH NMN ADENYLYLTRANSFERASE AND RIBOSYLNICOTINAMIDE KINASE ACTIVITIES Journal of Biological Chemistry. 277: 33291-33299. PMID 12068016 DOI: 10.1074/Jbc.M204368200 |
0.396 |
|
| 2002 |
Kinch LN, Grishin NV. Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity. Proteins. 48: 75-84. PMID 12012339 DOI: 10.1002/Prot.10110 |
0.495 |
|
| 2002 |
Qi Y, Pei J, Grishin NV. C-terminal domain of gyrase A is predicted to have a β-propeller structure Proteins. 47: 258-264. PMID 11948780 DOI: 10.1002/Prot.10090 |
0.392 |
|
| 2002 |
Kinch LN, Saier MH, Grishin NV. Sec61beta--a component of the archaeal protein secretory system. Trends in Biochemical Sciences. 27: 170-1. PMID 11943537 DOI: 10.1016/S0968-0004(01)02055-2 |
0.385 |
|
| 2002 |
Pei J, Grishin NV. Breaking the singleton of germination protease Protein Science. 11: 691-697. PMID 11847292 DOI: 10.1110/Ps.27302 |
0.409 |
|
| 2002 |
Wrabl JO, Grishin NV. Homology between O-linked GlcNAc transferases and proteins of the glycogen phosphorylase superfamily. Journal of Molecular Biology. 314: 365-74. PMID 11846551 DOI: 10.1006/Jmbi.2001.5151 |
0.485 |
|
| 2002 |
Sierra DA, Gilbert DJ, Householder D, Grishin NV, Yu K, Ukidwe P, Barker SA, He W, Wensel TG, Otero G, Brown G, Copeland NG, Jenkins NA, Wilkie TM. Evolution of the regulators of G-protein signaling multigene family in mouse and human. Genomics. 79: 177-85. PMID 11829488 DOI: 10.1006/Geno.2002.6693 |
0.407 |
|
| 2002 |
Zhang H, Zhou T, Kurnasov O, Cheek S, Grishin NV, Osterman A. Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Structure (London, England : 1993). 10: 69-79. PMID 11796112 DOI: 10.1016/S0969-2126(01)00693-1 |
0.333 |
|
| 2002 |
Makarova KS, Aravind L, Grishin NV, Rogozin IB, Koonin EV. A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis Nucleic Acids Research. 30: 482-496. PMID 11788711 DOI: 10.1093/Nar/30.2.482 |
0.347 |
|
| 2002 |
Zhou T, Kurnasov O, Tomchick DR, Binns DD, Grishin NV, Marquez VE, Osterman AL, Zhang H. Structure of Human Nicotinamide/Nicotinic Acid Mononucleotide Adenylyltransferase BASIS FOR THE DUAL SUBSTRATE SPECIFICITY AND ACTIVATION OF THE ONCOLYTIC AGENT TIAZOFURIN Journal of Biological Chemistry. 277: 13148-13154. PMID 11788603 DOI: 10.1074/Jbc.M111469200 |
0.351 |
|
| 2001 |
Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV. Genome trees constructed using five different approaches suggest new major bacterial clades Bmc Evolutionary Biology. 1: 8-8. PMID 11734060 DOI: 10.1186/1471-2148-1-8 |
0.384 |
|
| 2001 |
Grishin NV. Fold change in evolution of protein structures. Journal of Structural Biology. 134: 167-185. PMID 11551177 DOI: 10.1006/Jsbi.2001.4335 |
0.465 |
|
| 2001 |
Abbott JJ, Pei J, Ford JL, Qi Y, Grishin VN, Pitcher LA, Phillips MA, Grishin NV. Structure prediction and active site analysis of the metal binding determinants in gamma -glutamylcysteine synthetase. The Journal of Biological Chemistry. 276: 42099-107. PMID 11527962 DOI: 10.1074/Jbc.M104672200 |
0.318 |
|
| 2001 |
Pei J, Grishin NV. AL2CO: Calculation of positional conservation in a protein sequence alignment Bioinformatics. 17: 700-712. PMID 11524371 DOI: 10.1093/Bioinformatics/17.8.700 |
0.412 |
|
| 2001 |
Pei J, Grishin NV. Type II CAAX prenyl endopeptidases belong to a novel superfamily of putative membrane-bound metalloproteases Trends in Biochemical Sciences. 26: 275-277. PMID 11343912 DOI: 10.1016/S0968-0004(01)01813-8 |
