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PDB ID Mentions in PubMed Central Article count: 8

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Conformational changes in protein loops and helices induced by post-translational phosphorylation.

(2006) PLoS Comput Biol 2

PubMed: 16628247 | PubMedCentral: PMC1440919 | DOI: 10.1371/journal.pcbi.0020032

Accession Numbers The Protein Data Bank ( http://www.rcsb.org/pdb ) accession numbers for the proteins discussed in this paper are as follows: β PGM, (PDB ID: 1LVH); CDK2, phosphorylated (PDB ... D: 1JST); CDK2, unphosphorylated (PDB ID: 1FIN); CDK2/KAP complex (PDB ID: 1FQ1); cyclin A (PDB ID: 1B39); ERK2, phosphorylated (PDB ID: 2ERK); ERK2, unphosphorylated (PDB ID: 1ERK); FixJ, phosphorylated (PDB ID: 1D5W); FixJ, unphosphorylated (PDB ID: 1DCK); GLM, (PDB ID: 1MKI); Hpr, phosphorylated (PDB ID: 1FU0); Hpr, unphosphorylated (PDB ID: 1PTF); LCK, (PDB ID: 3LCK); Pim1, (PDB ID: 2BIK); PMM, (PDB ID: 1K35); Psp, phosphorylated (PDB ID: 1J97); Psp, unphosphorylated (PDB ID: 1L7O); P38 γ, (PDB ID: 1CM8); SpoIIAA, phosphorylated (PDB ID: 1H4X); and SpoIIAA, unphosphorylated (PDB ID: 1H4Z); Spo0A, (PDB ID: 1QMP).

Publication Year: 2006


Structural deformation upon protein-protein interaction: a structural alphabet approach.

(2008) BMC Struct Biol 8

PubMed: 18307769 | PubMedCentral: PMC2315654 | DOI: 10.1186/1472-6807-8-12

We consider the 3 classes from Table 3 , namely enzyme/substrate, antibody/antigen, and other; Table 3 Description of the complex set Type (number) Complexes PDB id Enzyme-substrate (23) 1ACB , 1AVX ,... 1AY7 , 1BVN , 1CGI , 1D6R , 1DFJ , 1E6E , 1EAW , 1EWY , 1EZU , 1F34 , 1HIA , 1KKL , 1MAH , 1PPE , 1TMQ , 1UDI , 2MTA , 2PCC , 2SIC , 2SNI , 7CEI Antibody-Antigen (10) 1AHW , 1BGX , 1BVK , 1DQJ , 1E6J , 1JPS , 1MLC , 1VFB , 1WEJ , 2VIS Other (35) 1A2K , 1AK4 , 1AKJ , 1ATN , 1B6C , 1BUH , 1DE4 , 1E96 , 1EER , 1F51 , 1FC2 , 1FQ1 , 1FQJ , 1GCQ , 1GP2 , 1GRN , 1H1V , 1HE1 , 1HE8 , 1I2M , 1I4D , 1IB1 , 1IBR , 1IJK , 1KLU , 1KTZ , 1KXP , 1M10 , 1ML0 , 1N2C , 1QA9 , 1RLB , 1SBB , 1WQ1 , 2BTF • the motif should be located in totality at the protein-protein interfaces of the complexes; • we do not consider runs of helical letters (A,a,V,W,Z,B,C) or extended letters (L,M,N,T,X,J,K).

Publication Year: 2008


A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys.

(2007) Proteins 69

PubMed: 17623864 | PubMedCentral: PMC2673351 | DOI: 10.1002/prot.21498

Table I The Number of Top 5 Decoys with rmsd < 10 Å given by EMPIRE and the RosettaDock scoring function Pdb ID a 1CGI 1CHO 2PTC 1TGS 2SNI 2SIC 1CSE 2KAI EMPIRE b 1 5 4 5 5 5 5 5 Roset... aDock c 4 3 2 5 4 5 2 4 Pdb ID 1BRC 1ACB 1BRS 1MAH 1UGH 1DFJ 1FSS 1AVW EMPIRE 5 3 4 5 5 5 3 5 RosettaDock 1 2 4 5 5 4 5 5 Pdb ID 1PPE 1TAB 1UDI 1STF 2TEC 4 HTC 1MLC 1WEJ EMPIRE 5 5 5 5 5 5 2 2 RosettaDock 5 5 5 5 5 5 0 0 Pdb ID 1AHW 1DQJ 1BVK 1FBI 2JEL 1BQL 1JHL 1NQA EMPIRE 0 1 1 5 5 2 1 5 RosettaDock 5 2 5 3 5 5 1 5 Pdb ID 1NMB 1MEL 2VIR 1EO8 1QFU 1IAI 2PCC 1WQ1 EMPIRE 5 5 3 1 4 3 4 4 RosettaDock 5 5 4 1 5 0 3 3 Pdb ID AVZ 1MDA 1IGC 1ATN 1GLA 1SPB 2BTF 1A0Q EMPIRE 0 4 1 5 5 5 3 4 RosettaDock 0 3 2 5 1 5 4 1 Pdb ID 1BTH 1FIN 1FQ1 1GOT 1EFU 3HHR #(≥3) d #(>) EMPIRE 0 0 4 5 2 2 39 21 e RosettaDock 0 0 2 0 0 0 34 10 f a Enzyme/Inhibitor: the first 22 protein complexes (1CGI-4HTC); antibody-antigen: the next 16 protein complexes (1MLC-1IAI); the others: (2PCC to 1A0Q); and the difficult set (1BTH to 3HHR).

