Citations in PubMed

Primary Citation PubMed: 11979279 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 18

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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Calculation of the free energy and cooperativity of protein folding.

(2007) PLoS One 2

PubMed: 17505540 | PubMedCentral: PMC1865387 | DOI: 10.1371/journal.pone.0000446

NMR structure of TC5b (PDB code 1L2Y; model 1) was used as the starting configuration for our studies.

Publication Year: 2007


An enhanced partial order curve comparison algorithm and its application to analyzing protein folding trajectories.

(2008) BMC Bioinformatics 9

PubMed: 18710565 | PubMedCentral: PMC2571979 | DOI: 10.1186/1471-2105-9-344

Following the definition from [ 32 ], a successful folding event has to satisfy the following two criteria: Figure 2 NMR structure of trp-cage protein 1l2y .

Neidigh J Fesinmeyer R Andersen N PDB ID: 1L2Y Mini-proteins Trp the light fantastic Nat Struct Biol 2002 9 425 430 11979279 Grasso C Lee C Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems Bioinformatics 2004 20 1546 1556 14962922 Lee C Grasso C Sharlow M Multiple sequence alignment using partial order graphs Bioinformatics 2002 18 452 464 11934745 Ota M Ikeguchi M Kidera A Phylogeny of protein-folding trajectories reveals a unique pathway to native structure PNAS 2004 101 17658 17663 15591340 Borreguero JM Ding F Buldyrev SV Stanley HE Dokholyan NV Multiple Folding Pathways of the SH3 Domain ArXiv Physics e-prints 2003 87 Levinthal C Are there pathways for protein folding?

Publication Year: 2008


An effective all-atom potential for proteins.

(2009) PMC Biophys 2

PubMed: 19356242 | PubMedCentral: PMC2696411 | DOI: 10.1186/1757-5036-2-2

Table 1 Amino acid sequences System PDB code Sequence Trp-cage 1L2Y NLYIQ WLKDG GPSSG RPPPS E6apn1 1RIJ Ac-ALQEL LGQWL KDGGP SSGRP PPS-NH 2 C Ac-KETAA AKFER AHA-NH 2 EK Ac-YAEAA KAAEA AKAF-NH 2 F s Su... -AAAAA AAARA AAARA AAARA A-NH 2 GCN4tp 2OVN NYHLE NEVAR LKKLV GE HPLC-6 1WFA DTASD AAAAA ALTAA NAKAA AELTA ANAAA AAAAT AR-NH 2 Chignolin 1UAO GYDPE TGTWG MBH12 1J4M RGKWT YNGIT YEGR GB1p GEWTY DDATK TFTVT E GB1m2 GEWTY NPATG KFTVT E GB1m3 KKWTY NPATG KFTVQ E trpzip1 1LE0 SWTWE GNKWT WK-NH 2 trpzip2 1LE1 SWTWE NGKWT WK-NH 2 betanova RGWSV QNGKY TNNGK TTEGR LLM RGWSL QNGKY TLNGK TMEGR beta3s TWIQN GSTKW YQNGS TKIYT AB zipper 1U2U Ac-EVAQL EKEVA QLEAE NYQLE QEVAQ LEHEG-NH 2 Ac-EVQAL KKRVQ ALKAR NYALK QKVQA LRHKG-NH 2 Top7-CFR 2GJH ERVRI SITAR TKKEA EKFAA ILIKV FAELG YNDIN VTWDG DTVTV EGQL GS- α 3 W 1LQ7 GSRVK ALEEK VKALE EKVKA LGGGG RIEEL KKKWE ELKKK IEELG GGGEV KKVEE EVKKL EEEIK KL Suc stands for succinylic acid.

Publication Year: 2009


A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

(2009) PLoS Comput Biol 5

PubMed: 19662155 | PubMedCentral: PMC2711228 | DOI: 10.1371/journal.pcbi.1000452

The NMR structure (1L2Y) [17] reveals a compact hydrophobic core, in which the Trp side chain is buried.

The RMSD is computed as the average RMSD between the cluster structures and all the structures in 1L2Y PDB entry.

The initial structure (pdb entry 1L2Y) [17] was solvated with 2075 TIP3P [62] water molecules in a 40×40×40 Å water box.

Publication Year: 2009


Detection of functional modes in protein dynamics.

(2009) PLoS Comput Biol 5

PubMed: 19714202 | PubMedCentral: PMC2721685 | DOI: 10.1371/journal.pcbi.1000480

Likewise, the first structure in the NMR ensemble derived by Neidigh et al. (PDB code 1L2Y [29] ) was used as initial structure for the simulations of Trp-cage.

Publication Year: 2009


On the zwitterionic nature of gas-phase peptides and protein ions.

(2010) PLoS Comput Biol 6

PubMed: 20463874 | PubMedCentral: PMC2865515 | DOI: 10.1371/journal.pcbi.1000775

Instead, the Trp-cage initial structure was obtained by a 20-ns MD simulation in aqueous solution at ambient conditions based on the NMR structure number 1 deposited in the protein data bank (PDB code... 1L2Y) [78] (see Text S1 ).

Publication Year: 2010


The effective fragment molecular orbital method for fragments connected by covalent bonds.

