Research graph
References from Bioinformatics tools for protein modeling in neurodegenerative diseases. Local targets link to admitted publications; unresolved targets remain external evidence.
α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation
10.1038/nature10324 · 2011 · External reference
QMEAN: a comprehensive scoring function for model quality assessment
10.1002/prot.21715 · 2008 · External reference
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
10.1093/nar/gku340 · 2014 · External reference
Data and sample sharing as an enabler for large-scale biomarker research and development: The EPND perspective
10.3389/fneur.2022.1031091 · 2022 · External reference
Protein misfolding, amyloid formation, and human disease: A summary of progress over the last decade
10.1146/annurev-biochem-061516-045115 · 2017 · External reference
Mechanical probes of SOD1 predict systematic trends in metal and dimer affinity of ALS-associated mutants
10.1016/j.jmb.2012.12.022 · 2013 · External reference
Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
10.1016/j.jmb.2009.07.008 · 2009 · External reference
Pathology of neurodegenerative diseases
10.1101/cshperspect.a028035 · 2017 · External reference
10.1002/0471250953.bi0506s15
10.1002/0471250953.bi0506s15 · External reference
Evaluating alphafold for clinical pharmacology and pharmacogenetics: a case-study of huntingtin variants linked to Huntington’s disease
10.1208/s12248-024-00969-9 · 2024 · External reference
Molecular docking and structure-based drug design strategies
10.3390/molecules200713384 · 2015 · External reference
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
10.1038/s41592-019-0666-6 · 2020 · External reference
Transforming neurodegenerative disorder care with machine learning: strategies and applications
10.1016/j.neuroscience.2025.03.036 · 2025 · External reference
A computational approach to investigate TDP-43C-terminal fragments aggregation in amyotrophic lateral sclerosis
10.3390/biom11121905 · 2021 · External reference
Advancing personalized medicine in neurodegenerative diseases: the role of epigenetics and pharmacoepigenomics in pharmacotherapy
10.1016/j.phrs.2024.107247 · 2024 · External reference
Homology modeling in the time of collective and artificial intelligence
10.1016/j.csbj.2020.11.007 · 2020 · External reference
Protein misfolding inside cells: the case of Huntingtin and Huntington's disease
10.1002/iub.111 · 2008 · External reference
GalaxyRefine: protein structure refinement driven by side-chain repacking
10.1093/nar/gkt458 · 2013 · External reference
Biomarkers for neurodegenerative diseases in regulatory decision-making by the European Medicines Agency
2025 · External reference
Critical aggregation concentration and reversibility of amyloid-β (1–40) oligomers
10.1016/j.abb.2024.110179 · 2024 · External reference
Structural bioinformatic study of six human olfactory receptors and their AlphaFold3 predicted water-soluble QTY variants and OR1A2 with an odorant octanoate and TAAR9 with spermidine
2024 · External reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · 2021 · External reference
Protein structure prediction on the Web: a case study using the Phyre server
10.1038/nprot.2009.2 · 2009 · External reference
The Phyre2 web portal for protein modeling, prediction and analysis
10.1038/nprot.2015.053 · 2015 · External reference
Protein structure prediction and analysis using the Robetta server
10.1093/nar/gkh468 · 2004 · External reference
The amyloid state and its association with protein misfolding diseases
10.1038/nrm3810 · 2014 · External reference
Computational and functional insights of protein misfolding in neurodegeneration
10.1007/978-3-031-31978-5_18 · 2023 · External reference
Advances in protein structure prediction and design
10.1038/s41580-019-0163-x · 2019 · External reference
Zebrafish an experimental model of Huntington’s disease: molecular aspects, therapeutic targets and current challenges
10.1007/s11033-021-06787-y · 2021 · External reference
Ab initio protein structure prediction
2009 · External reference
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
10.1093/nar/gkz288 · 2019 · External reference
Open science in precision medicine for neurodegenerative diseases
10.1038/d41573-024-00017-3 · 2024 · External reference
Unresolved reference
External reference
Protein fold recognition and threading
2008 · External reference
Mechanistic models of protein aggregation across length-scales and time-scales: from the test tube to neurodegenerative disease
10.3389/fnins.2022.909861 · 2022 · External reference
Molecular docking: a powerful approach for structure-based drug discovery
10.2174/157340911795677602 · 2011 · External reference
Protein structure prediction via deep learning: an in-depth review
