ArticleMethods in molecular biology (Clifton, N.J.)2024
AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses.
Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
4 citing papers in PubMed.
- Special Issue "Molecular Dynamics Simulations and Structural Analysis of Protein Domains (2nd Edition)".International journal of molecular sciences · 2026Article
- Comparative Analysis of Banana Lectins rBanLec-Like and H84T-BanLec: An In Silico and In Vitro Approach.The protein journal · 2026Article
- New Insights into Bioactive Peptides: Design, Synthesis, Structure-Activity Relationship.International journal of molecular sciences · 2024Article
- Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
AlphaFold2 (AF2) has emerged in recent years as a groundbreaking innovation that has revolutionized several scientific fields, in particular structural biology, drug design, and the elucidation of disease mechanisms. Many scientists now use AF2 on a daily basis, including non-specialist users. This chapter is aimed at the latter. Tips and tricks for getting the most out of AF2 to produce a high-quality biological model are discussed here. We suggest to non-specialist users how to maintain a critical perspective when working with AF2 models and provide guidelines on how to properly evaluate them. After showing how to perform our own structure prediction using ColabFold, we list several ways to improve AF2 models by adding information that is missing from the original AF2 model. By using software such as AlphaFill to add cofactors and ligands to the models, or MODELLER to add disulfide bridges between cysteines, we guide users to build a high-quality biological model suitable for applications such as drug design, protein interaction, or molecular dynamics studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.