Publications with the Minor Lab Go to top

1. Gucwa M, Bijak V, Zheng H, Murzyn K, Minor W (2024)
   CheckMyMetal (CMM): validating metal-binding sites in X-ray and cryo-EM data.
   IUCrJ 11(Pt 5): 871-877. [DOI:10.1107/S2052252524007073] [Pub Med ID: 39141478] [Pub Med Central ID: PMC11364027]
   Google Scholar Times Cited: 0
2. Zheng H, Zhang H, Zhong J, Gucwa M, Zhang Y, Ma H, Deng L, Mao L, Minor W, Wang N (2024)
   PinMyMetal: A hybrid learning system to accurately model metal binding sites in macromolecules.
   Res Sq [DOI:10.21203/rs.3.rs-3908734/v1] [Pub Med ID: 38463967] [Pub Med Central ID: PMC10925427]
   Google Scholar Times Cited: 1
3. Gucwa M, Lenkiewicz J, Zheng H, Cymborowski M, Cooper DR, Murzyn K, Minor W (2023)
   CMM-An enhanced platform for interactive validation of metal binding sites.
   Protein Sci 32(1): e4525. [DOI:10.1002/pro.4525] [Pub Med ID: 36464767] [Pub Med Central ID: PMC9794025]
   WoS Times Cited: 21 ; Google Scholar Times Cited: 36
4. Zhang H, Chen P, Ma H, Woińska M, Liu D, Cooper DR, Peng G, Peng Y, Deng L, Minor W, Zheng H (2021)
   virusMED: an atlas of hotspots of viral proteins.
   IUCrJ 8(Pt 6): 931-42. [DOI:10.1107/S2052252521009076] [Pub Med ID: 34614039] [Pub Med Central ID: PMC8479994]
   WoS Times Cited: 3 ; Google Scholar Times Cited: 8
5. Cooper DR, Grabowski M, Zimmerman MD, Porebski PJ, Shabalin IG, Woinska M, Domagalski MJ, Zheng H, Sroka P, Cymborowski M, Czub MP, Niedzialkowska E, Venkataramany BS, Osinski T, Fratczak Z, Bajor J, Gonera J, MacLean E, Wojciechowska K, Konina K, Wajerowicz W, Chruszcz M, Minor W (2020)
   State-of-the-Art Data Management: Improving the Reproducibility, Consistency, and Traceability of Structural Biology and in Vitro Biochemical Experiments.
   Methods Mol Biol 2199(): 209-236. [DOI:10.1007/978-1-0716-0892-0_13] [Pub Med ID: 33125653] [Pub Med Central ID: PMC8019398]
   WoS Times Cited: 4 ; Google Scholar Times Cited: 8
6. Majorek KA, Zimmerman MD, Shabalin I, Zheng H, Minor W, Grabowski M (2020)
   Assessment of Crystallographic Structure Quality and Protein–Ligand Complex Structure Validation
   in Structural Biology in Drug Discovery: Methods, Techniques, and Practices (): 253-275. [DOI:10.1002/9781118681121.ch11]
   WoS Times Cited: 5 ; Google Scholar Times Cited: 4
7. Lipowska J, Miks CD, Kwon K, Shuvalova L, Zheng H, Lewiński K, Cooper DR, Shabalin IG, Minor W (2019)
   Pyrimidine biosynthesis in pathogens - Structures and analysis of dihydroorotases from Yersinia pestis and Vibrio cholerae.
   Int J Biol Macromol 136(): 1176-1187. [DOI:10.1016/j.ijbiomac.2019.05.149] [Pub Med ID: 31207330] [Pub Med Central ID: PMC6686667]
   WoS Times Cited: 19 ; Google Scholar Times Cited: 23
8. Grabowski M, Shabalin I, Domagalski MJ, Zheng H, Cooper D, Bourne PE, Minor W, Porebski PJ, Venkataramany BS (2019)
   Data Sharing in Structural Biology: Advances and Challenges
   in Data Sharing: Recent Progress and Remaining Challenges - Computer Science, Technology and Applications, Nova Science Publishers, New York (): 29-68.