Publication Year: 2007


Designing coarse grained-and atom based-potentials for protein-protein docking.

(2010) BMC Struct Biol 10

PubMed: 21078143 | PubMedCentral: PMC2996388 | DOI: 10.1186/1472-6807-10-40

Table 4 Ranking ZDOCK2.3 decoys (IRMSD ≤4Å) by the jackknife test Complex a Rank b ADPs-II c Zdock2.3 DARS ACE 1AK4 - - 950 1744 1B6C 95 16 9 178 1BVK 12 268 610 - 1DQJ - 1490 - - 1EWY... 164 18 42 364 1FC2 484 - 24 797 1GHQ - - - 1308 1HIA 21 653 122 - 1IJK 1131 - 368 - 1KLU - - - - 1AVX 5 46 6 59 1D6R 1840 567 - - 1E96 39 399 42 490 1F34 13 26 666 5 1GCQ 1030 - 1057 1040 1GRN 210 102 - - 1I4D 84 403 965 616 1KXP 91 7 1 200 1NSN 53 445 - - 1SBB - - - - 1ACB 113 55 24 98 1AKJ 592 40 - - 1AY7 120 100 - - 1DFJ 37 1 - - 1EAW 65 13 33 309 1FQ1 - - - - 1GP2 4 389 58 1681 1I9R 184 14 589 - 1UDI 27 13 1 1 2PCC 203 193 821 120 1AHW 23 14 - - 1BUH 14 - 555 - 1E6E 2 103 44 520 1ML0 10 1 9 32 1PPE 3 1 1 1 1QFW 544 74 - - 1TMQ 9 126 12 22 1WEJ 3 42 1047 - 2JEL 307 86 76 579 7CEI 15 1 920 708 1ATN - - - - 1BJ1 6 18 18 85 1CGI 71 247 13 24 1F51 1 11 251 797 1KAC 121 1389 - - 1KKL 283 - 1 222 1NCA 4 4 - - 1QA9 687 - - - 2SNI 17 618 1 2 1RLB 48 302 5 7 a-Complex PDB code.

Publication Year: 2010


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Re-docking scheme for generating near-native protein complexes by assembling residue interaction fingerprints.

(2013) PLoS One 8

PubMed: 23874954 | PubMedCentral: PMC3712918 | DOI: 10.1371/journal.pone.0069365

Rigid-body (34) 1AK4 1AVX 1AY7 1B6C 1BUH 1BVN 1CGI 1D6R 1DFJ 1E6E 1E96 1EAW 1EWY 1F34 1FC2 1FQJ 1GCQ 1GHQ 1HE1 1KAC 1KTZ 1KXP 1KXQ 1MAH 1PPE 1QA9 1SBB 1TMQ 1UDI 2BTF 2PCC 2SIC 2SNI 7CEI Medium Difficu... ty (6) 1ACB 1GRN 1HE8 1I2M 1M10 1WQ1 Difficult (4) 1ATN 1FQ1 1H1V 1IBR Definition of IFP and Similarity between Decoys As suggested previously, it is sufficient to compare the interacting fragments rather than the whole structures to obtain information on near-native molecular interactions [9] , [10] .

Publication Year: 2013


A structure-guided approach for protein pocket modeling and affinity prediction.

(2013) J Comput Aided Mol Des 27

PubMed: 24214361 | PubMedCentral: PMC3851759 | DOI: 10.1007/s10822-013-9688-9

PDB codes of the pool of protein structures considered for model guidance in the CDK2 study: 1AQ1, 1FVT, 1FVV, 1GIH, 1B38, 1B39, 1FIN, 1FQ1, 1GY3, 1HCK, 1JST, 1QMZ, 1H08, 1DI8, 1H01, 1H00, 1E9H, 1JVP,... 1KE5, 1KE6, 1KE7, 1KE8, 1KE9, 1H07, 1E1X, 1JSV 26.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4443796

Rigid-body (34) 1AK4, 1AVX, 1AY7, 1B6C, 1BUH, 1BVN, 1CGI, 1D6R, 1DFJ, 1E6E, 1E96, 1EAW, 1EWY, 1F34, 1FC2, 1FQJ, 1GCQ, 1GHQ, 1HE1, 1KAC, 1KTZ, 1KXP, 1KXQ, 1MAH, 1PPE, 1QA9, 1SBB, 1TMQ, 1UDI, 2BTF, 2PCC... 2SIC, 2SNI, 7CEI Medium Difficulty (6) 1ACB, 1GRN, 1HE8, 1I2M, 1M10, 1WQ1 Difficult (4) 1ATN, 1FQ1, 1H1V, 1IBR Table 4 The 120 complex structures selected from the ZLAB Benchmark 4.0 dataset (large dataset).

Publication Year: 2014