Bioinformatics tools for protein modeling in neurodegenerative diseases

Global burden of Alzheimer’s disease and other dementias attributed to metabolic risks from 1990 to 2021: results from the global burden of disease study 2021

10.1186/s12888-024-06375-x · doi-reference

Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: a discrete molecular dynamics study

10.1529/biophysj.106.097766 · doi-reference

The I-TASSER Suite: protein structure and function prediction

10.1038/nmeth.3213 · doi-reference

Bioinformatics tools and data resources for assay development of fluid protein biomarkers

10.1186/s40364-022-00425-w · doi-reference

SWISS-MODEL: homology modelling of protein structures and complexes

10.1093/nar/gky427 · doi-reference

Ab initio discrete molecular dynamics approach to protein folding and aggregation

10.1016/s0076-6879(06)12019-4 · doi-reference

In silico study of amyloid β-protein folding and oligomerization

10.1073/pnas.0408153101 · doi-reference

AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

10.1002/jcc.21334 · doi-reference

αB-Crystallin chaperone inhibits Aβ aggregation by capping the β-sheet-rich oligomers and fibrils

10.1021/acs.jpcb.0c07256 · doi-reference

REMD simulations of full-length alpha-synuclein together with ligands reveal binding region and effect on amyloid conversion

10.3390/ijms231911545 · doi-reference

The amyloid hypothesis of Alzheimer's disease at 25 years

10.15252/emmm.201606210 · doi-reference

Comparative protein modelling by satisfaction of spatial restraints

10.1006/jmbi.1993.1626 · doi-reference

I-TASSER: a unified platform for automated protein structure and function prediction

10.1038/nprot.2010.5 · doi-reference

The future is precision medicine-guided diagnoses, preventions and treatments for neurodegenerative diseases

10.3389/fnagi.2023.1128619 · doi-reference

The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction

10.1093/nar/gkr184 · doi-reference

Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases

10.1186/s13024-023-00651-2 · doi-reference

UCSF Chimera - a visualization system for exploratory research and analysis

10.1002/jcc.20084 · doi-reference

Structure and engineering of tandem repeat lectins

10.1016/j.sbi.2019.11.006 · doi-reference

Protein structure prediction via deep learning: an in-depth review

10.3389/fphar.2025.1498662 · doi-reference

Molecular docking: a powerful approach for structure-based drug discovery

10.2174/157340911795677602 · doi-reference

Mechanistic models of protein aggregation across length-scales and time-scales: from the test tube to neurodegenerative disease

10.3389/fnins.2022.909861 · doi-reference

Open science in precision medicine for neurodegenerative diseases

10.1038/d41573-024-00017-3 · doi-reference

GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure

10.1093/nar/gkz288 · doi-reference

Zebrafish an experimental model of Huntington’s disease: molecular aspects, therapeutic targets and current challenges

10.1007/s11033-021-06787-y · doi-reference

Advances in protein structure prediction and design

10.1038/s41580-019-0163-x · doi-reference

Computational and functional insights of protein misfolding in neurodegeneration

10.1007/978-3-031-31978-5_18 · doi-reference

The amyloid state and its association with protein misfolding diseases

10.1038/nrm3810 · doi-reference

Protein structure prediction and analysis using the Robetta server

10.1093/nar/gkh468 · doi-reference

The Phyre2 web portal for protein modeling, prediction and analysis

10.1038/nprot.2015.053 · doi-reference

Protein structure prediction on the Web: a case study using the Phyre server

10.1038/nprot.2009.2 · doi-reference

Highly accurate protein structure prediction with AlphaFold

10.1038/s41586-021-03819-2 · doi-reference

Critical aggregation concentration and reversibility of amyloid-β (1–40) oligomers

10.1016/j.abb.2024.110179 · doi-reference

GalaxyRefine: protein structure refinement driven by side-chain repacking

10.1093/nar/gkt458 · doi-reference

Protein misfolding inside cells: the case of Huntingtin and Huntington's disease

10.1002/iub.111 · doi-reference

Homology modeling in the time of collective and artificial intelligence

10.1016/j.csbj.2020.11.007 · doi-reference

Advancing personalized medicine in neurodegenerative diseases: the role of epigenetics and pharmacoepigenomics in pharmacotherapy

10.1016/j.phrs.2024.107247 · doi-reference

A computational approach to investigate TDP-43C-terminal fragments aggregation in amyotrophic lateral sclerosis

10.3390/biom11121905 · doi-reference

Transforming neurodegenerative disorder care with machine learning: strategies and applications

10.1016/j.neuroscience.2025.03.036 · doi-reference

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

10.1038/s41592-019-0666-6 · doi-reference

Molecular docking and structure-based drug design strategies

10.3390/molecules200713384 · doi-reference