Improving the efficiency of evolutionary de novo peptide design: Strategies for probing configuration and parameter settings

Biosystems ◽  
2007 ◽  
Vol 88 (1-2) ◽  
pp. 35-55 ◽  
Author(s):  
Wuming Zhang ◽  
Kazuyoshi Yano ◽  
Isao Karube
Keyword(s):  
De Novo ◽  
Peptide Design ◽  
Design Strategies ◽  
De Novo Peptide Design ◽  
De Novo Peptide

Evolutionary algorithms and de novo peptide design

2005 ◽  
Vol 10 (4) ◽  
pp. 295-304 ◽  
Author(s):  
I. Belda ◽  
X. Llorà ◽  
E. Giralt
Keyword(s):  
Evolutionary Algorithms ◽  
De Novo ◽  
Peptide Design ◽  
De Novo Peptide Design ◽  
De Novo Peptide

scholarly journals De Novo Peptide Design and Experimental Validation of Histone Methyltransferase Inhibitors

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e90095 ◽  
Author(s):  
James Smadbeck ◽  
Meghan B. Peterson ◽  
Barry M. Zee ◽  
Shivani Garapaty ◽  
Aashna Mago ◽  
...  
Keyword(s):  
Experimental Validation ◽  
De Novo ◽  
Histone Methyltransferase ◽  
Peptide Design ◽  
De Novo Peptide Design ◽  
De Novo Peptide

ENPDA: an evolutionary structure-based de novo peptide design algorithm

2005 ◽  
Vol 19 (8) ◽  
pp. 585-601 ◽  
Author(s):  
Ignasi Belda ◽  
Sergio Madurga ◽  
Xavier Llorà ◽  
Marc Martinell ◽  
Teresa Tarragó ◽  
...  
Keyword(s):  
De Novo ◽  
Peptide Design ◽  
Design Algorithm ◽  
De Novo Peptide Design ◽  
De Novo Peptide

Constrained amino acid analogs in de novo peptide design

2006 ◽  
pp. 272-274
Author(s):  
Lars G. J. Hammarström ◽  
Ted J. Gauthier ◽  
Robert P. Hammer ◽  
Mark L. McLaughlin
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Peptide Design ◽  
Amino Acid Analogs ◽  
De Novo Peptide Design ◽  
De Novo Peptide

scholarly journals VitAL: Viterbi Algorithm for de novo Peptide Design

PLoS ONE ◽  
2010 ◽  
Vol 5 (6) ◽  
pp. e10926 ◽  
Author(s):  
E. Besray Unal ◽  
Attila Gursoy ◽  
Burak Erman
Keyword(s):  
Viterbi Algorithm ◽  
De Novo ◽  
Peptide Design ◽  
De Novo Peptide Design ◽  
De Novo Peptide

scholarly journals De Novo Peptide Design with C3a Receptor Agonist and Antagonist Activities: Theoretical Predictions and Experimental Validation

2012 ◽  
Vol 55 (9) ◽  
pp. 4159-4168 ◽  
Author(s):  
Meghan L. Bellows-Peterson ◽  
Ho Ki Fung ◽  
Christodoulos A. Floudas ◽  
Chris A. Kieslich ◽  
Li Zhang ◽  
...  
Keyword(s):  
Receptor Agonist ◽  
Experimental Validation ◽  
De Novo ◽  
Peptide Design ◽  
Theoretical Predictions ◽  
Agonist And Antagonist ◽  
De Novo Peptide Design ◽  
De Novo Peptide

In Machina Systems for the Rational De Novo Peptide Design

2009 ◽  
pp. 438-457
Author(s):  
Paul Wrede
Keyword(s):  
De Novo ◽  
Fitness Function ◽  
T Cell Epitopes ◽  
Cellular Functions ◽  
Guided Search ◽  
Weak Binding ◽  
Dilatative Cardiomyopathy ◽  
Computer Based ◽  
De Novo Peptide Design ◽  
De Novo Peptide

Peptides fulfill many tasks in controlling and regulating cellular functions and are key molecules in systems biology. There is a great demand in science and industry for a fast search of innovative peptide structures. In this chapter we introduce a combination of a computer-based guided search of novel peptides in sequence space with their biological experimental validation. The computer-based search uses an evolutionary algorithm that includes artificial neural networks as fitness function and a mutation operator, called the PepHarvester. Optimization occurs during 100 iterations. This system, called DARWINIZER, is applied in the de novo design of neutralizing peptides against autoantibodies from DCM (dilatative cardiomyopathy) patients. Another approach is the optimization of peptide sequences by an ant colony optimization process. This biologically-oriented system identified several novel weak binding T-cell epitopes.

Design of peptide affinity ligands for S-protein: a comparison of combinatorial and de novo design strategies

2013 ◽  
Vol 17 (2) ◽  
pp. 357-369 ◽  
Author(s):  
Divya Chandra ◽  
Christopher J. Morrison ◽  
James Woo ◽  
Steven Cramer ◽  
Pankaj Karande
Keyword(s):  
De Novo ◽  
Protein A ◽  
De Novo Design ◽  
Design Strategies ◽  
S Protein ◽  
Affinity Ligands ◽  
Peptide Affinity
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