Supervised learning with decision tree-based methods in computational and systems biology

P Geurts, A Irrthum, L Wehenkel - Molecular Biosystems, 2009 - pubs.rsc.org
At the intersection between artificial intelligence and statistics, supervised learning allows
algorithms to automatically build predictive models from just observations of a system …

A review on the development of bacterial multi-epitope recombinant protein vaccines via reverse vaccinology

Y Li, MHR Farhan, X Yang, Y Guo, Y Sui, J Chu… - International Journal of …, 2024 - Elsevier
Bacterial vaccines play a crucial role in combating bacterial infectious diseases. Apart from
the prevention of disease, bacterial vaccines also help to reduce the mortality rates in …

Biological Systems Discovery In Silico: Radical S-Adenosylmethionine Protein Families and Their Target Peptides for Posttranslational Modification

DH Haft, MK Basu - Journal of bacteriology, 2011 - journals.asm.org
Data mining methods in bioinformatics and comparative genomics commonly rely on
working definitions of protein families from prior computation. Partial phylogenetic profiling …

Metals in protein structures: a review of their principal features

MM Harding, MW Nowicki… - Crystallography …, 2010 - Taylor & Francis
Metals are present in more than one-third of all proteins as they occur in nature, and are
usually important in biological function or maintenance of the structure. Some are present as …

Diversity, structure and regulation of microbial metallothionein: metal resistance and possible applications in sequestration of toxic metals

S Chatterjee, S Kumari, S Rath, M Priyadarshanee… - Metallomics, 2020 - academic.oup.com
Metallothioneins (MTs) are a group of cysteine-rich, universal, low molecular weight proteins
distributed widely in almost all major taxonomic groups ranging from tiny microbes to highly …

Designing of a multi-epitopes based vaccine against Haemophilius parainfluenzae and its validation through integrated computational approaches

SA Ghaffar, H Tahir, S Muhammad, M Shahid… - Frontiers in …, 2024 - frontiersin.org
Haemophilus parainfluenzae is a Gram-negative opportunist pathogen within the mucus of
the nose and mouth without significant symptoms and has an ability to cause various …

Bioinformatical approaches to characterize intrinsically disordered/unstructured proteins

Z Dosztányi, B Mészáros, I Simon - Briefings in bioinformatics, 2010 - academic.oup.com
Intrinsically disordered/unstructured proteins exist without a stable three-dimensional (3D)
structure as highly flexible conformational ensembles. The available genome sequences …

The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function

M Punta, Y Ofran - PLoS computational biology, 2008 - journals.plos.org
Choosing the right function prediction tools. The vast majority of known proteins have not yet
been characterized experimentally, and there is very little that is known about their function …

Metalloproteomics: forward and reverse approaches in metalloprotein structural and functional characterization

W Shi, MR Chance - Current opinion in chemical biology, 2011 - Elsevier
About one-third of all proteins are associated with a metal. Metalloproteomics is defined as
the structural and functional characterization of metalloproteins on a genome-wide scale …

mebipred: identifying metal-binding potential in protein sequence

AA Aptekmann, J Buongiorno, D Giovannelli… - …, 2022 - academic.oup.com
Motivation metal-binding proteins have a central role in maintaining life processes. Nearly
one-third of known protein structures contain metal ions that are used for a variety of needs …