10.3389/fphar.2025.1498662 · 2025 · External reference
Structure and engineering of tandem repeat lectins
10.1016/j.sbi.2019.11.006 · 2020 · External reference
Unresolved reference
2016 · External reference
UCSF Chimera - a visualization system for exploratory research and analysis
10.1002/jcc.20084 · 2004 · External reference
Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases
10.1186/s13024-023-00651-2 · 2024 · External reference
Developing a molecular dynamics force field for both folded and disordered protein states
2018 · External 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 · 2011 · External reference
The future is precision medicine-guided diagnoses, preventions and treatments for neurodegenerative diseases
10.3389/fnagi.2023.1128619 · 2023 · External reference
I-TASSER: a unified platform for automated protein structure and function prediction
10.1038/nprot.2010.5 · 2010 · External reference
Comparative protein modelling by satisfaction of spatial restraints
10.1006/jmbi.1993.1626 · 1993 · External reference
The amyloid hypothesis of Alzheimer's disease at 25 years
10.15252/emmm.201606210 · 2016 · External reference
REMD simulations of full-length alpha-synuclein together with ligands reveal binding region and effect on amyloid conversion
10.3390/ijms231911545 · 2022 · External reference
Quantum computing and the future of neurodegeneration and mental health research
2024 · External reference
αB-Crystallin chaperone inhibits Aβ aggregation by capping the β-sheet-rich oligomers and fibrils
10.1021/acs.jpcb.0c07256 · 2020 · External reference
Protein homology detection by HMM–HMM comparison
2005 · External reference
Revolutionizing structural biology: AI-driven protein structure prediction from AlphaFold to next-generation innovations
2025 · External reference
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
10.1002/jcc.21334 · 2010 · External reference
In silico study of amyloid β-protein folding and oligomerization
10.1073/pnas.0408153101 · 2004 · External reference
Ab initio discrete molecular dynamics approach to protein folding and aggregation
10.1016/s0076-6879(06)12019-4 · 2006 · External reference
SWISS-MODEL: homology modelling of protein structures and complexes
10.1093/nar/gky427 · 2018 · External reference
Bioinformatics tools and data resources for assay development of fluid protein biomarkers
10.1186/s40364-022-00425-w · 2022 · External reference
Unresolved reference
2017 · External reference
The I-TASSER Suite: protein structure and function prediction
10.1038/nmeth.3213 · 2015 · External reference
Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: a discrete molecular dynamics study
10.1529/biophysj.106.097766 · 2007 · External reference
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 · 2024 · External reference
10.1002/0471250953.bi0506s15
10.1002/0471250953.bi0506s15 · ExternalCitation · doi-reference
Protein misfolding inside cells: the case of Huntingtin and Huntington's disease
10.1002/iub.111 · ExternalCitation · doi-reference
UCSF Chimera - a visualization system for exploratory research and analysis
10.1002/jcc.20084 · ExternalCitation · doi-reference
AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
10.1002/jcc.21334 · ExternalCitation · doi-reference
QMEAN: a comprehensive scoring function for model quality assessment
10.1002/prot.21715 · ExternalCitation · doi-reference
Comparative protein modelling by satisfaction of spatial restraints
10.1006/jmbi.1993.1626 · ExternalCitation · doi-reference
Computational and functional insights of protein misfolding in neurodegeneration
10.1007/978-3-031-31978-5_18 · ExternalCitation · doi-reference
Zebrafish an experimental model of Huntington’s disease: molecular aspects, therapeutic targets and current challenges
10.1007/s11033-021-06787-y · ExternalCitation · doi-reference
Critical aggregation concentration and reversibility of amyloid-β (1–40) oligomers
10.1016/j.abb.2024.110179 · ExternalCitation · doi-reference
Homology modeling in the time of collective and artificial intelligence
10.1016/j.csbj.2020.11.007 · ExternalCitation · doi-reference
Refinement of Protein Structures into Low-Resolution Density Maps Using Rosetta
10.1016/j.jmb.2009.07.008 · ExternalCitation · doi-reference
Mechanical probes of SOD1 predict systematic trends in metal and dimer affinity of ALS-associated mutants
10.1016/j.jmb.2012.12.022 · ExternalCitation · doi-reference
Transforming neurodegenerative disorder care with machine learning: strategies and applications
10.1016/j.neuroscience.2025.03.036 · ExternalCitation · doi-reference
Advancing personalized medicine in neurodegenerative diseases: the role of epigenetics and pharmacoepigenomics in pharmacotherapy
10.1016/j.phrs.2024.107247 · ExternalCitation · doi-reference
