ArticleBioinformatics (Oxford, England)2020
FASPR: an open-source tool for fast and accurate protein side-chain packing.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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55 citing papers in PubMed.
- OpenGerminal: an open-source implementation of the Germinal antibody design pipeline.bioRxiv : the preprint server for biology · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder.bioRxiv : the preprint server for biology · 2026Article
- Bioinformatic and computational biophysics tools for nanopore engineering: a review from standard approaches to machine learning advancements.Journal of nanobiotechnology · 2026Review
- Accurate conformational ensembles of intrinsically disordered proteins using reweighting based on NMR chemical shifts.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation.Mini reviews in medicinal chemistry · 2026Review
- Flexible protein-ligand docking with diffusion-based side-chain packing.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SAAINT-DB: a comprehensive structural antibody database for antibody modeling and design.Acta pharmacologica Sinica · 2025Article
- AlphaFlex: Ensembles of the human proteome representing disordered regions.bioRxiv : the preprint server for biology · 2025Article
- A structure-oriented kinetics dataset of enzyme-substrate interactions.Scientific data · 2025Article
- PackPPI: An integrated framework for protein-protein complex side-chain packing and ΔΔG prediction based on diffusion model.Protein science : a publication of the Protein Society · 2025Article
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- NOMPC ion channel hinge forms a gating spring that initiates mechanosensation.Nature neuroscience · 2025Article
- Connecting the dots: deep learning-based automated model building methods in cryo-EM.Frontiers in molecular biosciences · 2025Review
- Dissecting AlphaFold2's capabilities with limited sequence information.Bioinformatics advances · 2025Article
- Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- ADH1B, the adipocyte-enriched alcohol dehydrogenase, plays an essential, cell-autonomous role in human adipogenesis.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Characterization of the interaction between the Sec61 translocon complex and ppαF using optical tweezers.Protein science : a publication of the Protein Society · 2024Article
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3 authors.
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Abstract
motivationProtein structure and function are essentially determined by how the side-chain atoms interact with each other. Thus, accurate protein side-chain packing (PSCP) is a critical step toward protein structure prediction and protein design. Despite the importance of the problem, however, the accuracy and speed of current PSCP programs are still not satisfactory.
resultsWe present FASPR for fast and accurate PSCP by using an optimized scoring function in combination with a deterministic searching algorithm. The performance of FASPR was compared with four state-of-the-art PSCP methods (CISRR, RASP, SCATD and SCWRL4) on both native and non-native protein backbones. For the assessment on native backbones, FASPR achieved a good performance by correctly predicting 69.1% of all the side-chain dihedral angles using a stringent tolerance criterion of 20°, compared favorably with SCWRL4, CISRR, RASP and SCATD which successfully predicted 68.8%, 68.6%, 67.8% and 61.7%, respectively. Additionally, FASPR achieved the highest speed for packing the 379 test protein structures in only 34.3 s, which was significantly faster than the control methods. For the assessment on non-native backbones, FASPR showed an equivalent or better performance on I-TASSER predicted backbones and the backbones perturbed from experimental structures. Detailed analyses showed that the major advantage of FASPR lies in the optimal combination of the dead-end elimination and tree decomposition with a well optimized scoring function, which makes FASPR of practical use for both protein structure modeling and protein design studies. AVAILABILITY AND IMPLEMENTATION: The web server, source code and datasets are freely available at https://zhanglab.ccmb.med.umich.edu/FASPR and https://github.com/tommyhuangthu/FASPR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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