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Nick Grishin

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Genes & Molecular Sequences

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Sanae Shoji-Kawata; Stephen A Spector; Rhea Sumpter; Qihua Sun; Sharon A Tooze; Herbert W Virgin; Angela D Wilkins; Ramnik Xavier; Ai Yamamoto; Zhongju Zou; Grant R Campbell; Ruud Eerland; Nick V Grishin; J Bernd Helms; Carlos Huerta; Dora V Kaloyanova; Lisa Kinch; David King; Deborah J Lenschow; Matthew Leveno; Olivier Lichtarge; Donna MacDuff; Kathrin Pallauf; Beth Levine
Identification of a candidate therapeutic autophagy-inducing peptide.
Ivan K Huang; Jimin Pei; Nick V Grishin
Defining and predicting structurally conserved regions in protein superfamilies.
Wenlin Li; Lisa N Kinch; Qian Cong; Nick V Grishin
Seq2Ref: a web server to facilitate functional interpretation.

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All Publications

2013: Sanae Shoji-Kawata; Stephen A Spector; Rhea Sumpter; Qihua Sun; Sharon A Tooze; Herbert W Virgin; Angela D Wilkins; Ramnik Xavier; Ai Yamamoto; Zhongju Zou; Grant R Campbell; Ruud Eerland; Nick V Grishin; J Bernd Helms; Carlos Huerta; Dora V Kaloyanova; Lisa Kinch; David King; Deborah J Lenschow; Matthew Leveno; Olivier Lichtarge; Donna MacDuff; Kathrin Pallauf; Beth Levine
Identification of a candidate therapeutic autophagy-inducing peptide.
Nature 2013;494(7436):201-6.
2013: Ivan K Huang; Jimin Pei; Nick V Grishin
Defining and predicting structurally conserved regions in protein superfamilies.
Bioinformatics (Oxford, England) 2013;29(2):175-81.
2013: Wenlin Li; Lisa N Kinch; Qian Cong; Nick V Grishin
Seq2Ref: a web server to facilitate functional interpretation.
BMC bioinformatics 2013;14():30.
2012: Fabiana Quagliarini; David M Valenzuela; Yan Wang; Rhonda Hyde; Julia Kozlitina; Andrew J Murphy; Eric Boerwinkle; Jonathan C Cohen; Nick V Grishin; Helen H Hobbs
Atypical angiopoietin-like protein that regulates ANGPTL3.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(48):19751-6.
2012: Irina A Rodionova; David A Scott; Nick V Grishin; Andrei L Osterman; Dmitry A Rodionov
Tagaturonate-fructuronate epimerase UxaE, a novel enzyme in the hexuronate catabolic network in Thermotoga maritima.
Environmental microbiology 2012;14(11):2920-34.
2012: Wenlin Li; Jimin Pei; Qian Cong; Lisa N Kinch; Nick V Grishin
The ABC transporters in Candidatus Liberibacter asiaticus.
Proteins 2012;80(11):2614-28.
2012: Darui Xu; Garen Collett; Alicia Farmer; Nick V Grishin; YuhMin Chook
Sequence and structural analyses of nuclear export signals in the NESdb database.
Molecular biology of the cell 2012;23(18):3677-93.
2012: Darui Xu; Nick V Grishin; YuhMin Chook
NESdb: a database of NES-containing CRM1 cargoes.
Molecular biology of the cell 2012;23(18):3673-6.
2012: Jimin Pei; Nick V Grishin
Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins.
Protein science : a publication of the Protein Society 2012;21(8):1172-84.
2012: Xiaomo Jiang; Lisa N Kinch; Chad A Brautigam; Xiang Chen; Fenghe Du; Nick V Grishin; Zhijian J Chen
Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response.
Immunity 2012;36(6):959-73.
2012: Nick V Grishin
Membrane protein structure predictions for exploration.
Cell 2012;149(7):1424-5.
2012: Vincent S Tagliabracci; Jianzhong Wen; Sandra E Wiley; Carolyn A Worby; Junyu Xiao; James L Engel; Nick V Grishin; Lisa N Kinch; Jack E Dixon
Secreted kinase phosphorylates extracellular proteins that regulate biomineralization.
Science (New York, N.Y.) 2012;336(6085):1150-3.
2012: Masato Kato; Lin Li; Jamie Longgood; She Chen; Xinlin Du; David Eisenberg; Doug E Frantz; Elizabeth J Goldsmith; Nick V Grishin; Tina W Han; Hamid Mirzaei; Jimin Pei; Michael R Sawaya; Jay W Schneider; Kevin Shi; Robert Tycko; Leeju C Wu; Shanhai Xie; Steven L McKnight
Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels.
Cell 2012;149(4):753-67.
2012: Bong-Hyun Kim; Bhadrachalam Chitturi; Nick V Grishin
Self consistency grouping: a stringent clustering method.
BMC bioinformatics 2012;13 Suppl 13():S3.
2012: Qian Cong; Nick V Grishin
MESSA: MEta-Server for protein Sequence Analysis.
BMC biology 2012;10():82.
2012: Qian Cong; Bong-Hyun Kim; Lisa N Kinch; Nick V Grishin
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome.
PloS one 2012;7(7):e41071.
2012: Jeremy Semeiks; Nick V Grishin
A method to find longevity-selected positions in the mammalian proteome.
