메뉴 건너뛰기




Volumn 27, Issue 1, 2018, Pages 293-315

MolProbity: More and better reference data for improved all-atom structure validation

(18)  Williams, Christopher J a   Headd, Jeffrey J a,e   Moriarty, Nigel W b   Prisant, Michael G a   Videau, Lizbeth L a   Deis, Lindsay N a,f   Verma, Vishal c   Keedy, Daniel A a,g   Hintze, Bradley J a   Chen, Vincent B a   Jain, Swati a,h   Lewis, Steven M a,i   Arendall, W Bryan a   Snoeyink, Jack c   Adams, Paul D b   Lovell, Simon C d   Richardson, Jane S a   Richardson, David C a  


Author keywords

all atom contact analysis; Asn Gln His flip; CaBLAM; CCTBX; cis non proline; electron cloud hydrogen position; Top8000

Indexed keywords

HYDROGEN; PEPTIDE; RNA; PROTEIN;

EID: 85035199313     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.3330     Document Type: Article
Times cited : (2669)

References (74)
  • 1
    • 0000243829 scopus 로고
    • ProCheck: a program to check the stereochemical quality of protein structures
    • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) ProCheck: a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291.
    • (1993) J Appl Cryst , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 3
    • 0030497978 scopus 로고    scopus 로고
    • Efficient rebuilding of protein structures
    • Kleywegt GJ, Jones TA (1996) Efficient rebuilding of protein structures. Acta Cryst 52:829–832.
    • (1996) Acta Cryst , vol.52 , pp. 829-832
    • Kleywegt, G.J.1    Jones, T.A.2
  • 4
    • 0031059039 scopus 로고    scopus 로고
    • Detecting and overcoming crystal twinning
    • Yeates TO (1997) Detecting and overcoming crystal twinning. Methods Enzymol 276:344–358.
    • (1997) Methods Enzymol , vol.276 , pp. 344-358
    • Yeates, T.O.1
  • 6
    • 0026597444 scopus 로고
    • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger AT (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472–475.
    • (1992) Nature , vol.355 , pp. 472-475
    • Brünger, A.T.1
  • 9
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson DC (1999) Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 285:1735–1747.
    • (1999) J Mol Biol , vol.285 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 12
    • 3242886389 scopus 로고    scopus 로고
    • MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes
    • Davis IW, Murray LW, Richardson JS, Richardson DC (2004) MolProbity: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615–W619.
    • (2004) Nucleic Acids Res , vol.32 , pp. W615-W619
    • Davis, I.W.1    Murray, L.W.2    Richardson, J.S.3    Richardson, D.C.4
  • 19
    • 84860275453 scopus 로고    scopus 로고
    • Implementing an X-ray validation pipeline for the Protein Data Bank
    • Gore S, Velankar S, Kleywegt GJ (2012) Implementing an X-ray validation pipeline for the Protein Data Bank. Acta Cryst 68:478–483.
    • (2012) Acta Cryst , vol.68 , pp. 478-483
    • Gore, S.1    Velankar, S.2    Kleywegt, G.J.3
  • 23
    • 85017733780 scopus 로고    scopus 로고
    • Avoiding excess cis peptides at low resolution or high B
    • Williams CJ, Richardson JS (2015) Avoiding excess cis peptides at low resolution or high B. Comp Cryst Newsletter 6:2–6.
    • (2015) Comp Cryst Newsletter , vol.6 , pp. 2-6
    • Williams, C.J.1    Richardson, J.S.2
  • 24
    • 0036111645 scopus 로고    scopus 로고
    • The computational toolbox: crystallographic algorithms in a reusable software framework
    • Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD (2002) The computational toolbox: crystallographic algorithms in a reusable software framework. J Appl Cryst 35:126–136.
