Structural motif search across the protein universe with Folddisco

Highly accurate protein structure prediction with AlphaFold

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ColabFold - Making protein folding accessible to all

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Depth-First Search and Linear Graph Algorithms

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A statistical interpretation of term specificity and its application in retrieval

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Evolutionary-scale prediction of atomic level protein structure with a language model

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MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

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Fast and accurate protein structure search with Foldseek

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Fast and accurate protein structure search with Foldseek

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InterPro in 2022

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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

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The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

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Improved protein structure prediction using predicted interresidue orientations

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Design and Selection of Novel Cys2His2 Zinc Finger Proteins

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Common activation mechanism of class A GPCRs

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MMseqs2 desktop and local web server app for fast, interactive sequence searches

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Analysis of Catalytic Residues in Enzyme Active Sites

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Sampling alternative conformational states of transporters and receptors with AlphaFold2

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NGL Viewer: a web application for molecular visualization

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Advances and pitfalls of protein structural alignment

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Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

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A strong-connectivity algorithm and its applications in data flow analysis

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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

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Rapid calculation of RMSDs using a quaternion-based characteristic polynomial

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SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning

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Iron center, substrate recognition and mechanism of peptide deformylase

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Exploring the structure and function paradigm.

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Multiple protein structure alignment at scale with FoldMason

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Rapid search for tertiary fragments reveals protein sequence–structure relationships

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AFsample2 predicts multiple conformations and ensembles with AlphaFold2

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ProRule: a new database containing functional and structural information on PROSITE profiles

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Structural Characteristics of Novel Protein Folds

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Cross-phyla protein annotation by structural prediction and alignment

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Real-time structural motif searching in proteins using an inverted index strategy

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Foldcomp: a library and format for compressing and indexing large protein structure sets

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Functional annotation of a divergent genome using sequence and structure-based similarity

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pyScoMotif: discovery of similar 3D structural motifs across proteins

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Zero-shot design of a de novo metalloenzymePreprint

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RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

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“Visualize, Explore, and Select”: A Protein Language Model-based Approach Enabling Navigation of Protein Sequence Space for Enzyme Discovery and MiningPreprint

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SiteMatcher: A Web Server for Structure-Based Drug Design Using Protein–Ligand Interaction Patterns

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A universal cis-proline lock defines catalysis in thioredoxin-fold enzymes

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Alternative splicing expands and remodels the breast cancer proteoform landscapePreprint

Jiang, F. T., Chen, D., Wang, Z., Wang, X.-G., Hao, H., Zhang, Y.-H., Zhao, R., Liang, F., Cui, T.-Y., Tang, Z.-C., et al. (2026) · bioRxiv · doi:10.64898/2026.04.30.722115 · Cited by 1 · see citing works

PanRes: A database of latent and acquired antimicrobial resistance allowing 3D-based protein homology searchPreprint

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Computing complexity

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Investigating enzyme function by geometric matching of catalytic motifs

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Mimotope-Guided Molecular Dynamics Enables Precise Functional Epitope Mapping

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Real-time structural motif searching in proteins using an inverted index strategy

Bittrich, S., Burley, S. K., & Rose, A. (2020) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008502 · Cited by 37 · see citing works

AlphaFind v2: similarity search in AlphaFold DB and TED domains across structural contexts

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Foldseek gives AlphaFold protein database a rapid search tool

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Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data

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MotiveQuery: Language and Web Service for Fast Identification of Protein Structural Motifs in the Entire Protein Data Bank

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