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Literature DB >> 15073022

An interactive triple-helical collagen builder.

Abstract

UNLABELLED: To facilitate the building of triple-helical polypeptide structures, we provide an interactive, platform-independent Tcl/Tk script. User specified amino acid sequences are parsed to obtain localized melting temperature estimates corresponding to helical propensity. These propensities may be graphically examined prior to their automated use in combination with two separate statistical parameter sets to build the complete polypeptide backbone and, if desired, predict side-chain terminal atom locations. AVAILABILITY: The Tcl/Tk Triple Helical collagen Building Script (THe BuScr) and full documentation is freely available under the terms of the GNU General Public License at www.pence.ca/~jrainey/ or www.chem.utoronto.ca/staff/MCG/.

Entities: Gene

Mesh：

Substances：
Collagen

Year: 2004 PMID： 15073022 DOI： 10.1093/bioinformatics/bth247

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

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Cited

28 in total

1. Molecular mechanism of force induced stabilization of collagen against enzymatic breakdown.

Authors: Shu-Wei Chang; Brendan P Flynn; Jeffrey W Ruberti; Markus J Buehler
Journal: Biomaterials Date: 2012-03-06 Impact factor: 12.479

2. Atomistic modeling of collagen proteins in their fibrillar environment.

Authors: Ian Streeter; Nora H de Leeuw
Journal: J Phys Chem B Date: 2010-10-21 Impact factor: 2.991

Review 3. Designed triple-helical peptides as tools for collagen biochemistry and matrix engineering.

Authors: Takaki Koide
Journal: Philos Trans R Soc Lond B Biol Sci Date: 2007-08-29 Impact factor: 6.237

4. Structure and activation of C1, the complex initiating the classical pathway of the complement cascade.

Authors: Simon A Mortensen; Bjoern Sander; Rasmus K Jensen; Jan Skov Pedersen; Monika M Golas; Jens C Jensenius; Annette G Hansen; Steffen Thiel; Gregers R Andersen
Journal: Proc Natl Acad Sci U S A Date: 2017-01-19 Impact factor: 11.205

5. Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study.

Authors: Ming Tang; Xiaocong Wang; Neha S Gandhi; Bethany Lachele Foley; Kevin Burrage; Robert J Woods; YuanTong Gu
Journal: Glycobiology Date: 2020-09-28 Impact factor: 4.313

Review 6. Crafting of functional biomaterials by directed molecular self-assembly of triple helical peptide building blocks.

Authors: Jayati Banerjee; Helena S Azevedo
Journal: Interface Focus Date: 2017-10-20 Impact factor: 3.906

An interactive triple-helical collagen builder.

1. Molecular mechanism of force induced stabilization of collagen against enzymatic breakdown.

2. Atomistic modeling of collagen proteins in their fibrillar environment.

Review 3. Designed triple-helical peptides as tools for collagen biochemistry and matrix engineering.

4. Structure and activation of C1, the complex initiating the classical pathway of the complement cascade.

5. Effect of hydroxylysine-O-glycosylation on the structure of type I collagen molecule: A computational study.

Review 6. Crafting of functional biomaterials by directed molecular self-assembly of triple helical peptide building blocks.

7. Single molecule effects of osteogenesis imperfecta mutations in tropocollagen protein domains.

8. Collagen Gly missense mutations: Effect of residue identity on collagen structure and integrin binding.

9. Matriarch: A Python Library for Materials Architecture.

10. Investigation of mechanisms of viscoelastic behavior of collagen molecule.