   Google Scholar Times Cited: 28
9. Hou J, Zheng H, Tzou WS, Cooper DR, Chruszcz M, Chordia MD, Kwon K, Grabowski M, Minor W (2018)
   Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels.
   FEBS J 285(15): 2900-2921. [DOI:10.1111/febs.14588] [Pub Med ID: 29917313] [Pub Med Central ID: PMC6105497]
   WoS Times Cited: 3 ; Google Scholar Times Cited: 2
10. Handing KB, Niedzialkowska E, Shabalin IG, Kuhn ML, Zheng H, Minor W (2018)
    Characterizing metal-binding sites in proteins with X-ray crystallography.
    Nat Protoc 13(5): 1062-1090. [DOI:10.1038/nprot.2018.018] [Pub Med ID: 29674755] [Pub Med Central ID: PMC6235626]
    WoS Times Cited: 68 ; Google Scholar Times Cited: 110
    
11. Porebski PJ, Sroka P, Zheng H, Cooper DR, Minor W (2018)
    Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.
    Protein Sci 27(1): 86-94. [DOI:10.1002/pro.3272] [Pub Med ID: 28815771] [Pub Med Central ID: PMC5734276]
    WoS Times Cited: 26 ; Google Scholar Times Cited: 30
12. Zhang J, Zhu Y, Shi Y, Han Y, Liang C, Feng Z, Zheng H, Eng M, Wang J (2017)
    Fluoride-Induced Autophagy via the Regulation of Phosphorylation of Mammalian Targets of Rapamycin in Mice Leydig Cells.
    J. Agric. Food Chem. 65(40): 8966-8976. [DOI:10.1021/acs.jafc.7b03822] [Pub Med ID: 28927274]
    WoS Times Cited: 41 ; Google Scholar Times Cited: 51
13. Zheng H, Langner KM, Shields GP, Hou J, Kowiel M, Allen FH, Murshudov G, Minor W (2017)
    Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography.
    Acta Crystallogr D Struct Biol 73(Pt 4): 316-325. [DOI:10.1107/S2059798317000584] [Pub Med ID: 28375143] [Pub Med Central ID: PMC5503122]
    WoS Times Cited: 29 ; Google Scholar Times Cited: 36
14. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017)
    CheckMyMetal: a macromolecular metal-binding validation tool.
    Acta Crystallogr D Struct Biol 73(Pt 3): 223-233. [DOI:10.1107/S2059798317001061] [Pub Med ID: 28291757] [Pub Med Central ID: PMC5349434]
    WoS Times Cited: 227 ; Google Scholar Times Cited: 329
15. Zheng H, Porebski PJ, Grabowski M, Cooper DR, Minor W (2017)
    Databases, Repositories, and Other Data Resources in Structural Biology.
    Methods Mol Biol 1607(): 643-665. [DOI:10.1007/978-1-4939-7000-1_27] [Pub Med ID: 28573593] [Pub Med Central ID: PMC5587190]
    WoS Times Cited: 5 ; Google Scholar Times Cited: 12
16. Grabowski M, Langner KM, Cymborowski M, Porebski PJ, Sroka P, Zheng H, Cooper DR, Zimmerman MD, Elsliger MA, Burley SK, Minor W (2016)
    A public database of macromolecular diffraction experiments.
    Acta Crystallogr D Struct Biol 72(Pt 11): 1181-1193. [DOI:10.1107/S2059798316014716] [Pub Med ID: 27841751] [Pub Med Central ID: PMC5108346]
    WoS Times Cited: 95 ; Google Scholar Times Cited: 93
17. Zhang J, Zhang Y, Liang C, Wang N, Zheng H, Wang J (2016)
    Choline supplementation alleviates fluoride-induced testicular toxicity by restoring the NGF and MEK expression in mice.