    • (2002) J Appl Cryst , vol.35 , pp. 126-136
    • Grosse-Kunstleve, R.W.1    Sauter, N.K.2    Moriarty, N.W.3    Adams, P.D.4
  • 26
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: a quarter of a million crystal structures and rising
    • Allen FH (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst 58:380–388.
    • (2002) Acta Cryst , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 28
    • 0032475836 scopus 로고    scopus 로고
    • The low barrier hydrogen bond in enzymatic catalysis
    • Cleland WW, Frey PA, Gerlt JA (1998) The low barrier hydrogen bond in enzymatic catalysis. J Biol Chem 273:25529–-25532.
    • (1998) J Biol Chem , vol.273 , pp. 25529-25532
    • Cleland, W.W.1    Frey, P.A.2    Gerlt, J.A.3
  • 29
    • 84891894970 scopus 로고    scopus 로고
    • Proton transfer reactions and hydrogen-bond networks in protein environments
    • Ishikita H, Saito K (2013) Proton transfer reactions and hydrogen-bond networks in protein environments. J Royal Soc Interface 11:20130518.
    • (2013) J Royal Soc Interface , vol.11 , pp. 20130518
    • Ishikita, H.1    Saito, K.2
  • 31
    • 20544433165 scopus 로고
    • van der Waals volumes and radii
    • Bondi A (1964) van der Waals volumes and radii. J Phys Chem 68:441–451.
    • (1964) J Phys Chem , vol.68 , pp. 441-451
    • Bondi, A.1
  • 32
    • 0020799931 scopus 로고
    • The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity
    • Gavezzotti A (1983) The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity. J Am Chem Soc 105:5220–5225.
    • (1983) J Am Chem Soc , vol.105 , pp. 5220-5225
    • Gavezzotti, A.1
  • 33
    • 0002928871 scopus 로고
    • Atoms in molecules
    • Bader RFW (1985) Atoms in molecules. Acc Chem Res 18:9–15.
    • (1985) Acc Chem Res , vol.18 , pp. 9-15
    • Bader, R.F.W.1
  • 34
    • 37549039510 scopus 로고    scopus 로고
    • A short history of ShelX
    • Sheldrick GM (2008) A short history of ShelX. Acta Cryst 64:112–122.
    • (2008) Acta Cryst , vol.64 , pp. 112-122
    • Sheldrick, G.M.1
  • 36
    • 19944425329 scopus 로고
    • Coherent X-ray scattering for the hydrogen atom in the hydrogen molecule
    • Stewart RF, Davidson ER, Simpson WT (1965) Coherent X-ray scattering for the hydrogen atom in the hydrogen molecule. J Chem Phys 42:3175–3318.
    • (1965) J Chem Phys , vol.42 , pp. 3175-3318
    • Stewart, R.F.1    Davidson, E.R.2    Simpson, W.T.3
  • 37
    • 0002599287 scopus 로고
    • Calculation of the crystal structures of hydrocarbons by molecular packing analysis
    • Williams DE, Starr TL (1977) Calculation of the crystal structures of hydrocarbons by molecular packing analysis. Comput Chem 1:173–177.
    • (1977) Comput Chem , vol.1 , pp. 173-177
    • Williams, D.E.1    Starr, T.L.2
  • 38
    • 84912956010 scopus 로고
    • A systematic pairwise comparison of geometric parameters obtained by X-ray and neutron diffraction
    • Allen FH (1986) A systematic pairwise comparison of geometric parameters obtained by X-ray and neutron diffraction. Acta Cryst 42:515–522.
    • (1986) Acta Cryst , vol.42 , pp. 515-522
    • Allen, F.H.1
  • 40
    • 0343777190 scopus 로고
    • Equilibrium bond lengths in methane and deuteromethane as determined by electron diffraction and spectroscopic methods
    • Bartell LS, Kuchitsu K, deNeui RJ (1960) Equilibrium bond lengths in methane and deuteromethane as determined by electron diffraction and spectroscopic methods. J Chem Phys 33:1254–1255.
    • (1960) J Chem Phys , vol.33 , pp. 1254-1255