PloS one 2012;7(6):e38595.
2011: Lisa Kinch; Nick V Grishin; James Brugarolas
Succination of Keap1 and activation of Nrf2-dependent antioxidant pathways in FH-deficient papillary renal cell carcinoma type 2.
Cancer cell 2011;20(4):418-20.
2011: Jimin Pei; Douglas A Mitchell; Jack E Dixon; Nick V Grishin
Expansion of type II CAAX proteases reveals evolutionary origin of γ-secretase subunit APH-1.
Journal of molecular biology 2011;410(1):18-26.
2011: Daniel Quiat; Kevin A Voelker; Jimin Pei; Rhonda Bassel-Duby; Robert W Grange; Nick V Grishin; Eric N Olson
Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(25):10196-201.
2011: Lisa N Kinch; Valerio Mariani; Jimin Pei; Torsten Schwede; Shuoyong Shi; Hua Cheng; Qian Cong; Nick V Grishin
CASP9 target classification.
Proteins 2011;79 Suppl 10():21-36.
2011: Lisa N Kinch; Yuxing Liao; Shuo Yong Shi; Hua Cheng; Qian Cong; Nick V Grishin
CASP9 assessment of free modeling target predictions.
Proteins 2011;79 Suppl 10():59-73.
2010: Phi Luong; Lisa N Kinch; Chad A Brautigam; Nick V Grishin; Diana R Tomchick; Kim Orth
Kinetic and structural insights into the mechanism of AMPylation by VopS Fic domain.
The Journal of biological chemistry 2010;285(26):20155-63.
2010: Bong-Hyun Kim; Qian Cong; Nick V Grishin
HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
Bioinformatics (Oxford, England) 2010;26(12):1564-5.
2010: Silvia Vega-Rubin-de-Celis; Zeina Abdallah; Lisa Kinch; Nick V Grishin; James Brugarolas; Xuewu Zhang
Structural analysis and functional implications of the negative mTORC1 regulator REDD1.
Biochemistry 2010;49(11):2491-501.
2010: Shaoqing He; Christopher McPhaul; John Zhong Li; Rita Garuti; Lisa Kinch; Nick V Grishin; Jonathan C Cohen; Helen H Hobbs
A sequence variation (I148M) in PNPLA3 associated with nonalcoholic fatty liver disease disrupts triglyceride hydrolysis.
The Journal of biological chemistry 2010;285(9):6706-15.
2009: Ruslan I Sadreyev; Jamison D Feramisco; Hensin Tsao; Nick V Grishin
Phenotypic categorization of genetic skin diseases reveals new relations between phenotypes, genes and pathways.
Bioinformatics (Oxford, England) 2009;25(22):2891-6.
2009: Jamison D Feramisco; Ruslan I Sadreyev; Mitzi L Murray; Nick V Grishin; Hensin Tsao
Phenotypic and genotypic analyses of genetic skin disease through the Online Mendelian Inheritance in Man (OMIM) database.
The Journal of investigative dermatology 2009;129(11):2628-36.
2009: Jimin Pei; Nick V Grishin
The Rho GTPase inactivation domain in Vibrio cholerae MARTX toxin has a circularly permuted papain-like thiol protease fold.
Proteins 2009;77(2):413-9.
2009: Ameen A Salahudeen; Joel W Thompson; Julio C Ruiz; He-Wen Ma; Lisa N Kinch; Qiming Li; Nick V Grishin; Richard K Bruick
An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis.
Science (New York, N.Y.) 2009;326(5953):722-6.
2009: Jimin Pei; Cong Ma; Josep Rizo; Nick V Grishin
Remote homology between Munc13 MUN domain and vesicle tethering complexes.
Journal of molecular biology 2009;391(3):509-17.
2009: Yong Wang; Ruslan I Sadreyev; Nick V Grishin
PROCAIN server for remote protein sequence similarity search.
Bioinformatics (Oxford, England) 2009;25(16):2076-7.
2009: Ying Liu; Xuecheng Ye; Feng Jiang; Chunyang Liang; Dongmei Chen; Junmin Peng; Lisa N Kinch; Nick V Grishin; Qinghua Liu
C3PO, an endoribonuclease that promotes RNAi by facilitating RISC activation.
Science (New York, N.Y.) 2009;325(5941):750-3.
2009: Ruslan I Sadreyev; Ming Tang; Bong-Hyun Kim; Nick V Grishin
COMPASS server for homology detection: improved statistical accuracy, speed and functionality.
Nucleic acids research 2009;37(Web Server issue):W90-4.
2009: Shuoyong Shi; Bhadrachalam Chitturi; Nick V Grishin
ProSMoS server: a pattern-based search using interaction matrix representation of protein structures.
Nucleic acids research 2009;37(Web Server issue):W526-31.
2009: Bong-Hyun Kim; Hua Cheng; Nick V Grishin
HorA web server to infer homology between proteins using sequence and structural similarity.
Nucleic acids research 2009;37(Web Server issue):W532-8.
2009: Carlos Huerta; Dominika Borek; Mischa Machius; Nick V Grishin; Hong Zhang
Structure and mechanism of a eukaryotic FMN adenylyltransferase.
Journal of molecular biology 2009;389(2):388-400.
2009: Ruslan I Sadreyev; Bong-Hyun Kim; Nick V Grishin
Discrete-continuous duality of protein structure space.
