Citations in PubMed

Primary Citation PubMed: 1557349 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

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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Tools for integrated sequence-structure analysis with UCSF Chimera.

(2006) BMC Bioinformatics 7

PubMed: 16836757 | PubMedCentral: PMC1570152 | DOI: 10.1186/1471-2105-7-339

Table 2 Results from different programs for difficult structure pairs pair PDB ID PDB ID Chimera TOPOFIT CE CE/MA 1 3chy 2fox 88/2.2 19/0.7 108/3.6 93/2.6 2 2aza A 1paz 79/2.0 72/1.7 84/2.9 81/2.4 3 1... ew I 1mol A 73/1.9 73/1.6 81/2.3 78/1.9 4 1cid 2rhe 90/2.0 69/1.5 97/2.9 88/1.9 5 1crl 1ede 184/2.5 143/1.9 219/3.8 183/2.3 6 2sim 1nsb A 257/2.6 207/2.0 275/3.0 266/2.5 7 1ten 3hhr B 82/1.3 81/1.4 87/1.9 85/1.6 8 1tie 4fgf 73/2.2 88/1.6 116/2.9 105/2.1 9 2snv 5ptp 118/2.3 83/1.8 130/3.1 118/2.4 10 1gp1 A 2trx A 89/1.8 96/1.6 64/5.2 54/2.7 Results are of the form N/RMSD, where N is the number of residue pairs matched and RMSD is the corresponding alpha-carbon root-mean-square deviation.

Publication Year: 2006


Detection of protein catalytic residues at high precision using local network properties.

(2008) BMC Bioinformatics 9

PubMed: 19055796 | PubMedCentral: PMC2632678 | DOI: 10.1186/1471-2105-9-517

violaceum (E.C. 1.14.16.1, PDB entry 1ltv, iron cofactor bound), human peptidyl-prolyl isomerase (E.C. 5.2.1.8, PDB entry 1pin, substrate Ala-Pro bound), ferric binding protein from Hæm. influ... nzae (PDB entry 1mrp, iron and phosphate bound) and bovine β-trypsin (E.C. 3.4.21.4, PDB entry 5ptp, calcium bound).

Publication Year: 2008


Unfolding simulations reveal the mechanism of extreme unfolding cooperativity in the kinetically stable alpha-lytic protease.

(2010) PLoS Comput Biol 6

PubMed: 20195497 | PubMedCentral: PMC2829044 | DOI: 10.1371/journal.pcbi.1000689

Materials and Methods Simulations 1SSX and 5PTP PDBs were used for αLP and trypsin, respectively.

Publication Year: 2010


Generalized spring tensor models for protein fluctuation dynamics and conformation changes.

(2010) BMC Struct Biol 10 Suppl 1

PubMed: 20487510 | PubMedCentral: PMC2873826 | DOI: 10.1186/1472-6807-10-S1-S3

Two proteins, 1CYO and 5PTP, are removed from the dataset because they no longer exist in the current Protein Data Bank [ 28 ].

Publication Year: 2010


Predicting protein interactions by Brownian dynamics simulations.

(2012) J Biomed Biotechnol 2012

PubMed: 22500075 | PubMedCentral: PMC3303761 | DOI: 10.1155/2012/121034

Crystal structures for proteins, Trypsin and BPTI, are available in both bound (Trypsin/BPTI, PDB : 2PTC) and unbound (Trypsin, PDB : 5PTP; BPTI, PDB : ... BPI) forms, which provide us an opportunity to further evaluate our BD approach.

Publication Year: 2012


Crystal structures of a plant trypsin inhibitor from Enterolobium contortisiliquum (EcTI) and of its complex with bovine trypsin.

(2013) PLoS One 8

PubMed: 23626794 | PubMedCentral: PMC3633903 | DOI: 10.1371/journal.pone.0062252

A comparison of the trypsin component of the complex with the structure of the inactivated enzyme containing monoisopropylphoshoserine instead of the catalytic Ser195 (PDB ID: 5PTP) indicates the abse... ce of any significant conformational changes in the enzyme that could be traced to binding of EcTI (RMSD 0.50 Å for a superposition of all 223 Cα atoms).

Publication Year: 2013