afdb_clusters v1.0: AlphaFold-derived structure-based dataset for benchmarking MSA tools
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| Formato: | Recurso digital |
| Lenguaje: | inglés |
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Zenodo
2025
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| _version_ | 1866902271904710656 |
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| author | Zielezinski, Andrzej Gudyś, Adam Deorowicz, Sebastian |
| author_facet | Zielezinski, Andrzej Gudyś, Adam Deorowicz, Sebastian |
| contents | <p>This dataset contains 1,166 protein families derived from AlphaFold Database Clusters. The families vary in size, ranging from approximately 1,000 to 680,000 sequences.</p> <p>For each family, the dataset provides:</p> <ul> <li>protein sequences (FASTA format)</li> <li>download URLs for AlphaFold-predicted PDB structures corresponding to each protein sequence</li> </ul> <p>These paired sequences and structures enable structure-based benchmarking of multiple sequence alignment (MSA) tools using the Local Distance Difference Test (LDDT) score, computed with the FoldMason tool.</p> <h3><strong>Directory structure</strong></h3> <p>The dataset contains two main directories:</p> <ul> <li><code>fasta/</code> – protein sequences for each cluster [FASTA format]</li> <li><code>pdb_urls/</code> – text files containing download URLs for AlphaFold PDB structures for each sequence in the cluster [TXT format]</li> </ul> <p>A metadata file (<code>metadata.tsv</code>) is also included, providing detailed information for each cluster.</p> <h3><strong>Metadata</strong></h3> <p>A metadata file (<code>metadata.tsv</code>) provides:</p> <ul> <li><strong>cluster_id</strong> – Cluster identifier</li> <li><strong>seqs_count</strong> – total number of sequences in the cluster</li> <li><strong>min_seq_length</strong> – minimum sequence length within the cluster</li> <li><strong>mean_seq_length</strong> – average sequence length within the cluster</li> <li><strong>max_seq_length</strong> – maximum sequence length within the cluster</li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_16082639 |
| institution | Zenodo |
| language | eng |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | afdb_clusters v1.0: AlphaFold-derived structure-based dataset for benchmarking MSA tools Zielezinski, Andrzej Gudyś, Adam Deorowicz, Sebastian multiple sequence alignment protein sequences AlphaFold protein structures benchmark <p>This dataset contains 1,166 protein families derived from AlphaFold Database Clusters. The families vary in size, ranging from approximately 1,000 to 680,000 sequences.</p> <p>For each family, the dataset provides:</p> <ul> <li>protein sequences (FASTA format)</li> <li>download URLs for AlphaFold-predicted PDB structures corresponding to each protein sequence</li> </ul> <p>These paired sequences and structures enable structure-based benchmarking of multiple sequence alignment (MSA) tools using the Local Distance Difference Test (LDDT) score, computed with the FoldMason tool.</p> <h3><strong>Directory structure</strong></h3> <p>The dataset contains two main directories:</p> <ul> <li><code>fasta/</code> – protein sequences for each cluster [FASTA format]</li> <li><code>pdb_urls/</code> – text files containing download URLs for AlphaFold PDB structures for each sequence in the cluster [TXT format]</li> </ul> <p>A metadata file (<code>metadata.tsv</code>) is also included, providing detailed information for each cluster.</p> <h3><strong>Metadata</strong></h3> <p>A metadata file (<code>metadata.tsv</code>) provides:</p> <ul> <li><strong>cluster_id</strong> – Cluster identifier</li> <li><strong>seqs_count</strong> – total number of sequences in the cluster</li> <li><strong>min_seq_length</strong> – minimum sequence length within the cluster</li> <li><strong>mean_seq_length</strong> – average sequence length within the cluster</li> <li><strong>max_seq_length</strong> – maximum sequence length within the cluster</li> </ul> |
| title | afdb_clusters v1.0: AlphaFold-derived structure-based dataset for benchmarking MSA tools |
| topic | multiple sequence alignment protein sequences AlphaFold protein structures benchmark |
| url | https://doi.org/10.5281/zenodo.16082639 |