Current opinion in structural biology 2009;19(3):321-8.
2009: Yong Wang; Ruslan I Sadreyev; Nick V Grishin
PROCAIN: protein profile comparison with assisting information.
Nucleic acids research 2009;37(11):3522-30.
2009: Ruslan I Sadreyev; ShuoYong Shi; David Baker; Nick V Grishin
Structure similarity measure with penalty for close non-equivalent residues.
Bioinformatics (Oxford, England) 2009;25(10):1259-63.
2009: Wu Yin; Stefano Romeo; Shurong Chang; Nick V Grishin; Helen H Hobbs; Jonathan C Cohen
Genetic variation in ANGPTL4 provides insights into protein processing and function.
The Journal of biological chemistry 2009;284(19):13213-22.
2009: Jimin Pei; Nick V Grishin
Prediction of a caspase-like fold in Tannerella forsythia virulence factor PrtH.
Cell cycle (Georgetown, Tex.) 2009;8(9):1453-5.
2009: Jimin Pei; Patrick J Lupardus; K Christopher Garcia; Nick V Grishin
CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins.
Protein science : a publication of the Protein Society 2009;18(4):856-62.
2009: Junmei Zhang; Robert W. Sprung; Jimin Pei; Xiaohong Tan; Sungchan Kim; Heng Zhu; Chuan-Fa Liu; Nick V Grishin; Yingming Zhao
Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli.
Molecular & cellular proteomics : MCP 2009;8(2):215-25.
2009: Melanie L Yarbrough; Yan Li; Lisa N Kinch; Nick V Grishin; Haydn L Ball; Kim Orth
AMPylation of Rho GTPases by Vibrio VopS disrupts effector binding and downstream signaling.
Science (New York, N.Y.) 2009;323(5911):269-72.
2009: Ruslan I Sadreyev; Yong Wang; Nick V Grishin
Considering scores between unrelated proteins in the search database improves profile comparison.
BMC bioinformatics 2009;10():399.
2009: Srivatsan Raman; Robert Vernon; James Thompson; Michael Tyka; Ruslan Sadreyev; Jimin Pei; David Kim; Elizabeth Kellogg; Frank DiMaio; oliver lange; Lisa Kinch; Will Sheffler; Bong-Hyun Kim; Rhiju Das; Nick V Grishin; David Baker
Structure prediction for CASP8 with all-atom refinement using Rosetta.
Proteins 2009;77 Suppl 9():89-99.
2009: Lisa N Kinch; Melanie L Yarbrough; Kim Orth; Nick V Grishin
Fido, a novel AMPylation domain common to fic, doc, and AvrB.
PloS one 2009;4(6):e5818.
2009: Indraneel Majumdar; Lisa N Kinch; Nick V Grishin
A database of domain definitions for proteins with complex interdomain geometry.
PloS one 2009;4(4):e5084.
2009: Lisa N Kinch; Nick V Grishin
The human Ago2 MC region does not contain an eIF4E-like mRNA cap binding motif.
Biology direct 2009;4():2.
2009: Yongyu Wang; Phillip J Kuan; Chao Xing; Jennifer T Cronkhite; Fernando Torres; Randall L Rosenblatt; J Michael DiMaio; Lisa N Kinch; Nick V Grishin; Christine Kim Garcia
Genetic defects in surfactant protein A2 are associated with pulmonary fibrosis and lung cancer.
American journal of human genetics 2009;84(1):52-9.
2008: Jimin Pei; Ming Tang; Nick V Grishin
PROMALS3D web server for accurate multiple protein sequence and structure alignments.
Nucleic acids research 2008;36(Web Server issue):W30-4.
2008: Sarah A Teichmann; Nick V Grishin
Sequences and topology: from genome structure to protein structure.
Current opinion in structural biology 2008;18(3):340-1.
2008: Marc F Bolliger; Jimin Pei; Stephan Maxeiner; Antony A Boucard; Nick V Grishin; Thomas C Südhof
Unusually rapid evolution of Neuroligin-4 in mice.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(17):6421-6.
2008: Yanjie Liu; Rita Tewari; Jue Ning; Andrew M Blagborough; Sara Garbom; Jimin Pei; Nick V Grishin; Robert E Steele; Robert E Sinden; William J Snell; Oliver Billker
The conserved plant sterility gene HAP2 functions after attachment of fusogenic membranes in Chlamydomonas and Plasmodium gametes.
Genes & development 2008;22(8):1051-68.
2008: Hua Cheng; Bong-Hyun Kim; Nick V Grishin
Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets.
Journal of molecular biology 2008;377(4):1265-78.
2008: James O Wrabl; Nick V Grishin
Statistics of random protein superpositions: p-values for pairwise structure alignment.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(3):317-55.
2008: Jimin Pei; Bong-Hyun Kim; Nick V Grishin
PROMALS3D: a tool for multiple protein sequence and structure alignments.
Nucleic acids research 2008;36(7):2295-300.
2008: Ruslan I Sadreyev; Nick V Grishin
Accurate statistical model of comparison between multiple sequence alignments.
Nucleic acids research 2008;36(7):2240-8.
2008: Hua Cheng; Bong-Hyun Kim; Nick V Grishin
MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs.
Proteins 2008;70(4):1162-6.
