Substitution scoring matrices for proteins‐An overview

R Trivedi, HA Nagarajaram - Protein Science, 2020 - Wiley Online Library
Sequence analysis is the primary and simplest approach to discover structural, functional
and evolutionary details of related proteins. All the alignment based approaches of …

Computational approaches for identifying disease-causing mutations in proteins

M Pandey, SK Shah, MM Gromiha - Advances in protein chemistry and …, 2024 - Elsevier
Advancements in genome sequencing have expanded the scope of investigating mutations
in proteins across different diseases. Amino acid mutations in a protein alter its structure …

The distal-proximal relationships among the human moonlighting proteins: Evolutionary hotspots and darwinian checkpoints

D Nawn, SS Hassan, M Sil, A Ghosh… - International Journal of …, 2024 - Elsevier
Moonlighting proteins, known for their ability to perform multiple, often unrelated functions
within a single polypeptide chain, challenge the traditional “one gene, one protein, one …

Rooting the ribosomal tree of life

GP Fournier, JP Gogarten - Molecular biology and evolution, 2010 - academic.oup.com
The origin of the genetic code and the rooting of the tree of life (ToL) are two of the most
challenging problems in the study of life's early evolution. Although both have been the …

Expansion of lysine-rich repeats in Plasmodium proteins generates novel localization sequences that target the periphery of the host erythrocyte

HM Davies, K Thalassinos, AR Osborne - Journal of Biological Chemistry, 2016 - jbc.org
Repetitive low complexity sequences, mostly assumed to have no function, are common in
proteins that are exported by the malaria parasite into its host erythrocyte. We identify a …

Exploring genomes for glycosyltransferases

SF Hansen, E Bettler, Å Rinnan, SB Engelsen… - Molecular …, 2010 - pubs.rsc.org
Glycosyltransferases are one of the largest and most diverse enzyme groups in Nature. They
catalyse the synthesis of glycosidic linkages by the transfer of a sugar residue from a donor …

The evolution of genomic GC content undergoes a rapid reversal within the genus Plasmodium

H Nikbakht, X **a, DA Hickey - Genome, 2014 - cdnsciencepub.com
The genome of the malarial parasite Plasmodium falciparum is extremely AT rich. This bias
toward a low GC content is a characteristic of several, but not all, species within the genus …

GC bias lead to increased small amino acids and random coils of proteins in cold-water fishes

D Zhang, P Hu, T Liu, J Wang, S Jiang, Q Xu, L Chen - BMC genomics, 2018 - Springer
Background Temperature adaptation of biological molecules is fundamental in evolutionary
studies but remains unsolved. Fishes living in cold water are adapted to low temperatures …

A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model

AI Castillo, ADL Nelson, AK Haug-Baltzell, E Lyons - Database, 2018 - academic.oup.com
Integrated platforms for storage, management, analysis and sharing of large quantities of
omics data have become fundamental to comparative genomics. CoGe (https …

Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction

E Bultrini, K Brick, S Mukherjee, Y Zhang, F Silvestrini… - BMC genomics, 2009 - Springer
Background Subtelomeric RIFIN genes constitute the most abundant multigene family in
Plasmodium falciparum. RIFIN products are targets for the human immune response and …