    • Bartell, L.S.1    Kuchitsu, K.2    deNeui, R.J.3
  • 41
    • 0000522778 scopus 로고
    • Representations of molecular force fields. V. On the equilibrium structure of methane
    • Bartell LS, Kuchitsu K (1978) Representations of molecular force fields. V. On the equilibrium structure of methane. J Chem Phys 68:1213–1215.
    • (1978) J Chem Phys , vol.68 , pp. 1213-1215
    • Bartell, L.S.1    Kuchitsu, K.2
  • 42
    • 0032477283 scopus 로고    scopus 로고
    • N, N-C', Cα-C', and Cα-Hα effective bond lengths in a protein by NMR in a dilute liquid crystalline phase
    • N, N-C', Cα-C', and Cα-Hα effective bond lengths in a protein by NMR in a dilute liquid crystalline phase. J Am Chem Soc 120:12334–12341.
    • (1998) J Am Chem Soc , vol.120 , pp. 12334-12341
    • Ottiger, M.1    Bax, A.2
  • 43
    • 0006228808 scopus 로고
    • Structure of N-acetyl-L-cysteine: X-ray (T=295 K) and neutron (T=16 K) diffraction studies
    • Takusagawa F, Koetzle TF, Kou WWH, Parthasarathy R (1981) Structure of N-acetyl-L-cysteine: X-ray (T=295 K) and neutron (T=16 K) diffraction studies. Acta Cryst 37:1591–1596.
    • (1981) Acta Cryst , vol.37 , pp. 1591-1596
    • Takusagawa, F.1    Koetzle, T.F.2    Kou, W.W.H.3    Parthasarathy, R.4
  • 44
    • 84981541214 scopus 로고    scopus 로고
    • Molprobity's ultimate rotamer-library distributions for model validation
    • Hintze BJ, Lewis SM, Richardson JS, Richardson DC (2016) Molprobity's ultimate rotamer-library distributions for model validation. Proteins 84:1177–1189.
    • (2016) Proteins , vol.84 , pp. 1177-1189
    • Hintze, B.J.1    Lewis, S.M.2    Richardson, J.S.3    Richardson, D.C.4
  • 47
    • 77954450582 scopus 로고    scopus 로고
    • Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins
    • Tronrud DE, Berkholz DS, Karplus PA (2010) Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins. Acta Cryst 66:834–842.
    • (2010) Acta Cryst , vol.66 , pp. 834-842
    • Tronrud, D.E.1    Berkholz, D.S.2    Karplus, P.A.3
  • 48
    • 84909977680 scopus 로고    scopus 로고
    • Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement
    • Moriarty NW, Tronrud DE, Adams PD, Karplus PA (2014) Conformation-dependent backbone geometry restraints set a new standard for protein crystallographic refinement. febs J 281:4061–4071.
    • (2014) febs J , vol.281 , pp. 4061-4071
    • Moriarty, N.W.1    Tronrud, D.E.2    Adams, P.D.3    Karplus, P.A.4
  • 49
    • 84924787043 scopus 로고    scopus 로고
    • The rate of cis–trans conformation errors is increasing in low-resolution crystal structures
    • Croll TI (2015) The rate of cis–trans conformation errors is increasing in low-resolution crystal structures. Acta Cryst 71:706–709.
    • (2015) Acta Cryst , vol.71 , pp. 706-709
    • Croll, T.I.1
  • 53
    • 85042312251 scopus 로고    scopus 로고
    • Using C-alpha geometry to describe protein secondary structure and motifs
    • Williams CJ (2016) Using C-alpha geometry to describe protein secondary structure and motifs. Doctoral Dissertation, Duke University 248. pages.
    • (2016) Doctoral Dissertation, Duke University , pp. 248
    • Williams, C.J.1
  • 54
    • 84935023279 scopus 로고    scopus 로고
    • Computational methods for RNA structure validation and improvement. Chapter 7
    • In, Woodson S, Allain F, Eds (, Elsevier, Oxford UK, Methods Enzymol series, vol
    • Jain S, Richardson DC, Richardson JS, Computational methods for RNA structure validation and improvement. Chapter 7 In: Woodson S, Allain F, Eds (2015) Structures of large RNA molecules and their complexes. Elsevier, Oxford UK, Methods Enzymol series, vol 558:181–212.