2008: Jing Yang; Michael S Brown; Guosheng Liang; Nick V Grishin; Joseph L Goldstein
Identification of the acyltransferase that octanoylates ghrelin, an appetite-stimulating peptide hormone.
Cell 2008;132(3):387-96.
2008: Erik D Nelson; Nick V Grishin
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 2008;105(5):1489-93.
2008: Nian Huang; Leonardo Sorci; Xuejun Zhang; Chad A Brautigam; Xiaoqing Li; Nadia Raffaelli; Giulio Magni; Nick V Grishin; Andrei Osterman; Hong Zhang
Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.
Structure (London, England : 1993) 2008;16(2):196-209.
2008: Rodney E Infante; Arun Radhakrishnan; Lina Abi-Mosleh; Lisa N Kinch; Michael L Wang; Nick V Grishin; Joseph L Goldstein; Michael S Brown
Purified NPC1 protein: II. Localization of sterol binding to a 240-amino acid soluble luminal loop.
The Journal of biological chemistry 2008;283(2):1064-75.
2008: Hua Cheng; Bong-Hyun Kim; Nick V Grishin
MALISAM: a database of structurally analogous motifs in proteins.
Nucleic acids research 2008;36(Database issue):D211-7.
2007: Kimberly M Szymanski; Derk D Binns; René Bartz; Nick V Grishin; Wei-Ping Li; Anil K Agarwal; Abhimanyu Garg; Richard G W Anderson; Joel M Goodman
The lipodystrophy protein seipin is found at endoplasmic reticulum lipid droplet junctions and is important for droplet morphology.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(52):20890-5.
2007: Nathan B Holladay; Lisa N Kinch; Nick V Grishin
Optimization of linear disorder predictors yields tight association between crystallographic disorder and hydrophobicity.
Protein science : a publication of the Protein Society 2007;16(10):2140-52.
2007: Ruslan I Sadreyev; Ming Tang; Bong-Hyun Kim; Nick V Grishin
COMPASS server for remote homology inference.
Nucleic acids research 2007;35(Web Server issue):W653-8.
2007: Jimin Pei; Bong-Hyun Kim; Ming Tang; Nick V Grishin
PROMALS web server for accurate multiple protein sequence alignments.
Nucleic acids research 2007;35(Web Server issue):W649-52.
2007: Alexander Dikiy; Sergey V Novoselov; Dmitri E Fomenko; Aniruddha Sengupta; Bradley A Carlson; Ronald L Cerny; Krzysztof Ginalski; Nick V Grishin; Dolph L Hatfield; Vadim N Gladyshev
SelT, SelW, SelH, and Rdx12: genomics and molecular insights into the functions of selenoproteins of a novel thioredoxin-like family.
Biochemistry 2007;46(23):6871-82.
2007: Shuoyong Shi; Yi Zhong; Indraneel Majumdar; S Sri Krishna; Nick V Grishin
Searching for three-dimensional secondary structural patterns in proteins with ProSMoS.
Bioinformatics (Oxford, England) 2007;23(11):1331-8.
2007: Georgiy A Belogurov; Marina N Vassylyeva; Vladimir Svetlov; Sergiy Klyuyev; Nick V Grishin; Dmitry G Vassylyev; Irina Artsimovitch
Structural basis for converting a general transcription factor into an operon-specific virulence regulator.
Molecular cell 2007;26(1):117-29.
2007: Jimin Pei; Nick V Grishin
PROMALS: towards accurate multiple sequence alignments of distantly related proteins.
Bioinformatics (Oxford, England) 2007;23(7):802-8.
2007: Yuan Qi; Ruslan I Sadreyev; Yong Wang; Bong-Hyun Kim; Nick V Grishin
A comprehensive system for evaluation of remote sequence similarity detection.
BMC bioinformatics 2007;8():314.
2007: Lukasz Knizewski; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.
BMC structural biology 2007;7():40.
2006: Kamil Steczkiewicz; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Eukaryotic domain of unknown function DUF738 belongs to Gcn5-related N-acetyltransferase superfamily.
Cell cycle (Georgetown, Tex.) 2006;5(24):2927-30.
2006: Lisa N Kinch; Nick V Grishin
Longin-like folds identified in CHiPS and DUF254 proteins: vesicle trafficking complexes conserved in eukaryotic evolution.
Protein science : a publication of the Protein Society 2006;15(11):2669-74.
2006: Kira S Makarova; Nick V Grishin; Eugene V Koonin
The HicAB cassette, a putative novel, RNA-targeting toxin-antitoxin system in archaea and bacteria.
Bioinformatics (Oxford, England) 2006;22(21):2581-4.
2006: Sung Chan Kim; Robert W. Sprung; Yue Chen; Yingda Xu; Haydn Ball; Jimin Pei; Tzuling Cheng; Yoonjung Kho; Hao Xiao; Lin Xiao; Nick V Grishin; Michael White; Xiang-Jiao Yang; Yingming Zhao
Substrate and functional diversity of lysine acetylation revealed by a proteomics survey.
Molecular cell 2006;23(4):607-18.
2006: Sara Cheek; S Sri Krishna; Nick V Grishin
Structural classification of small, disulfide-rich protein domains.
Journal of molecular biology 2006;359(1):215-37.
2006: Erik D Nelson; Nick V Grishin
Alternate pathways for folding in the flavodoxin fold family revealed by a nucleation-growth model.