Structure and engineering of tandem repeat lectins
10.1016/j.sbi.2019.11.006 · ExternalCitation · doi-reference
Ab initio discrete molecular dynamics approach to protein folding and aggregation
10.1016/s0076-6879(06)12019-4 · ExternalCitation · doi-reference
αB-Crystallin chaperone inhibits Aβ aggregation by capping the β-sheet-rich oligomers and fibrils
10.1021/acs.jpcb.0c07256 · ExternalCitation · doi-reference
Open science in precision medicine for neurodegenerative diseases
10.1038/d41573-024-00017-3 · ExternalCitation · doi-reference
α-Synuclein occurs physiologically as a helically folded tetramer that resists aggregation
10.1038/nature10324 · ExternalCitation · doi-reference
The I-TASSER Suite: protein structure and function prediction
10.1038/nmeth.3213 · ExternalCitation · doi-reference
Protein structure prediction on the Web: a case study using the Phyre server
10.1038/nprot.2009.2 · ExternalCitation · doi-reference
I-TASSER: a unified platform for automated protein structure and function prediction
10.1038/nprot.2010.5 · ExternalCitation · doi-reference
The Phyre2 web portal for protein modeling, prediction and analysis
10.1038/nprot.2015.053 · ExternalCitation · doi-reference
The amyloid state and its association with protein misfolding diseases
10.1038/nrm3810 · ExternalCitation · doi-reference
Advances in protein structure prediction and design
10.1038/s41580-019-0163-x · ExternalCitation · doi-reference
Highly accurate protein structure prediction with AlphaFold
10.1038/s41586-021-03819-2 · ExternalCitation · doi-reference
Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
10.1038/s41592-019-0666-6 · ExternalCitation · doi-reference
In silico study of amyloid β-protein folding and oligomerization
10.1073/pnas.0408153101 · ExternalCitation · doi-reference
Protein structure prediction and analysis using the Robetta server
10.1093/nar/gkh468 · ExternalCitation · 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 · ExternalCitation · doi-reference
GalaxyRefine: protein structure refinement driven by side-chain repacking
10.1093/nar/gkt458 · ExternalCitation · doi-reference
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
10.1093/nar/gku340 · ExternalCitation · doi-reference
SWISS-MODEL: homology modelling of protein structures and complexes
10.1093/nar/gky427 · ExternalCitation · doi-reference
GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure
10.1093/nar/gkz288 · ExternalCitation · doi-reference
Pathology of neurodegenerative diseases
10.1101/cshperspect.a028035 · ExternalCitation · doi-reference
Protein misfolding, amyloid formation, and human disease: A summary of progress over the last decade
10.1146/annurev-biochem-061516-045115 · ExternalCitation · doi-reference
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 · ExternalCitation · doi-reference
Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases
10.1186/s13024-023-00651-2 · ExternalCitation · doi-reference
Bioinformatics tools and data resources for assay development of fluid protein biomarkers
10.1186/s40364-022-00425-w · ExternalCitation · doi-reference
Evaluating alphafold for clinical pharmacology and pharmacogenetics: a case-study of huntingtin variants linked to Huntington’s disease
10.1208/s12248-024-00969-9 · ExternalCitation · doi-reference
The amyloid hypothesis of Alzheimer's disease at 25 years
10.15252/emmm.201606210 · ExternalCitation · doi-reference
Role of electrostatic interactions in amyloid β-protein (Aβ) oligomer formation: a discrete molecular dynamics study
10.1529/biophysj.106.097766 · ExternalCitation · doi-reference
Molecular docking: a powerful approach for structure-based drug discovery
10.2174/157340911795677602 · ExternalCitation · doi-reference
The future is precision medicine-guided diagnoses, preventions and treatments for neurodegenerative diseases
10.3389/fnagi.2023.1128619 · ExternalCitation · doi-reference
Data and sample sharing as an enabler for large-scale biomarker research and development: The EPND perspective
10.3389/fneur.2022.1031091 · ExternalCitation · 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 · ExternalCitation · doi-reference
Protein structure prediction via deep learning: an in-depth review
10.3389/fphar.2025.1498662 · ExternalCitation · doi-reference
A computational approach to investigate TDP-43C-terminal fragments aggregation in amyotrophic lateral sclerosis
10.3390/biom11121905 · ExternalCitation · doi-reference
REMD simulations of full-length alpha-synuclein together with ligands reveal binding region and effect on amyloid conversion
10.3390/ijms231911545 · ExternalCitation · doi-reference
Molecular docking and structure-based drug design strategies
10.3390/molecules200713384 · ExternalCitation · doi-reference