    Toxicol Appl Pharmacol. 310(): 205-214. [DOI:10.1016/j.taap.2016.09.018] [Pub Med ID: 27664006]
    WoS Times Cited: 10 ; Google Scholar Times Cited: 93
18. Hou J, Zheng H, Zimmerman MD, Shumilin IA, Osinski T, Demas M, Minor W, Grimshaw S, Chruszcz M (2015)
    Dissecting the Structural Elements for the Activation of β-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
    J. Bacteriol. 198(3): 463-76. [DOI:10.1128/JB.00360-15] [Pub Med ID: 26553852] [Pub Med Central ID: PMC4719456]
    WoS Times Cited: 14 ; Google Scholar Times Cited: 21
19. Zheng H, Mandal A, Shumilin IA, Chordia MD, Panneerdoss S, Herr JC, Minor W (2015)
    Sperm Lysozyme-Like Protein 1 (SLLP1), an intra-acrosomal oolemmal-binding sperm protein, reveals filamentous organization in protein crystal form.
    Andrology 3(4): 756-71. [DOI:10.1111/andr.12057] [Pub Med ID: 26198801] [Pub Med Central ID: PMC5040164]
    WoS Times Cited: 8 ; Google Scholar Times Cited: 11
20. Zheng H, Shabalin IG, Handing KB, Minor W, Bujnicki JM (2015)
    Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection.
    Nucleic Acids Res 43(7): 3789-801. [DOI:10.1093/nar/gkv225] [Pub Med ID: 25800744] [Pub Med Central ID: PMC4402538]
    WoS Times Cited: 67 ; Google Scholar Times Cited: 96
21. Zheng H, Handing KB, Zimmerman MD, Shabalin IG, Minor W, Almo SC (2015)
    X-ray crystallography over the past decade for novel drug discovery - where are we heading next?
    Expert Opin Drug Discov 10(9): 975-89. [DOI:10.1517/17460441.2015.1061991] [Pub Med ID: 26177814] [Pub Med Central ID: PMC4655606]
    WoS Times Cited: 57 ; Google Scholar Times Cited: 116
22. Zheng H, Hou J, Zimmerman MD, Minor W, Wlodawer A (2014)
    The future of crystallography in drug discovery.
    Expert Opin Drug Discov 9(2): 125-37. [DOI:10.1517/17460441.2014.872623] [Pub Med ID: 24372145] [Pub Med Central ID: PMC4106240]
    WoS Times Cited: 64 ; Google Scholar Times Cited: 116
23. Zheng H, Chordia MD, Cooper DR, Chruszcz M, Minor W, Müller P, Sheldrick GM (2014)
    Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.
    Nat Protoc 9(1): 156-70. [DOI:10.1038/nprot.2013.172] [Pub Med ID: 24356774] [Pub Med Central ID: PMC4410975]
    WoS Times Cited: 229 ; Google Scholar Times Cited: 307
24. Domagalski MJ, Zheng H, Zimmerman MD, Minor W, Wlodawer A, Dauter Z (2014)
    The quality and validation of structures from structural genomics.
    Methods Mol Biol 1091(): 297-314. [DOI:10.1007/978-1-62703-691-7_21] [Pub Med ID: 24203341] [Pub Med Central ID: PMC4081469]
    WoS Times Cited: 22 ; Google Scholar Times Cited: 29
25. Luo HB, Knapik AA, Petkowski JJ, Demas M, Shumilin IA, Zheng H, Minor W, Chruszcz M (2013)
    Biophysical analysis of the putative acetyltransferase SACOL2570 from methicillin-resistant Staphylococcus aureus.
    J. Struct. Funct. Genomics 14(3): 97-108. [DOI:10.1007/s10969-013-9158-6] [Pub Med ID: 23963951] [Pub Med Central ID: PMC3923901]
    Google Scholar Times Cited: 6
26. Hou J, Wojciechowska K, Zheng H, Chruszcz M, Cooper DR, Cymborowski M, Luo H, Minor W, Savchenko A, Gordon E, Skarina T (2012)
    Structure of a short-chain dehydrogenase/reductase from Bacillus anthracis.
    Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 68(Pt 6): 632-7. [DOI:10.1107/S1744309112017939] [Pub Med ID: 22684058] [Pub Med Central ID: PMC3370898]
    WoS Times Cited: 5 ; Google Scholar Times Cited: 7
27. Zheng H, Tkaczuk KL, Dworzynski P, Chruszcz M, Porebski PJ, Wawrzak Z, Minor W, Savchenko A, Grimshaw S, Onopriyenko O, Filippova EV, Kudritska M, Anderson WF (2012)
    Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.
    J. Struct. Funct. Genomics 13(1): 15-26. [DOI:10.1007/s10969-012-9131-9] [Pub Med ID: 22403005] [Pub Med Central ID: PMC4485498]
    Google Scholar Times Cited: 8
28. Sledz P, Zheng H, Chruszcz M, Zimmerman MD, Chordia MD, Minor W, Murzyn K, Joachimiak A (2010)
    New surface contacts formed upon reductive lysine methylation: improving the probability of protein crystallization.
    Protein Sci 19(7): 1395-404. [DOI:10.1002/pro.420] [Pub Med ID: 20506323] [Pub Med Central ID: PMC2974831]
    WoS Times Cited: 27 ; Google Scholar Times Cited: 45
29. Zheng H, Zimmerman MD, Chruszcz M, Egorova O, Edwards AM, Minor W, Savchenko A, Skarina T, Luo HB (2010)
    Crystal structure and molecular modeling study of N-carbamoylsarcosine amidase Ta0454 from Thermoplasma acidophilum.
    J Struct Biol 169(3): 304-11. [DOI:10.1016/j.jsb.2009.11.008] [Pub Med ID: 19932181] [Pub Med Central ID: PMC2830209]
    WoS Times Cited: 12 ; Google Scholar Times Cited: 15
30. Savchenko A, Chruszcz M, Zimmerman MD, Wang S, Koclega KD, Zheng H, Cymborowski M, Minor W, Edwards A, Evdokimova E, Kudritska M (2008)
    Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.
    Cryst Growth Des 8(11): 4054-4061. [DOI:10.1021/cg800430f] [Pub Med ID: 19898606] [Pub Med Central ID: PMC2700756]
    WoS Times Cited: 2 ; Google Scholar Times Cited: 5
31. Zheng H, Chruszcz M, Lasota P, Minor W, Lebioda L (2008)
    Data mining of metal ion environments present in protein structures.
    J. Inorg. Biochem. 102(9): 1765-76. [DOI:10.1016/j.jinorgbio.2008.05.006] [Pub Med ID: 18614239] [Pub Med Central ID: PMC2872550]
    WoS Times Cited: 250 ; Google Scholar Times Cited: 327
32. Jha KN, Shumilin IA, Digilio LC, Chertihin O, Zheng H, Flickinger CJ, Minor W, Herr JC, Schmitz G, Visconti PE (2008)
    Biochemical and structural characterization of apolipoprotein A-I binding protein, a novel phosphoprotein with a potential role in sperm capacitation.
    Endocrinology 149(5): 2108-20. [DOI:10.1210/en.2007-0582] [Pub Med ID: 18202122] [Pub Med Central ID: PMC2329272]
    WoS Times Cited: 42 ; Google Scholar Times Cited: 57
33. Chruszcz M, Potrzebowski W, Zimmerman MD, Grabowski M, Zheng H, Lasota P, Minor W (2008)
    Analysis of solvent content and oligomeric states in protein crystals--does symmetry matter?
    Protein Sci 17(4): 623-32. [DOI:10.1110/ps.073360508] [Pub Med ID: 18359856] [Pub Med Central ID: PMC2271157]
    WoS Times Cited: 52 ; Google Scholar Times Cited: 77
34. Zheng H, Gawlicka-Chruszcz A, Cymborowski M, Minor W (2007)
    trans-1-Hydroxycyclopentan-2-aminium chloride.
    Acta Crystallogr Sect E Struct Rep Online 63(): O2697-O2698. [DOI:10.1107/S1600536807018958]
    WoS Times Cited: 0 ; Google Scholar Times Cited: 0
35. Savchenko A, Dong A, Edwards AM, Chang C, Chruszcz M, Cuff M, Cymborowski M, Di Leo R, Egorova O, Filippova E, Guthrie J, Ignatchenko A, Joachimiak A, Klostermann N, Korniyenko Y, Minor W, Que Q, Tan K, Yakunin A, Yee A, Yim V, Zhang R, Zheng H, Akutsu M, Arrowsmith C, Avvakumov GV, Bochkarev A, Dahlgren LG, Dhe-Paganon S, Dimov S, Dombrovski L, Finerty P, Flodin S, Flores A, Gräslund S, Hammerström M, Herman MD, Hong BS, Hui R, Johansson I, Liu Y, Nilsson M, Nedyalkova L, Nordlund P, Nyman T, Min J, Ouyang H, Park HW, Qi C, Kim Y, Skarina T, Gu J, Evdokimova E, Xu X, Rabeh W, Shen L, Shen Y, Sukumard D, Tempel W, Tong Y, Tresagues L, Vedadi M, Walker JR, Weigelt J, Welin M, Wu H, Xiao T, Zeng H, Zhu H (2007)
    In situ proteolysis for protein crystallization and structure determination.
    Nat. Methods 4(12): 1019-21. [DOI:10.1038/nmeth1118] [Pub Med ID: 17982461] [Pub Med Central ID: PMC3366506]
    WoS Times Cited: 163 ; Google Scholar Times Cited: 292
    
36. Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Cymborowski MT, Koclega KD, Minor W, Savchenko A, Edwards A, Onopriyenko O, Skarina T (2007)
    Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit.
    Protein Sci 16(7): 1360-7. [DOI:10.1110/ps.072793807] [Pub Med ID: 17586771] [Pub Med Central ID: PMC2206681]
    WoS Times Cited: 17 ; Google Scholar Times Cited: 24
37. Zheng H, Chruszcz M, Cymborowski M, Minor W, Savchenko A, Wang Y, Malhotra A, Zuo Y, Skarina T (2007)
    Crystal structure of RNase T, an exoribonuclease involved in tRNA maturation and end turnover.
    Structure 15(4): 417-28. [DOI:10.1016/j.str.2007.02.004] [Pub Med ID: 17437714] [Pub Med Central ID: PMC1907377]
    WoS Times Cited: 36 ; Google Scholar Times Cited: 66
38. Zimmerman MD, Chruszcz M, Cymborowski M, Zheng HP, Minor W (2006)
    Disodium 4-nitrophenylphosphate hexahydrate.
    Acta Crystallogr Sect E Struct Rep Online 62(): M884-M886. [DOI:10.1107/S160053680600941X]
    WoS Times Cited: 1 ; Google Scholar Times Cited: 1
39. Gawlicka-Chruszcz A, Zheng H, Hyacinth M, Cymborowski M, Sabat M, Minor W (2006)
    Crystal structure of 2,6-dichlorobenzaldehyde,C7H4Cl2O.
    Zeitschrift fur Kristallographie 221(): 545-546. [DOI:10.1524/ncrs.2006.0192]
    WoS Times Cited: 2 ; Google Scholar Times Cited: 2
40. Chruszcz M, Zheng HP, Cymborowski M, Gawlicka-Chruszcz A, Minor W (2005)
    3-(Morpholinium-1-yl)propanesulfonate.
    Acta Crystallogr Sect E Struct Rep Online 61(): O3190-O3191. [DOI:10.1107/S1600536805027728]
    WoS Times Cited: 5 ; Google Scholar Times Cited: 5

Structures with the Minor Lab Go to top