Journal of molecular biology 2006;358(3):646-53.
2006: Lukasz Knizewski; Lisa N Kinch; Nick V Grishin; Leszek Rychlewski; Krzysztof Ginalski
Human herpesvirus 1 UL24 gene encodes a potential PD-(D/E)XK endonuclease.
Journal of virology 2006;80(5):2575-7.
2006: Jimin Pei; Wei Cai; Lisa N Kinch; Nick V Grishin
Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.
Bioinformatics (Oxford, England) 2006;22(2):164-71.
2006: Kumar Singh Saikatendu; Xuejun Zhang; Lisa N Kinch; Matthew Leybourne; Nick V Grishin; Hong Zhang
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 2006;6():27.
2006: Jimin Pei; Nick V Grishin
MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information.
Nucleic acids research 2006;34(16):4364-74.
2006: S Sri Krishna; Ruslan I Sadreyev; Nick V Grishin
A tale of two ferredoxins: sequence similarity and structural differences.
BMC structural biology 2006;6():8.
2006: Ruslan I Sadreyev; Nick V Grishin
Exploring dynamics of protein structure determination and homology-based prediction to estimate the number of superfamilies and folds.
BMC structural biology 2006;6():6.
2006: Kira S Makarova; Nick V Grishin; Svetlana A Shabalina; Yuri I Wolf; Eugene V Koonin
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 2006;1():7.
2006: Erik D Nelson; Nick V Grishin
Scaling approach to the folding kinetics of large proteins.
Physical review. E, Statistical, nonlinear, and soft matter physics 2006;73(1 Pt 1):011904.
2006: Lisa N Kinch; Krzysztof Ginalski; Nick V Grishin
Site-2 protease regulated intramembrane proteolysis: sequence homologs suggest an ancient signaling cascade.
Protein science : a publication of the Protein Society 2006;15(1):84-93.
2005: James O Wrabl; Nick V Grishin
Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization.
Proteins 2005;61(3):523-34.
2005: Jayeeta Basu; Nan Shen; Irina Dulubova; Jun Lu; Rong Guan; Oleg Guryev; Nick V Grishin; christian rosenmund; Josep Rizo
A minimal domain responsible for Munc13 activity.
Nature structural & molecular biology 2005;12(11):1017-8.
2005: Jimin Pei; Nick V Grishin
COG3926 and COG5526: a tale of two new lysozyme-like protein families.
Protein science : a publication of the Protein Society 2005;14(10):2574-81.
2005: Bong-Hyun Kim; Ruslan I Sadreyev; Nick V Grishin
COG4849 is a novel family of nucleotidyltransferases.
Journal of molecular recognition : JMR 2005;18(5):422-5.
2005: Hua Cheng; Nick V Grishin
DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain.
Protein science : a publication of the Protein Society 2005;14(7):1902-10.
2005: Jimin Pei; Nick V Grishin
The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases.
Protein science : a publication of the Protein Society 2005;14(5):1370-4.
2005: S Sri Krishna; Nick V Grishin
Structural drift: a possible path to protein fold change.
Bioinformatics (Oxford, England) 2005;21(8):1308-10.
2005: Mingzhu Zheng; Krzysztof Ginalski; Leszek Rychlewski; Nick V Grishin
Protein domain of unknown function DUF1023 is an alpha/beta hydrolase.
Proteins 2005;59(1):1-6.
2005: Demet Araç; Irina Dulubova; Jimin Pei; Iryna Huryeva; Nick V Grishin; Josep Rizo
Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5.
Journal of molecular biology 2005;346(2):589-601.
2005: Lisa N Kinch; Sara Cheek; Nick V Grishin
EDD, a novel phosphotransferase domain common to mannose transporter EIIA, dihydroxyacetone kinase, and DegV.
Protein science : a publication of the Protein Society 2005;14(2):360-7.
2005: Yuan Qi; Nick V Grishin
Structural classification of thioredoxin-like fold proteins.
Proteins 2005;58(2):376-88.
2005: Indraneel Majumdar; S Sri Krishna; Nick V Grishin
PALSSE: a program to delineate linear secondary structural elements from protein structures.
BMC bioinformatics 2005;6():202.
2005: Lisa N Kinch; Krzysztof Ginalski; Leszek Rychlewski; Nick V Grishin
Identification of novel restriction endonuclease-like fold families among hypothetical proteins.
Nucleic acids research 2005;33(11):3598-605.
2005: Krzysztof Ginalski; Nick V Grishin; Adam Godzik; Leszek Rychlewski
Practical lessons from protein structure prediction.
Nucleic acids research 2005;33(6):1874-91.
2005: Sara Cheek; Krzysztof Ginalski; Hong Zhang; Nick V Grishin
A comprehensive update of the sequence and structure classification of kinases.
BMC structural biology 2005;5():6.
2004: Sara Cheek; Yuan Qi; S Sri Krishna; Lisa N Kinch; Nick V Grishin
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
BMC bioinformatics 2004;5():197.
2004: Yuan Qi; Nick V Grishin
PCOAT: positional correlation analysis using multiple methods.
Bioinformatics (Oxford, England) 2004;20(18):3697-9.
2004: Erik D Nelson; Nick V Grishin
Efficient expansion, folding, and unfolding of proteins.
