ArticleProteins2009
Building and assessing atomic models of proteins from structural templates: learning and benchmarks.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Diversity, expression, and structural modeling of sugar transporters inFrontiers in cellular and infection microbiology · 2025Article
- Tandem Mass Tagging (TMT) Reveals Tissue-Specific Proteome of L4 Larvae ofInternational journal of molecular sciences · 2022Article
- Structural modelling of the DNAJB6 oligomeric chaperone shows a peptide-binding cleft lined with conserved S/T-residues at the dimer interface.Scientific reports · 2018Article
- Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking.PloS one · 2017Article
- Are protein-protein interfaces special regions on a protein's surface?The Journal of chemical physics · 2015Article
- Fast evolutionary rates associated with functional loss in class I glucose transporters of Schistosoma mansoni.BMC genomics · 2015Article
- Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection.Parasites & vectors · 2015Article
- Control of carotenoid biosynthesis through a heme-based cis-trans isomerase.Nature chemical biology · 2015Article
- Article
- The catalytic domain of topological knot tRNA methyltransferase (TrmH) discriminates between substrate tRNA and nonsubstrate tRNA via an induced-fit process.The Journal of biological chemistry · 2013Article
- Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.PloS one · 2013Article
- Article
- Crystal structure of the central axis DF complex of the prokaryotic V-ATPase.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Fast geometric consensus approach for protein model quality assessment.Journal of computational biology : a journal of computational molecular cell biology · 2011Article
- Designing coarse grained-and atom based-potentials for protein-protein docking.BMC structural biology · 2010Article
- A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins.Proteins · 2009Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
One approach to predict a protein fold from a sequence (a target) is based on structures of related proteins that are used as templates. We present an algorithm that examines a set of candidates for templates, builds from each of the templates an atomically detailed model, and ranks the models. The algorithm performs a hierarchical selection of the best model using a diverse set of signals. After a quick and suboptimal screening of template candidates from the protein data bank, the current method fine-tunes the selection to a few models. More detailed signals test the compatibility of the sequence and the proposed structures, and are merged to give a global fitness measure using linear programming. This algorithm is a component of the prediction server LOOPP (http://www.loopp.org). Large-scale training and tests sets were designed and are presented. Recent results of the LOOPP server in CASP8 are discussed.
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Registered trials
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.