ArticleProteins2016
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI.
Article in Proteins, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Which Metrics Best Capture Protein Structural Changes in Molecular Dynamics Simulations? Evaluating Score Combinations and Force-Field Effects.Journal of chemical information and modeling · 2026Article
- Deep-learning-based single-domain and multidomain protein structure prediction with D-I-TASSER.Nature biotechnology · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- Assessment of Nucleic Acid Structure Prediction in CASP16.Proteins · 2026Article
- Assessment of nucleic acid structure prediction in CASP16.bioRxiv : the preprint server for biology · 2025Article
- Host-guest systems for the SAMPL9 blinded prediction challenge: phenothiazine as a privileged scaffold for binding to cyclodextrins.Physical chemistry chemical physics : PCCP · 2024Article
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- AlphaFold developers Demis Hassabis and John Jumper share the 2023 Albert Lasker Basic Medical Research Award.The Journal of clinical investigation · 2023Article
- Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15.bioRxiv : the preprint server for biology · 2023Article
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Ensemble deep learning models for protein secondary structure prediction using bidirectional temporal convolution and bidirectional long short-term memory.Frontiers in bioengineering and biotechnology · 2023Article
- DLBLS_SS: protein secondary structure prediction using deep learning and broad learning system.RSC advances · 2022Article
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- Using steered molecular dynamic tension for assessing quality of computational protein structure models.Journal of computational chemistry · 2022Article
- A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models.Bioengineering (Basel, Switzerland) · 2022Article
- Refined Contact Map Prediction of Peptides Based on GCN and ResNet.Frontiers in genetics · 2022Article
- An Overview of Alphafold's Breakthrough.Frontiers in artificial intelligence · 2022Review
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32 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Modeling of protein structure from amino acid sequence now plays a major role in structural biology. Here we report new developments and progress from the CASP11 community experiment, assessing the state of the art in structure modeling. Notable points include the following: (1) New methods for predicting three dimensional contacts resulted in a few spectacular template free models in this CASP, whereas models based on sequence homology to proteins with experimental structure continue to be the most accurate. (2) Refinement of initial protein models, primarily using molecular dynamics related approaches, has now advanced to the point where the best methods can consistently (though slightly) improve nearly all models. (3) The use of relatively sparse NMR constraints dramatically improves the accuracy of models, and another type of sparse data, chemical crosslinking, introduced in this CASP, also shows promise for producing better models. (4) A new emphasis on modeling protein complexes, in collaboration with CAPRI, has produced interesting results, but also shows the need for more focus on this area. (5) Methods for estimating the accuracy of models have advanced to the point where they are of considerable practical use. (6) A first assessment demonstrates that models can sometimes successfully address biological questions that motivate experimental structure determination. (7) There is continuing progress in accuracy of modeling regions of structure not directly available by comparative modeling, while there is marginal or no progress in some other areas. Proteins 2016; 84(Suppl 1):4-14. © 2016 Wiley Periodicals, Inc.
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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.