Physical review. E, Statistical, nonlinear, and soft matter physics 2004;70(5 Pt 1):051906.
2004: Tim A Rand; Krzysztof Ginalski; Nick V Grishin; Xiaodong Wang
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 2004;101(40):14385-9.
2004: Krzysztof Ginalski; Hong Zhang; Nick V Grishin
Raptor protein contains a caspase-like domain.
Trends in biochemical sciences 2004;29(10):522-4.
2004: Wei Cai; Jimin Pei; Nick V Grishin
Reconstruction of ancestral protein sequences and its applications.
BMC evolutionary biology 2004;4():33.
2004: Jimin Pei; Nick V Grishin
Combining evolutionary and structural information for local protein structure prediction.
Proteins 2004;56(4):782-94.
2004: Rahul Shah; Catherine S Coleman; Kiran Mir; Jeffrey Baldwin; James L Van Etten; Nick V Grishin; Anthony E Pegg; Bruce Stanley; Margaret A Phillips
Paramecium bursaria chlorella virus-1 encodes an unusual arginine decarboxylase that is a close homolog of eukaryotic ornithine decarboxylases.
The Journal of biological chemistry 2004;279(34):35760-7.
2004: Ruslan I Sadreyev; Nick V Grishin
Estimates of statistical significance for comparison of individual positions in multiple sequence alignments.
BMC bioinformatics 2004;5():106.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases.
Trends in biochemical sciences 2004;29(8):392-5.
2004: Hua Cheng; Nan Shen; Jimin Pei; Nick V Grishin
Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease.
Protein science : a publication of the Protein Society 2004;13(8):2260-9.
2004: S Sri Krishna; Nick V Grishin
The finger domain of the human deubiquitinating enzyme HAUSP is a zinc ribbon.
Cell cycle (Georgetown, Tex.) 2004;3(8):1046-9.
2004: S Sri Krishna; Nick V Grishin
Structurally analogous proteins do exist!
Structure (London, England : 1993) 2004;12(7):1125-7.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
DCC proteins: a novel family of thiol-disulfide oxidoreductases.
Trends in biochemical sciences 2004;29(7):339-42.
2004: Krzysztof Ginalski; Marcin von Grotthuss; Nick V Grishin; Leszek Rychlewski
Detecting distant homology with Meta-BASIC.
Nucleic acids research 2004;32(Web Server issue):W576-81.
2004: Krzysztof Ginalski; Lisa N Kinch; Leszek Rychlewski; Nick V Grishin
BOF: a novel family of bacterial OB-fold proteins.
FEBS letters 2004;567(2-3):297-301.
2004: Ruslan I Sadreyev; Nick V Grishin
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.
Bioinformatics (Oxford, England) 2004;20(6):818-28.
2004: Krzysztof Ginalski; Leszek Rychlewski; David Baker; Nick V Grishin
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 2004;101(8):2305-10.
2004: Shide Liang; Nick V Grishin
Effective scoring function for protein sequence design.
Proteins 2004;54(2):271-81.
2004: James O Wrabl; Nick V Grishin
Gaps in structurally similar proteins: towards improvement of multiple sequence alignment.
Proteins 2004;54(1):71-87.
2003: Ruslan I Sadreyev; David Baker; Nick V Grishin
Profile-profile comparisons by COMPASS predict intricate homologies between protein families.
Protein science : a publication of the Protein Society 2003;12(10):2262-72.
2003: Jimin Pei; Nikolay V Dokholyan; Eugene I Shakhnovich; Nick V Grishin
Using protein design for homology detection and active site searches.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(20):11361-6.
2003: Lisa N Kinch; David Baker; Nick V Grishin
Deciphering a novel thioredoxin-like fold family.
Proteins 2003;52(3):323-31.
2003: David Mittelman; Ruslan I Sadreyev; Nick V Grishin
Probabilistic scoring measures for profile-profile comparison yield more accurate short seed alignments.
Bioinformatics (Oxford, England) 2003;19(12):1531-9.
2003: Jimin Pei; Nick V Grishin
Peptidase family U34 belongs to the superfamily of N-terminal nucleophile hydrolases.
Protein science : a publication of the Protein Society 2003;12(5):1131-5.
2003: Xuejun Zhang; Oleg V Kurnasov; Subburamu Karthikeyan; Nick V Grishin; Andrei Osterman; Hong Zhang
Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis.
The Journal of biological chemistry 2003;278(15):13503-11.
2003: Subburamu Karthikeyan; Qingxian Zhou; Faika Mseeh; Nick V Grishin; Andrei Osterman; Hong Zhang
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch.
Structure (London, England : 1993) 2003;11(3):265-73.
2003: Jimin Pei; Ruslan I Sadreyev; Nick V Grishin
PCMA: fast and accurate multiple sequence alignment based on profile consistency.
Bioinformatics (Oxford, England) 2003;19(3):427-8.
2003: Ruslan I Sadreyev; Nick V Grishin
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance.
Journal of molecular biology 2003;326(1):317-36.
2003: S Sri Krishna; Indraneel Majumdar; Nick V Grishin
Structural classification of zinc fingers: survey and summary.
Nucleic acids research 2003;31(2):532-50.
2003: Lisa N Kinch; James O Wrabl; S Sri Krishna; Indraneel Majumdar; Ruslan I Sadreyev; Yuan Qi; Jimin Pei; Hua Cheng; Nick V Grishin
CASP5 assessment of fold recognition target predictions.
