Folding protein-like structures with open L-systems

Gemma B. Danks; Susan Stepney; Leo S. D. Caves

Folding protein-like structures with open L-systems

Gemma B. Danks, Susan Stepney, Leo S. D. Caves

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Proteins, under native conditions, fold to specific 3D structures according to their ID amino acid sequence, which in turn is defined by the genetic code. The specific shape of a folded protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding are not well understood and predicting the final conformation of a folded protein from its amino acid sequence alone is not yet achievable despite extensive research efforts, both theoretical and experimental. The protein folding process may be viewed as an emergent phenomenon, a result of underlying physics controlling the interaction of amino acids with their local environment, leading to the complex global fold. In this spirit we present a model for investigating protein folding using open L-systems, local rewriting rules with environmental interaction.

Original language	English
Title of host publication	Advances in Artificial Life, Proceedings
Editors	FAE Costa, LM Rocha, E Costa, I Harvey, A Coutinho
Place of Publication	BERLIN
Publisher	Springer
Pages	1100-1109
Number of pages	10
ISBN (Print)	978-3-540-74912-7
Publication status	Published - 2007
Event	9th European Conference on Artificial Life - Lisbon Duration: 10 Sept 2007 → 14 Sept 2007

Conference

Conference	9th European Conference on Artificial Life
City	Lisbon
Period	10/09/07 → 14/09/07

Keywords

protein-folding
L-systems
open-L-systems
MODELS
PRINCIPLES
LATTICE

Cite this

@inproceedings{399a9050086c435aa1d2931204da1805,

title = "Folding protein-like structures with open L-systems",

abstract = "Proteins, under native conditions, fold to specific 3D structures according to their ID amino acid sequence, which in turn is defined by the genetic code. The specific shape of a folded protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding are not well understood and predicting the final conformation of a folded protein from its amino acid sequence alone is not yet achievable despite extensive research efforts, both theoretical and experimental. The protein folding process may be viewed as an emergent phenomenon, a result of underlying physics controlling the interaction of amino acids with their local environment, leading to the complex global fold. In this spirit we present a model for investigating protein folding using open L-systems, local rewriting rules with environmental interaction.",

keywords = "protein-folding, L-systems, open-L-systems, MODELS, PRINCIPLES, LATTICE",

author = "Danks, {Gemma B.} and Susan Stepney and Caves, {Leo S. D.}",

year = "2007",

language = "English",

isbn = "978-3-540-74912-7",

pages = "1100--1109",

editor = "FAE Costa and LM Rocha and E Costa and I Harvey and A Coutinho",

booktitle = "Advances in Artificial Life, Proceedings",

publisher = "Springer",

address = "Germany",

note = "9th European Conference on Artificial Life ; Conference date: 10-09-2007 Through 14-09-2007",

}

TY - GEN

T1 - Folding protein-like structures with open L-systems

AU - Danks, Gemma B.

AU - Stepney, Susan

AU - Caves, Leo S. D.

PY - 2007

Y1 - 2007

N2 - Proteins, under native conditions, fold to specific 3D structures according to their ID amino acid sequence, which in turn is defined by the genetic code. The specific shape of a folded protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding are not well understood and predicting the final conformation of a folded protein from its amino acid sequence alone is not yet achievable despite extensive research efforts, both theoretical and experimental. The protein folding process may be viewed as an emergent phenomenon, a result of underlying physics controlling the interaction of amino acids with their local environment, leading to the complex global fold. In this spirit we present a model for investigating protein folding using open L-systems, local rewriting rules with environmental interaction.

AB - Proteins, under native conditions, fold to specific 3D structures according to their ID amino acid sequence, which in turn is defined by the genetic code. The specific shape of a folded protein is a strong indicator of its function in the cell. The mechanisms involved in protein folding are not well understood and predicting the final conformation of a folded protein from its amino acid sequence alone is not yet achievable despite extensive research efforts, both theoretical and experimental. The protein folding process may be viewed as an emergent phenomenon, a result of underlying physics controlling the interaction of amino acids with their local environment, leading to the complex global fold. In this spirit we present a model for investigating protein folding using open L-systems, local rewriting rules with environmental interaction.

KW - protein-folding

KW - L-systems

KW - open-L-systems

KW - MODELS

KW - PRINCIPLES

KW - LATTICE

M3 - Conference contribution

SN - 978-3-540-74912-7

SP - 1100

EP - 1109

BT - Advances in Artificial Life, Proceedings

A2 - Costa, FAE

A2 - Rocha, LM

A2 - Costa, E

A2 - Harvey, I

A2 - Coutinho, A

PB - Springer

CY - BERLIN

T2 - 9th European Conference on Artificial Life

Y2 - 10 September 2007 through 14 September 2007

ER -