    • (2015) Structures of large RNA molecules and their complexes , vol.558 , pp. 181-212
    • Jain, S.1    Richardson, D.C.2    Richardson, J.S.3
  • 57
    • 70350509577 scopus 로고    scopus 로고
    • KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program
    • Chen VB, Davis IW, Richardson DC (2009) KiNG (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program. Protein Sci 18:2403–2409.
    • (2009) Protein Sci , vol.18 , pp. 2403-2409
    • Chen, V.B.1    Davis, I.W.2    Richardson, D.C.3
  • 61
    • 84979865146 scopus 로고    scopus 로고
    • NGL viewer: A web application for molecular visualization
    • Rose AS, Hildebrand PW (2015) NGL viewer: A web application for molecular visualization. Nucleic Acids Res 43:W576–W579.
    • (2015) Nucleic Acids Res , vol.43 , pp. W576-W579
    • Rose, A.S.1    Hildebrand, P.W.2
  • 64
    • 84871957573 scopus 로고    scopus 로고
    • Correcting pervasive errors in RNA crystallography through enumerative structure prediction
    • Chou FC, Sripakdeevong P, Dibrov SM, Hermann T, Das R (2013) Correcting pervasive errors in RNA crystallography through enumerative structure prediction. Nat Methods 10:74–76.
    • (2013) Nat Methods , vol.10 , pp. 74-76
    • Chou, F.C.1    Sripakdeevong, P.2    Dibrov, S.M.3    Hermann, T.4    Das, R.5
  • 68
    • 24644520019 scopus 로고    scopus 로고
    • Ultra-high resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 Å x-ray structure of mutant W4L/R5S
    • Bonisch H, Schmidt CL, Bianco P, Ladenstein R (2005) Ultra-high resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 Å x-ray structure of mutant W4L/R5S. Acta Cryst 61:990–1004.
    • (2005) Acta Cryst , vol.61 , pp. 990-1004
    • Bonisch, H.1    Schmidt, C.L.2    Bianco, P.3    Ladenstein, R.4
  • 69
    • 0032533444 scopus 로고    scopus 로고
    • Structural comparisons of calponin homology domains: implications for actin binding
    • Banuelos S, Saraste M, Carugo KD (1998) Structural comparisons of calponin homology domains: implications for actin binding. Structure 6:1419–1431.
    • (1998) Structure , vol.6 , pp. 1419-1431
    • Banuelos, S.1    Saraste, M.2    Carugo, K.D.3
  • 71
    • 2942615089 scopus 로고    scopus 로고
    • The roles of ribosomal proteins in the structure, assembly, and evolution of the large ribosomal subunit
    • Klein DJ, Moore PB, Steitz TA (2004) The roles of ribosomal proteins in the structure, assembly, and evolution of the large ribosomal subunit. J Mol Biol 340:141–177.
    • (2004) J Mol Biol , vol.340 , pp. 141-177
    • Klein, D.J.1    Moore, P.B.2    Steitz, T.A.3
  • 72
    • 34247576821 scopus 로고    scopus 로고
    • The structure of a plant photosystem I supercomplex at 3.4Å resolution
    • Amunts A, Drory O, Nelson N (2007) The structure of a plant photosystem I supercomplex at 3.4Å resolution. Nature 447:58–63.
    • (2007) Nature , vol.447 , pp. 58-63
    • Amunts, A.1    Drory, O.2    Nelson, N.3
  • 73
    • 17644434949 scopus 로고    scopus 로고
    • Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase
    • Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, Schomburg D (2003) Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. embo J 22:4922–4932.
    • (2003) embo J , vol.22 , pp. 4922-4932
    • Hövel, K.1    Shallom, D.2    Niefind, K.3    Belakhov, V.4    Shoham, G.5    Baasov, T.6    Shoham, Y.7    Schomburg, D.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.