Proteins 2003;53 Suppl 6():395-409.
2003: Lisa N Kinch; Yuan Qi; Tim Hubbard; Nick V Grishin
CASP5 target classification.
Proteins 2003;53 Suppl 6():340-51.
2002: Vyacheslav N Grishin; Nick V Grishin
Euclidian space and grouping of biological objects.
Bioinformatics (Oxford, England) 2002;18(11):1523-34.
2002: S Kumar Singh; Oleg V Kurnasov; Baozhi Chen; Howard Robinson; Nick V Grishin; Andrei Osterman; Hong Zhang
Crystal structure of Haemophilus influenzae NadR protein. A bifunctional enzyme endowed with NMN adenyltransferase and ribosylnicotinimide kinase activities.
The Journal of biological chemistry 2002;277(36):33291-9.
2002: Yuri I Wolf; Igor Rogozin; Nick V Grishin; Eugene V Koonin
Genome trees and the tree of life.
Trends in genetics : TIG 2002;18(9):472-9.
2002: Sara Cheek; Hong Zhang; Nick V Grishin
Sequence and structure classification of kinases.
Journal of molecular biology 2002;320(4):855-81.
2002: Lisa N Kinch; Nick V Grishin
Expanding the nitrogen regulatory protein superfamily: Homology detection at below random sequence identity.
Proteins 2002;48(1):75-84.
2002: Lisa N Kinch; Nick V Grishin
Evolution of protein structures and functions.
Current opinion in structural biology 2002;12(3):400-8.
2002: Yuan Qi; Jimin Pei; Nick V Grishin
C-terminal domain of gyrase A is predicted to have a beta-propeller structure.
Proteins 2002;47(3):258-64.
2002: Tianjun Zhou; Oleg V Kurnasov; Diana R Tomchick; Derk D Binns; Nick V Grishin; Victor E Marquez; Andrei Osterman; Hong Zhang
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
The Journal of biological chemistry 2002;277(15):13148-54.
2002: Lisa N Kinch; Milton H Saier; Nick V Grishin
Sec61beta--a component of the archaeal protein secretory system.
Trends in biochemical sciences 2002;27(4):170-1.
2002: Jimin Pei; Nick V Grishin
Breaking the singleton of germination protease.
Protein science : a publication of the Protein Society 2002;11(3):691-7.
2002: David A Sierra; Debra J Gilbert; Deborah Householder; Nick V Grishin; Kan Yu; Pallavi Ukidwe; Sheryll A Barker; Wei He; Theodore G Wensel; Glen Otero; Greg Brown; Neal G Copeland; Nancy A Jenkins; Thomas Wilkie
Evolution of the regulators of G-protein signaling multigene family in mouse and human.
Genomics 2002;79(2):177-85.
2002: Shide Liang; Nick V Grishin
Side-chain modeling with an optimized scoring function.
Protein science : a publication of the Protein Society 2002;11(2):322-31.
2002: Kira S Makarova; L Aravind; Nick V Grishin; Igor Rogozin; Eugene V Koonin
A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.
Nucleic acids research 2002;30(2):482-96.
2002: Hong Zhang; Tianjun Zhou; Oleg V Kurnasov; Sara Cheek; Nick V Grishin; Andrei Osterman
Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD.
Structure (London, England : 1993) 2002;10(1):69-79.
2001: James O Wrabl; Nick V Grishin
Homology between O-linked GlcNAc transferases and proteins of the glycogen phosphorylase superfamily.
Journal of molecular biology 2001;314(3):365-74.
2001: Jared J Abbott; J Pei; J L Ford; Y Qi; V N Grishin; Lisa A Pitcher; Margaret A Phillips; Nick V Grishin
Structure prediction and active site analysis of the metal binding determinants in gamma -glutamylcysteine synthetase.
The Journal of biological chemistry 2001;276(45):42099-107.
2001: Yuri I Wolf; Igor Rogozin; Nick V Grishin; Roman L Tatusov; Eugene V Koonin
Genome trees constructed using five different approaches suggest new major bacterial clades.
BMC evolutionary biology 2001;1():8.
2001: Jimin Pei; Nick V Grishin
AL2CO: calculation of positional conservation in a protein sequence alignment.
Bioinformatics (Oxford, England) 2001;17(8):700-12.
2001: J Pei; Nick V Grishin
Type II CAAX prenyl endopeptidases belong to a novel superfamily of putative membrane-bound metalloproteases.
Trends in biochemical sciences 2001;26(5):275-7.
2001: Nick V Grishin
Treble clef finger--a functionally diverse zinc-binding structural motif.
Nucleic acids research 2001;29(8):1703-14.
2001: Nick V Grishin
Mh1 domain of Smad is a degraded homing endonuclease.
Journal of molecular biology 2001;307(1):31-7.
2001: Nick V Grishin
KH domain: one motif, two folds.
Nucleic acids research 2001;29(3):638-43.
2001: Monica M Horvath; Nick V Grishin
The C-terminal domain of HPII catalase is a member of the type I glutamine amidotransferase superfamily.
Proteins 2001;42(2):230-6.
2001: Jimin Pei; Nick V Grishin
GGDEF domain is homologous to adenylyl cyclase.
Proteins 2001;42(2):210-6.
