Computational methods and tools in antimicrobial peptide research

PGA Aronica, LM Reid, N Desai, J Li… - Journal of Chemical …, 2021 - ACS Publications
The evolution of antibiotic-resistant bacteria is an ongoing and troubling development that
has increased the number of diseases and infections that risk going untreated. There is an …

Rational design of stapled antimicrobial peptides

YH You, HY Liu, YZ Zhu, H Zheng - Amino Acids, 2023 - Springer
The global increase in antimicrobial drug resistance has dramatically reduced the
effectiveness of traditional antibiotics. Structurally diverse antibiotics are urgently needed to …

[HTML][HTML] Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm

P Chacon, F Moran, JF Diaz, E Pantos, JM Andreu - Biophysical Journal, 1998 - cell.com
Small-angle x-ray solution scattering (SAXS) is analyzed with a new method to retrieve
convergent model structures that fit the scattering profiles. An arbitrary hexagonal packing of …

[PDF][PDF] Genetic and evolutionary algorithms

G Jones - Encyclopedia of computational chemistry, 1998 - Citeseer
Genetic and Evolutionary Algorithms Page 1 CGA04- Genetic and Evolutionary Algorithms
Gareth Jones University of Sheffield, UK 1 Introduction 2 Evolutionary Algorithms 3 Applications …

Progress in protein structure prediction

DT Jones - Current Opinion in Structural Biology, 1997 - Elsevier
If protein structure prediction methods are to make any impact on the impending onerous
task of analyzing the large numbers of unknown protein sequences generated by the …

Evolutionary algorithms in computer-aided molecular design

DE Clark, DR Westhead - Journal of Computer-Aided Molecular Design, 1996 - Springer
In recent years, search and optimisation algorithms inspired by evolutionary processes have
been applied with marked success to a wide variety of problems in diverse fields of study. In …

CODA: a combined algorithm for predicting the structurally variable regions of protein models

CM Deane, TL Blundell - Protein Science, 2001 - Wiley Online Library
CODA, an algorithm for predicting the variable regions in proteins, combines FREAD a
knowledge based approach, and PETRA, which constructs the region ab initio. FREAD …

Genetic algorithms for protein structure prediction

JT Pedersen, J Moult - Current Opinion in Structural Biology, 1996 - Elsevier
Genetic algorithms are a general class of search methods that mimic natural gene-based
optimization mechanisms. Mutation, cross-over and replication operations are performed on …

The current state of the art in protein structure prediction

J Moult - Current opinion in biotechnology, 1996 - Elsevier
The capabilities of current protein structure prediction methods have been assessed from
the outcome of a set of blind tests. In comparative modeling, many of the numerical methods …

Protein folding simulations with genetic algorithms and a detailed molecular description

JT Pedersen, J Moult - Journal of Molecular Biology, 1997 - Elsevier
We have explored the application of genetic algorithms (GA) to the determination of protein
structure from sequence, using a full atom representation. A free energy function with point …