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PDB ID Mentions in PubMed Central Article count: 10

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Solute transport in orthorhombic lysozyme crystals: a molecular simulation study.

(2007) Biotechnol Lett 29

PubMed: 17641823 | PubMedCentral: PMC2045120 | DOI: 10.1007/s10529-007-9466-7

The crystal structures of lysozyme, entry 1AKI (Artymiuk et al.

The surface representation in ( a ) was computed from the electron density calculations using the crystal structure data (1AKI) available in the Brookhaven protein data bank.

Publication Year: 2007


Automatic multiple-zone rigid-body refinement with a large convergence radius.

(2009) J Appl Crystallogr 42

PubMed: 19649324 | PubMedCentral: PMC2712840 | DOI: 10.1107/S0021889809023528

NA PDB ID NB group2-intron 3.5 1497 1kxk 1 synaptotagmin 3.2 2186 1dqv   1029B 3.0 9230 1n0e   1038B 3.0 11038 1lql 5 1071B 3.0 6558 1nf2 6 proteasome 2.9 24927 1q5q   sec17 2.... 2217 1qqe   cp-synthase 2.8 4331 1l1e   penicillopepsin 2.8 2366 3app   s-hydrolase 2.8 6666 1a7a   ut-synthase 2.8 7504 1e8c   gere 2.7 3060 1fse   groel 2.7 26957 1oel   aep-transaminase 2.6 16698 1m32 4 rab3a 2.6 2431 1zbd   a2u-globulin 2.5 5148 2a2u 4 flavin-reductase 2.5 3385 1bkj   p32 2.5 4265 1p32   psd-95 2.5 2180 1jxm   qaprtase 2.5 12570 1qpo 1 rnase-s 2.5 1488 1rge   1102B 2.5 2662 1l2f   rh-dehalogenase 2.45 2336 1bn7   armadillo 2.4 3458 3bct   cyanase 2.4 11970 1dw9   fusion-complex 2.4 7025 1sfc   human-otc 2.4 2528 1ep9   mev-kinase 2.4 2506 1kkh   nsf-d2 2.4 1943 1nsf   granulocyte 2.35 1908 2gmf   oat-gabaculine 2.3 9450 1gbn 2 vmp 2.3 7992 1l8w   gpatase 2.25 7786 1ecf   hn-rnp 2.2 1338 1ha1   antitrypsin 2.1 2985 1hp7   pdz 2.1 1372 1kwa   1167B 2.0 2920 1s12   apoferritin 2.0 1354 1gwg   cobd 2.0 2738 1lkc   synapsin 2.0 4636 1auv 1 tryparedoxin 2.0 1145 1qk8   myoglobin 1.9 1227 1n9x   nsf-n 1.9 1518 1qcs   rop 1.9 850 1f4n   epsin 1.8 1210 1edu   gene-5 1.8 673 1vqb 2 ic lyase 1.8 6484 1f61   mbp 1.8 1760 1ytt   p9 1.75 1062 1bkb   1063B 1.7 1926 1lfp   nitrite-reduct 1.7 2582 1et7   insulin 1.7 400 2bn3   lysozyme 1.5 982 1aki   rnase-p 1.5 3607 1nz0   calmodulin 1.1 1150 1exr 2 hipip 0.8 616 1iua   Table 2 Comparison of success rates for different values of the n_ref(1) 1 parameter (§3.2.1 ) The first row and the first column show the parameter values.

Publication Year: 2009


Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics.

(2010) J Chem Theory Comput 6

PubMed: 20148176 | PubMedCentral: PMC2817915 | DOI: 10.1021/ct9005294

Figure 1 The HEWL enzyme (PDB ID: 1AKI ) with titratable groups highlighted in liquorice style (aspartates, blue; glutamates, red; and histidine, orange).

All simulations were started from the minimized 1AKI (PDB ID) crystal structure, as prepared by Mongan et al. (details given in ref ( 4 )).

Publication Year: 2010


Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations.

(2012) J Chem Theory Comput 8

PubMed: 23180979 | PubMedCentral: PMC3503459 | DOI: 10.1021/ct200390j

o 115.04 63.77 51.27 1.91 0.38 0.12 a The test proteins (PDB code) are trp ( 1l2y ), drk ( 2a36 ), ubq ( 1ubq ), if3c ( 1tig ), lys ( 1aki ), and talin ( 2jsw ).

Publication Year: 2012


In silico Evaluation of Crosslinking Effects on Denaturant m(eq) values and ?Cp upon Protein Unfolding.

(2012) Avicenna J Med Biotechnol 4

PubMed: 23408172 | PubMedCentral: PMC3558204 | DOI: null

Figure 4 Molecular dynamics simulation of lysozyme (hen egg white) (PDB code 1AKI) solvated in 4.4 M urea in water at 500 °K for 10 ns using GROMOS-96 force field parameters As shown in Table ... , the SASAs of the investigated proteins increased at the end of MD simulation.

Publication Year: 2012


Testing of the GROMOS Force-Field Parameter Set 54A8: Structural Properties of Electrolyte Solutions, Lipid Bilayers, and Proteins.

(2013) J Chem Theory Comput 9

PubMed: 23418406 | PubMedCentral: PMC3572754 | DOI: 10.1021/ct300874c

Starting configurations for HEWL, FOX, CM and GCN were provided by the authors of ref ( 21 ) who used these systems for testing the GROMOS 54A7 force field, i.e., these starting configurations are rig... rously identical to those used in ref ( 21 ) and correspond to entries 1AKI (HEWL; X-ray diffraction structure at 1.5 Å resolution), 56 2ERR (FOX; entry number 1 from a solution-NMR structure bundle), 57 2FP2 (CM; X-ray diffraction structure at 1.6 Å resolution), 58 and 2OVN (GCN; entry number 1 from a solution-NMR structure bundle) 59 in the Protein Data Bank (PDB).

Publication Year: 2013


Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation.

(2014) J Chem Theory Comput 10

PubMed: 24803862 | PubMedCentral: PMC3985686 | DOI: 10.1021/ct401042b

37 We used the HEWL structure solved in PDB code 1AKI( 38 ) as our starting structure.

Publication Year: 2014


Structural basis of protein oxidation resistance: a lysozyme study.

(2014) PLoS One 9

PubMed: 24999730 | PubMedCentral: PMC4085010 | DOI: 10.1371/journal.pone.0101642

Protein (PDB: 1AKI) was placed into cubic boxes filled with water molecules.

g004 Figure 4 Lysozyme tertiary structure (PDB:1AKI).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4095916

47 The structure of lysozyme was taken from PDB entry 1AKI.

Publication Year: 2014


A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

(2014) J Comput Chem 35

PubMed: 25220475 | PubMedCentral: PMC4263261 | DOI: 10.1002/jcc.23728

To account for the secondary structures of proteins, we first optimized the PB radii for the alanine residue using 14 polyalanine structures described in the previous study by Swanson et al. 23 These ... tructures were constructed using the specific regions of two X-ray crystallographic structures (Protein Data Bank (PDB) 31 ID: 1AKI 32 and 1EJG 33 ).

Publication Year: 2014