Protein contacts, inter-residue interactions and side-chain modelling

G Faure, A Bornot, AG de Brevern - Biochimie, 2008 - Elsevier
Three-dimensional structures of proteins are the support of their biological functions. Their
folds are stabilized by contacts between residues. Inner protein contacts are generally …

A unified approach to protein domain parsing with inter-residue distance matrix

K Zhu, H Su, Z Peng, J Yang - Bioinformatics, 2023 - academic.oup.com
Motivation It is fundamental to cut multi-domain proteins into individual domains, for precise
domain-based structural and functional studies. In the past, sequence-based and structure …

SWORD2: hierarchical analysis of protein 3D structures

G Cretin, T Galochkina, Y Vander Meersche… - Nucleic acids …, 2022 - academic.oup.com
Understanding the functions and origins of proteins requires splitting these macromolecules
into fragments that could be independent in terms of folding, activity, or evolution. For that …

Evolutionary transitions in protein fold space

WR Taylor - Current opinion in structural biology, 2007 - Elsevier
With the number of known protein folds potentially approaching completion, the problems
associated with their systematic classification are evaluated. It is argued that it will be …

Auditory attention state decoding for the quiet and hypothetical environment: a comparison between bLSTM and SVM

F Nasrin, NI Ahmed, MA Rahman - Proceedings of International …, 2020 - Springer
Auditory attention is a cognitive process that involves listeners to give their attention, which
the listener wants to focus on. Consequently, the auditory attention processes their stimulus …

Local protein structures

B Offmann, M Tyagi, AG de Brevern - Current Bioinformatics, 2007 - ingentaconnect.com
Protein structures are classically described as composed of two regular states, the α-helices
and the β-strands and one non-regular and variable state, the coil. Nonetheless, this simple …

SARS-CoV 2 spike protein S1 subunit as an ideal target for stable vaccines: A bioinformatic study

SN Nagesha, BN Ramesh, C Pradeep… - Materials Today …, 2022 - Elsevier
The Covid-19 a pandemic infectious disease and affected life across the world resulting in
over 188.65 million confirmed cases across 223 countries, territories and areas with 4.06 …

An ambiguity principle for assigning protein structural domains

G Postic, Y Ghouzam, R Chebrek, JC Gelly - Science advances, 2017 - science.org
Ambiguity is the quality of being open to several interpretations. For an image, it arises when
the contained elements can be delimited in two or more distinct ways, which may cause …

ICARUS: flexible protein structural alignment based on Protein Units

G Cretin, C Périn, N Zimmermann, T Galochkina… - …, 2023 - academic.oup.com
Motivation Alignment of protein structures is a major problem in structural biology. The first
approach commonly used is to consider proteins as rigid bodies. However, alignment of …

ProCKSI: a decision support system for protein (structure) comparison, knowledge, similarity and information

D Barthel, JD Hirst, J Błażewicz, EK Burke… - BMC …, 2007 - Springer
Background We introduce the decision support system for Protein (Structure) Comparison,
Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein …