Search strategies and evaluation in protein–protein docking: principles, advances and challenges

SY Huang - Drug discovery today, 2014 - Elsevier
Highlights•Search strategies of current protein–protein docking algorithms were
reviewed.•Challenges and future directions of established approaches were discussed.•Post …

Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

SY Huang - Drug discovery today, 2015 - Elsevier
Highlights•The development and trend of global protein–protein docking was briefly
reviewed.•18 global docking/scoring protocols were assessed on the latest docking …

Contacts-based prediction of binding affinity in protein–protein complexes

A Vangone, AMJJ Bonvin - elife, 2015 - elifesciences.org
Almost all critical functions in cells rely on specific protein–protein interactions.
Understanding these is therefore crucial in the investigation of biological systems. Despite …

Identification of shared tumor epitopes from endogenous retroviruses inducing high-avidity cytotoxic T cells for cancer immunotherapy

P Bonaventura, V Alcazer, V Mutez, L Tonon… - Science …, 2022 - science.org
Human endogenous retroviruses (HERVs) represent 8% of the human genome. HERV
products may represent tumor antigens relevant for cancer immunotherapy. We developed a …

Immunoinformatics-aided design of a peptide based multiepitope vaccine targeting glycoproteins and membrane proteins against monkeypox virus

N Akhtar, V Kaushik, RK Grewal, AK Wani… - Viruses, 2022 - mdpi.com
Monkeypox is a self-limiting zoonotic viral disease and causes smallpox-like symptoms. The
disease has a case fatality ratio of 3–6% and, recently, a multi-country outbreak of the …

[PDF][PDF] Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons

AT Tuukkanen, A Spilotros, DI Svergun - IUCrJ, 2017 - journals.iucr.org
Small-angle X-ray scattering (SAXS) is an established technique that provides low-
resolution structural information on macromolecular solutions. Recent decades have …

Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies

G Poli, A Martinelli, T Tuccinardi - Journal of Enzyme Inhibition and …, 2016 - Taylor & Francis
Ligand-protein docking is one of the most common techniques used in virtual screening
campaigns. Despite the large number of docking software available, there is still the need of …

PPCheck: A webserver for the quantitative analysis of protein-protein interfaces and prediction of residue hotspots

A Sukhwal, R Sowdhamini - Bioinformatics and biology …, 2015 - journals.sagepub.com
Background Modeling protein-protein interactions (PPIs) using docking algorithms is useful
for understanding biomolecular interactions and mechanisms. Typically, a docking algorithm …

Docking approaches for modeling multi-molecular assemblies

M Rosell, J Fernández-Recio - Current opinion in structural biology, 2020 - Elsevier
Highlights•Computational docking methods can provide relevant structural data on protein
complexes.•Template-based docking and integrative modeling are currently the most …

T cell epitope based vaccine design while targeting outer capsid proteins of rotavirus strains infecting neonates: an immunoinformatics approach

AD Sharma, RK Grewal, S Gorle… - Journal of …, 2024 - Taylor & Francis
Gastrointestinal diarrhea is majorly caused by the rotavirus (RV) in the children who
generally are under the age group of 5 years. WHO estimates that∼ 95% of the children …