Primary Citation PubMed: 1557349
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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. 126.96.36.199, PDB entry 1ltv, iron cofactor bound), human peptidyl-prolyl isomerase (E.C. 188.8.131.52, 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. 184.108.40.206, 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 ].
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
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