ArticlePLoS computational biology2010
Accuracy of protein-protein binding sites in high-throughput template-based modeling.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Computational Methods and Deep Learning for Elucidating Protein Interaction Networks.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RL-MLZerD: Multimeric protein docking using reinforcement learning.Frontiers in molecular biosciences · 2022Article
- Effects of SARS-CoV-2 mutations on protein structures and intraviral protein-protein interactions.Journal of medical virology · 2021Article
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- Integrating ab initio and template-based algorithms for protein-protein complex structure prediction.Bioinformatics (Oxford, England) · 2020Article
- Modeling complexes of modeled proteins.Proteins · 2017Article
- Modeling, molecular docking, probing catalytic binding mode of acetyl-CoA malate synthase G inBiochemistry and biophysics reports · 2016Article
- AraPPISite: a database of fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.Plant molecular biology · 2016Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- Progress and challenges in predicting protein interfaces.Briefings in bioinformatics · 2016Review
- Algorithmic approaches to protein-protein interaction site prediction.Algorithms for molecular biology : AMB · 2015Article
- Protein-protein docking: from interaction to interactome.Biophysical journal · 2014Review
- Evaluating template-based and template-free protein-protein complex structure prediction.Briefings in bioinformatics · 2014Article
- Protein models: the Grand Challenge of protein docking.Proteins · 2014Article
- Low-resolution structural modeling of protein interactome.Current opinion in structural biology · 2013Review
- A computational framework for boosting confidence in high-throughput protein-protein interaction datasets.Genome biology · 2012Article
- Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement.Proteins · 2012Article
- Article
- Protein-protein interaction site predictions with three-dimensional probability distributions of interacting atoms on protein surfaces.PloS one · 2012Article
- Study of protein complexes via homology modeling, applied to cysteine proteases and their protein inhibitors.Journal of molecular modeling · 2011Article
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2 authors.
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Abstract
The accuracy of protein structures, particularly their binding sites, is essential for the success of modeling protein complexes. Computationally inexpensive methodology is required for genome-wide modeling of such structures. For systematic evaluation of potential accuracy in high-throughput modeling of binding sites, a statistical analysis of target-template sequence alignments was performed for a representative set of protein complexes. For most of the complexes, alignments containing all residues of the interface were found. The full interface alignments were obtained even in the case of poor alignments where a relatively small part of the target sequence (as low as 40%) aligned to the template sequence, with a low overall alignment identity (<30%). Although such poor overall alignments might be considered inadequate for modeling of whole proteins, the alignment of the interfaces was strong enough for docking. In the set of homology models built on these alignments, one third of those ranked 1 by a simple sequence identity criteria had RMSD<5 A, the accuracy suitable for low-resolution template free docking. Such models corresponded to multi-domain target proteins, whereas for single-domain proteins the best models had 5 A<RMSD<10 A, the accuracy suitable for less sensitive structure-alignment methods. Overall, approximately 50% of complexes with the interfaces modeled by high-throughput techniques had accuracy suitable for meaningful docking experiments. This percentage will grow with the increasing availability of co-crystallized protein-protein complexes.
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