Patrick Timmons

Patrick Timmons
Nuritas Inc.

Doctor of Philosophy

About

24
Publications
3,892
Reads
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122
Citations
Introduction
Patrick completed his PhD research at the University College Dublin Conway Insitute. He is most interested in the study of the structure and function of therapeutic peptides. He specialises in the application of NMR methods for the determination of tertiary structures, molecular dynamics for studying peptide-membrane interactions, and the development of novel neural networks for prediction of peptide structure and function from the primary sequence. https://research.timmons.eu
Additional affiliations
November 2021 - present
Nuritas
Position
  • Bioinformatician
September 2017 - August 2021
University College Dublin
Position
  • Research Assistant
September 2017 - November 2021
University College Dublin
Position
  • PhD Student
Education
September 2017 - August 2021
University College Dublin
Field of study
  • Biochemistry
September 2013 - May 2017
Trinity College Dublin
Field of study
  • Medicinal Chemistry

Publications

Publications (24)
Article
Maximin 3 is a 27-residue-long cationic antimicrobial peptide found in the skin secretion and brain of the Chinese red-belly toad Bombina maxima. The peptide is of biological interest as it possesses anti-HIV activity, not found in the other maximin peptides, in addition to antimicrobial, antitumor and spermicidal activities. The three-dimensional...
Preprint
Full-text available
Good knowledge of a peptide's tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational method that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works fo...
Preprint
Full-text available
Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the de...
Article
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC), first isolated from skin secretions of the foothill yellow-legged frog Rana boylii, shows broad-spectrum activity, being particularly effective against opportunistic yeast pathogens. The structure of brevinin-1BYa was investigated in various solution and membrane-mimicking environments by proton nuclear mag...
Article
Brevinin-1BYa is a 24-amino acid residue host-defense peptide, first isolated from skin secretions of the foothill yellow-legged frog Rana boylii. The peptide is of interest, as it shows broad-spectrum antimicrobial activity, and is particularly effective against opportunistic yeast pathogens. Its potential for clinical use, however, is hindered by...
Article
Full-text available
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defence peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus. The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-dim...
Article
Full-text available
Maximin 1 is a cationic, amphipathic antimicrobial peptide found in the skin secretions and brains of the Chinese red belly toad Bombina maxima. The 27 amino acid residue-long peptide is biologically interesting as it possesses a variety of biological activities, including antibacterial, antifungal, antiviral, antitumour and spermicidal activities....
Article
Full-text available
Good knowledge of a peptide's tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational protocol that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works...
Article
Full-text available
Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the de...
Preprint
Full-text available
Palustrin-Ca (GFLDIIKDTGKEFAVKILNNLKCKLAGGCPP) is a host defense peptide with potent antimicrobial and anticancer activities, first isolated from the skin of the American bullfrog Lithobates catesbeianus . The peptide is 31 amino acid residues long, cationic and amphipathic. Two-dimensional NMR spectroscopy was employed to characterise its three-di...
Article
Full-text available
The prevalence of cancer as a threat to human life, responsible for 9.6 million deaths worldwide in 2018, motivates the search for new anticancer agents. While many options are currently available for treatment, these are often expensive and impact the human body unfavourably. Anticancer peptides represent a promising emerging field of anticancer t...
Conference Paper
The search for novel anticancer agents is motivated by the prevalent threat to human life posed by cancer, responsible for 9.6 million deaths worldwide in 2018. Although a number of treatment options are currently available, these are typically costly and have severe impact on the human body. Antimicrobial peptides are a diversiform class of well-s...
Preprint
Full-text available
The prevalence of cancer as a threat to human life, responsible for 9.6 million deaths worldwide in 2018, motivates the search for new anticancer agents. While many options are currently available for treatment, these are often expensive and impact the human body unfavourably. Anticancer peptides represent a promising emerging field of anticancer t...
Article
Full-text available
The growing prevalence of resistance to antibiotics motivates the search for new antibacterial agents. Antimicrobial peptides are a diverse class of well-studied membrane-active peptides which function as part of the innate host defence system, and form a promising avenue in antibiotic drug research. Some antimicrobial peptides exhibit toxicity aga...
Conference Paper
The increasing prevalence of multi-drug antibiotic resistance provides the motivation for the pursuit of new antibacterial agents. As few cases of bacterial resistance to antimicrobial peptides (AMPs) have been identified to-date, this diversiform class of membrane-active peptides, which in nature function as part of the innate host defence system,...
Conference Paper
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC) is a 24-amino acid residue host-defence peptide, first isolated from the skin secretions of the foothill yellow-legged frog Rana boylii. The peptide is of interest as it shows broad-spectrum antimicrobial activity, and is particularly effective against opportunistic yeast pathogens. Its potential for clinica...
Conference Paper
We have studied structural properties of maximin 3, a 27-residue long cationic antimicrobial peptide which possesses antimicrobial, antitumor, spermicidal and anti-HIV activities. The three-dimensional structural model was obtained using NMR and molecular modelling techniques. Maximin 3 possesses amphipathic character and adopts α-helical conformat...
Conference Paper
Maximin-3 (GIGGKILSGLKTALKGAAKELASTYLH) is a 27-residue long cationic antimicrobial peptide found in the skin secretion and brain of the Chinese red belly toad Bombina maxima. The peptide is interesting as it possesses anti-HIV activity, not found in the other maximin peptides, in addition to its antimicrobial, antitumor, and spermicidal activities...
Conference Paper
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC), first isolated from skin secretions of the foothill yellow-legged frog Rana boylii, is particularly effective against C. albicans, and is also active against E. coli and S. aureus. The structures of brevinin-1BYa and its less-potent analogue [C18S,C24S]brevinin-1BYa were investigated in various solution and...
Conference Paper
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC), first isolated from skin secretions of the foothill yellow-legged frog Rana boylii, is particularly effective against C. albicans, and is also active against E. coli and S. aureus. The structures of brevinin-1BYa and its less-potent analogue [C18S,C24S]brevinin-1BYa were investigated in various solution and...
Conference Paper
Brevinin-1BYa (FLPILASLAAKFGPKLFCLVTKKC), first isolated from skin secretions of the foothill yellow-legged frog Rana boylii, is particularly effective against C. albicans, and is also active against E. coli and S. aureus. The structures of brevinin-1BYa and its less-potent analogue [C18S,C24S]brevinin-1BYa were investigated in various solution and...

Questions

Question (1)
Question
Hi all,
I am interested in peptide structure prediction services, both secondary structure and tertiary structure. Protein prediction services that can predict structures of short peptides are also of interest to me.
Could anybody provide me with a list of such structure prediction services, or name services that they are familiar with?
Many thanks,
Patrick

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Projects

Projects (2)
Project
Characterise the three-dimensional structures of antimicrobial peptides, characterise their interactions with membranes, and develop an understanding of the relationship between the peptide structures and their biological activities.