0.374 |
|
| 2001 |
Garcia CK, Wilund K, Arca M, Zuliani G, Fellin R, Maioli M, Calandra S, Bertolini S, Cossu F, Grishin N, Barnes R, Cohen JC, Hobbs HH. Autosomal recessive hypercholesterolemia caused by mutations in a putative LDL receptor adaptor protein. Science (New York, N.Y.). 292: 1394-8. PMID 11326085 DOI: 10.1126/Science.1060458 |
0.337 |
|
| 2001 |
Grishin NV. Treble clef finger—a functionally diverse zinc-binding structural motif Nucleic Acids Research. 29: 1703-1714. PMID 11292843 DOI: 10.1093/Nar/29.8.1703 |
0.458 |
|
| 2001 |
Grishin NV. MH1 domain of Smad is a degraded homing endonuclease Journal of Molecular Biology. 307: 31-37. PMID 11243801 DOI: 10.1006/Jmbi.2000.4486 |
0.424 |
|
| 2001 |
Grishin NV. KH domain: one motif, two folds Nucleic Acids Research. 29: 638-643. PMID 11160884 DOI: 10.1093/Nar/29.3.638 |
0.442 |
|
| 2001 |
Horvath MM, Grishin NV. The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily. Proteins. 42: 230-236. PMID 11119647 DOI: 10.1002/1097-0134(20010201)42:2<230::Aid-Prot100>3.0.Co;2-J |
0.464 |
|
| 2001 |
Pei J, Grishin NV. GGDEF domain is homologous to adenylyl cyclase Proteins: Structure, Function and Genetics. 42: 210-216. PMID 11119645 DOI: 10.1002/1097-0134(20010201)42:2<210::Aid-Prot80>3.0.Co;2-8 |
0.439 |
|
| 2000 |
Galperin MY, Grishin NV. The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase. Proteins. 41: 238-247. PMID 10966576 DOI: 10.1002/1097-0134(20001101)41:2<238::Aid-Prot80>3.0.Co;2-L |
0.389 |
|
| 2000 |
Shao X, Grishin NV. Common fold in helix-hairpin-helix proteins. Nucleic Acids Research. 28: 2643-2650. PMID 10908318 DOI: 10.1093/Nar/28.14.2643 |
0.43 |
|
| 2000 |
Grishin NV, Wolf YI, Koonin EV. From Complete Genomes to Measures of Substitution Rate Variability Within and Between Proteins Genome Research. 10: 991-1000. PMID 10899148 DOI: 10.1101/Gr.10.7.991 |
0.327 |
|
| 2000 |
Grishin NV. C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily. Journal of Molecular Biology. 299: 1165-1177. PMID 10873443 DOI: 10.1006/Jmbi.2000.3841 |
0.395 |
|
| 2000 |
Grishin NV. Two tricks in one bundle: helix–turn–helix gains enzymatic activity Nucleic Acids Research. 28: 2229-2233. PMID 10871343 DOI: 10.1093/Nar/28.11.2229 |
0.415 |
|
| 2000 |
Wolf YI, Grishin NV, Koonin EV. Estimating the number of protein folds and families from complete genome data Journal of Molecular Biology. 299: 897-905. PMID 10843846 DOI: 10.1006/Jmbi.2000.3786 |
0.392 |
|
| 2000 |
Zhang H, Huang K, Li Z, Banerjei L, Fisher KE, Grishin NV, Eisenstein E, Herzberg O. Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications. Proteins. 40: 86-97. PMID 10813833 DOI: 10.1002/(Sici)1097-0134(20000701)40:1<86::Aid-Prot100>3.0.Co;2-Y |
0.487 |
|
| 2000 |
Ye J, Davé UP, Grishin NV, Goldstein JL, Brown MS. Asparagine-proline sequence within membrane-spanning segment of SREBP triggers intramembrane cleavage by site-2 protease. Proceedings of the National Academy of Sciences of the United States of America. 97: 5123-8. PMID 10805775 DOI: 10.1073/Pnas.97.10.5123 |
0.355 |
|
| 2000 |
Almrud JJ, Oliveira MA, Kern AD, Grishin NV, Phillips MA, Hackert ML. Crystal structure of human ornithine decarboxylase at 2.1 A resolution: structural insights to antizyme binding. Journal of Molecular Biology. 295: 7-16. PMID 10623504 DOI: 10.1006/Jmbi.1999.3331 |