(2012) PLoS One 7

PubMed: 22844433 | PubMedCentral: PMC3402534 | DOI: 10.1371/journal.pone.0041117

[32] , [34] , [41] This includes -helices ( ) and -sheets ( ) of alanine, Chignolin (PDB code: 1UAO) and the Trp-cage (PDB code: 1L2Y).

Publication Year: 2012


Atomic-level structure characterization of an ultrafast folding mini-protein denatured state.

(2012) PLoS One 7

PubMed: 22848459 | PubMedCentral: PMC3407199 | DOI: 10.1371/journal.pone.0041301

The previously reported, high resolution NMR structure (PDB entry: 1L2Y, Figure 1 ) of TC5b’s (NLYIQ WLKDG GPSSG RPPPS) native state reveals a compact hydrophobic core where three proline resi... ues – namely Pro 12, Pro 18, and Pro 19– and a glycine residue (Gly 11) pack against the aromatic side chains of Tyr 3 and, in particular, Trp 6 which lies in the centre of the hydrophobic cage, well shielded from solvent exposure [9] .

g001 Figure 1 NMR-derived native state structure of TC5b (PDB entry: 1L2Y).

Publication Year: 2012


FragIt: a tool to prepare input files for fragment based quantum chemical calculations.

(2012) PLoS One 7

PubMed: 23028546 | PubMedCentral: PMC3445547 | DOI: 10.1371/journal.pone.0044480

Description of the Test Dataset To illustrate the applicability of FragIt to different molecules using different patterns, we show results for a molecular cluster consisting of water and a solute, Chi... nolin (PDB: 1UAO), Tryptophan-cage (PDB: 1L2Y), Human Parathyroid Hormone (HPH) residues 1–34 (PDB: 1ET1A), Crambine (PDB: 1CRN), GluR2 ligand binding core (PDB: 1FTJ) as well as several neutral methyl-capped -helix and -sheet alanine structures from Fedorov et al. [6] and finally a -cyclodextrin (extracted from PDB: 3CGT).

Publication Year: 2012


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


Interface of the polarizable continuum model of solvation with semi-empirical methods in the GAMESS program.

(2013) PLoS One 8

PubMed: 23844075 | PubMedCentral: PMC3699639 | DOI: 10.1371/journal.pone.0067725

The Mean Absolute Deviations (MADs) of vibrational frequencies between solvated (s) and gas-phase (g) calculations were calculated by (16) We also carried out single point energies and gradients calcu... ations for Chignolin (PDB: 1UAO), Trypthophan-cage (PDB: 1L2Y), Crambine (PDB: 1CRN), Trypsin Inhibitor (PDB: 5PTI) and Ubiquitin (PDB: 1UBI).

Publication Year: 2013


Dynamic folding pathway models of the Trp-cage protein.

(2013) Biomed Res Int 2013

PubMed: 23865078 | PubMedCentral: PMC3707288 | DOI: 10.1155/2013/973867

The Trp-cage protein has the amino-acid sequence of NLYIQ WLKDG GPSSG RPPPS (PDB code: 1L2Y).

Publication Year: 2013


Role of tryptophan side chain dynamics on the Trp-cage mini-protein folding studied by molecular dynamics simulations.

(2014) PLoS One 9

PubMed: 24563686 | PubMedCentral: PMC3921895 | DOI: 10.1371/journal.pone.0088383

(B) Root-mean –square deviation (RMSD) of C α –atoms with respect to native structure and (C) distance between Asp9-Arg16 (salt bridge) of sampled Trp-cage conformations in exp... icit solvent starting from the native structure (1 st entry of pdb 1L2Y) versus simulation time.

Publication Year: 2014


Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

(2013) BMC Struct Biol 13 Suppl 1

PubMed: 24565158 | PubMedCentral: PMC3952944 | DOI: 10.1186/1472-6807-13-S1-S8

On Trp-Cage, we connect an extended conformation to the native structure (PDB id 1l2y ).

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC3999791

Figure 1 (A) From the unfolded strand to folded cage structure of a Trp-cage protein (PDB code: 1L2Y).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4020588

19 , 36 In this work, we used the energy-term weights from the force field calibrated in our earlier work 36 with the tryptophan cage (PDB code: 1L2Y) 39 and the tryptophan zipper 2 (PDB code: 1LE1).

Publication Year: 2014


A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+.

(2014) PeerJ 2

PubMed: 25024918 | PubMedCentral: PMC4081274 | DOI: 10.7717/peerj.449

Geometry optimizations of Chignolin (PDB: 1UAO) and the Tryptophan-cage (PDB: 1L2Y) using PM6-D3H+ were also carried out.

Publication Year: 2014


High-temperature unfolding of a trp-cage mini-protein: a molecular dynamics simulation study.

(2005) Theor Biol Med Model 2

PubMed: 15760474 | PubMedCentral: PMC555740 | DOI: 10.1186/1742-4682-2-7

Results and Discussion Molecular dynamics simulations of the Trp-cage mini-protein construct (PDB ID: 1L2Y) were carried out using the OPLS-AA force-field incorporated in the freely available program,... GROMACS.

Methods The starting structures for the simulations were obtained from PDB 1L2Y [ 3 ].

Publication Year: 2005