2000: Tianjun Zhou; Matthew D Daugherty; Nick V Grishin; Andrei Osterman; Hong Zhang
Structure and mechanism of homoserine kinase: prototype for the GHMP kinase superfamily.
Structure (London, England : 1993) 2000;8(12):1247-57.
2000: Michael Galperin; Nick V Grishin
The synthetase domains of cobalamin biosynthesis amidotransferases cobB and cobQ belong to a new family of ATP-dependent amidoligases, related to dethiobiotin synthetase.
Proteins 2000;41(2):238-47.
2000: X Shao; Nick V Grishin
Common fold in helix-hairpin-helix proteins.
Nucleic acids research 2000;28(14):2643-50.
2000: Nick V Grishin; Yuri I Wolf; Eugene V Koonin
From complete genomes to measures of substitution rate variability within and between proteins.
Genome research 2000;10(7):991-1000.
2000: Nick V Grishin
C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily.
Journal of molecular biology 2000;299(5):1165-77.
2000: Yuri I Wolf; Nick V Grishin; Eugene V Koonin
Estimating the number of protein folds and families from complete genome data.
Journal of molecular biology 2000;299(4):897-905.
2000: Nick V Grishin
Two tricks in one bundle: helix-turn-helix gains enzymatic activity.
Nucleic acids research 2000;28(11):2229-33.
2000: Jin Ye; UP Davé; Nick V Grishin; Joseph L Goldstein; Michael S Brown
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 2000;97(10):5123-8.
2000: Detlef D Leipe; L Aravind; Nick V Grishin; Eugene V Koonin
The bacterial replicative helicase DnaB evolved from a RecA duplication.
Genome research 2000;10(1):5-16.
1999: Nick V Grishin; Andrei Osterman; Harold B Brooks; Margaret A Phillips; Elizabeth J Goldsmith
X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine.
Biochemistry 1999;38(46):15174-84.
1999: Kira S Makarova; Nick V Grishin
Thermolysin and mitochondrial processing peptidase: how far structure-functional convergence goes.
Protein science : a publication of the Protein Society 1999;8(11):2537-40.
1999: Kira S Makarova; Nick V Grishin
The Zn-peptidase superfamily: functional convergence after evolutionary divergence.
Journal of molecular biology 1999;292(1):11-7.
1999: Nick V Grishin
Phosphatidylinositol phosphate kinase: a link between protein kinase and glutathione synthase folds.
Journal of molecular biology 1999;291(2):239-47.
1999: Yuri I Wolf; L Aravind; Nick V Grishin; Eugene V Koonin
Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events.
Genome research 1999;9(8):689-710.
1999: Kira S Makarova; L Aravind; Michael Galperin; Nick V Grishin; Roman L Tatusov; Yuri I Wolf; Eugene V Koonin
Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell.
Genome research 1999;9(7):608-28.
1999: Nick V Grishin
A novel approach to phylogeny reconstruction from protein sequences.
Journal of molecular evolution 1999;48(3):264-73.
1998: Nick V Grishin
The R3H motif: a domain that binds single-stranded nucleic acids.
Trends in biochemical sciences 1998;23(9):329-30.
1997: Nick V Grishin
Estimation of evolutionary distances from protein spatial structures.
Journal of molecular evolution 1997;45(4):359-69.
1996: Nick V Grishin; Andrei Osterman; Elizabeth J Goldsmith; Margaret A Phillips
Crystallization and preliminary X-ray studies of ornithine decarboxylase from Trypanosoma brucei.
Proteins 1996;24(2):272-3.
1995: Nick V Grishin; Margaret A Phillips; Elizabeth J Goldsmith
Modeling of the spatial structure of eukaryotic ornithine decarboxylases.
Protein science : a publication of the Protein Society 1995;4(7):1291-304.
1995: Andrei Osterman; L N Kinch; Nick V Grishin; Margaret A Phillips
Acidic residues important for substrate binding and cofactor reactivity in eukaryotic ornithine decarboxylase identified by alanine scanning mutagenesis.
The Journal of biological chemistry 1995;270(20):11797-802.
1994: Nick V Grishin; Margaret A Phillips
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 1994;3(12):2455-8.
1994: Andrei Osterman; Nick V Grishin; L N Kinch; Margaret A Phillips
Formation of functional cross-species heterodimers of ornithine decarboxylase.
Biochemistry 1994;33(46):13662-7.
1992: A L Osterman; Nick V Grishin; S V Smulevitch; M V Matz; O P Zagnitko; Lyudmila P Revina; VM Stepanov
Primary structure of carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family.
Journal of protein chemistry 1992;11(5):561-70.
1992: Alexey Teplyakov; K Polyakov; Galina Obmolova; B Strokopytov; I Kuranova; A Osterman; Nick V Grishin; S Smulevitch; O Zagnitko; O Galperina
Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris.
European journal of biochemistry / FEBS 1992;208(2):281-8.
1991: S V Smulevitch; A L Osterman; O V Galperina; M V Matz; O P Zagnitko; R M Kadyrov; I A Tsaplina; Nick V Grishin; Galina G Chestukhina; VM Stepanov
Molecular cloning and primary structure of Thermoactinomyces vulgaris carboxypeptidase T. A metalloenzyme endowed with dual substrate specificity.
FEBS letters 1991;291(1):75-8.