0.349 |
|
| 2000 |
Leipe DD, Aravind L, Grishin NV, Koonin EV. The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Research. 10: 5-16. DOI: 10.1101/Gr.10.1.5 |
0.4 |
|
| 1999 |
Grishin NV, Osterman AL, Brooks HB, Phillips MA, Goldsmith EJ. X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine. Biochemistry. 38: 15174-84. PMID 10563800 DOI: 10.1021/Bi9915115 |
0.348 |
|
| 1999 |
Makarova KS, Grishin NV. The Zn-peptidase superfamily: functional convergence after evolutionary divergence. Journal of Molecular Biology. 292: 11-17. PMID 10493853 DOI: 10.1006/Jmbi.1999.3059 |
0.359 |
|
| 1999 |
Zhang H, Grishin NV. The α-subunit of protein prenyltransferases is a member of the tetratricopeptide repeat family Protein Science. 8: 1658-1667. PMID 10452610 DOI: 10.1110/Ps.8.8.1658 |
0.458 |
|
| 1999 |
Grishin NV. Phosphatidylinositol phosphate kinase: a link between protein kinase and glutathione synthase folds. Journal of Molecular Biology. 291: 239-247. PMID 10438618 DOI: 10.1006/Jmbi.1999.2973 |
0.382 |
|
| 1999 |
Grishin NV. A Novel Approach to Phylogeny Reconstruction from Protein Sequences Journal of Molecular Evolution. 48: 264-273. PMID 10093215 DOI: 10.1007/Pl00006469 |
0.32 |
|
| 1999 |
Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events Genome Research. 9: 689-710. DOI: 10.1101/Gr.9.8.689 |
0.384 |
|
| 1999 |
Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV. Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell Genome Research. 9: 608-628. DOI: 10.1101/Gr.9.7.608 |
0.434 |
|
| 1998 |
Kurvari V, Grishin NV, Snell WJ. A gamete-specific, sex-limited homeodomain protein in Chlamydomonas. The Journal of Cell Biology. 143: 1971-80. PMID 9864368 DOI: 10.1083/Jcb.143.7.1971 |
0.318 |
|
| 1997 |
Grishin NV. Estimation of evolutionary distances from protein spatial structures Journal of Molecular Evolution. 45: 359-369. PMID 9321415 DOI: 10.1007/Pl00006241 |
0.372 |
|
| 1995 |
Osterman AL, Kinch LN, Grishin NV, Phillips MA. Acidic residues important for substrate binding and cofactor reactivity in eukaryotic ornithine decarboxylase identified by alanine scanning mutagenesis. The Journal of Biological Chemistry. 270: 11797-802. PMID 7744828 DOI: 10.1074/Jbc.270.20.11797 |
0.323 |
|
| 1995 |
Grishin NV, Phillips MA, Goldsmith EJ. Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Science : a Publication of the Protein Society. 4: 1291-304. PMID 7670372 DOI: 10.1002/Pro.5560040705 |
0.425 |
|
| 1994 |
Osterman A, Grishin NV, Kinch LN, Phillips MA. Formation of functional cross-species heterodimers of ornithine decarboxylase. Biochemistry. 33: 13662-7. PMID 7947774 DOI: 10.1021/Bi00250A016 |
0.304 |
|
| 1994 |
Grishin NV, Phillips MA. The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. Protein Science : a Publication of the Protein Society. 3: 2455-8. PMID 7757001 DOI: 10.1002/Pro.5560031231 |
0.405 |
|
| 1992 |
Osterman AL, Grishin NV, Smulevitch SV, Matz MV, Zagnitko OP, Revina LP, Stepanov VM. Primary structure of carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family. Journal of Protein Chemistry. 11: 561-70. PMID 1449602 DOI: 10.1007/Bf01025034 |
0.367 |
|
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