ArticlePloS one2012
BCL::Fold--de novo prediction of complex and large protein topologies by assembly of secondary structure elements.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
28 citing papers in PubMed.
- IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.Journal of molecular biology · 2024Article
- Integration of software tools for integrative modeling of biomolecular systems.Journal of structural biology · 2022Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.Structure (London, England : 1993) · 2019Article
- BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.Journal of chemical information and modeling · 2019Article
- Identification and Verification of Ubiquitin-Activated Bacterial Phospholipases.Journal of bacteriology · 2019Article
- Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.Structure (London, England : 1993) · 2018Article
- Integrated Structural Biology for α-Helical Membrane Protein Structure Determination.Structure (London, England : 1993) · 2018Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Improving prediction of helix-helix packing in membrane proteins using predicted contact numbers as restraints.Proteins · 2017Article
- Article
- Membrane protein contact and structure prediction using co-evolution in conjunction with machine learning.PloS one · 2017Article
- Pushing the size limit of de novo structure ensemble prediction guided by sparse SDSL-EPR restraints to 200 residues: The monomeric and homodimeric forms of BAX.Journal of structural biology · 2016Article
- Protonation-dependent conformational dynamics of the multidrug transporter EmrE.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Characterization of the Domain Orientations of E. coli 5'-Nucleotidase by Fitting an Ensemble of Conformers to DEER Distance Distributions.Structure (London, England : 1993) · 2016Article
- CASP11--An Evaluation of a Modular BCL::Fold-Based Protein Structure Prediction Pipeline.PloS one · 2016Article
- Article
- Protein structure prediction guided by crosslinking restraints--A systematic evaluation of the impact of the crosslinking spacer length.Methods (San Diego, Calif.) · 2015Article
- BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles.Proteins · 2015Article
- Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.Journal of chemical theory and computation · 2015Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Computational de novo protein structure prediction is limited to small proteins of simple topology. The present work explores an approach to extend beyond the current limitations through assembling protein topologies from idealized α-helices and β-strands. The algorithm performs a Monte Carlo Metropolis simulated annealing folding simulation. It optimizes a knowledge-based potential that analyzes radius of gyration, β-strand pairing, secondary structure element (SSE) packing, amino acid pair distance, amino acid environment, contact order, secondary structure prediction agreement and loop closure. Discontinuation of the protein chain favors sampling of non-local contacts and thereby creation of complex protein topologies. The folding simulation is accelerated through exclusion of flexible loop regions further reducing the size of the conformational search space. The algorithm is benchmarked on 66 proteins with lengths between 83 and 293 amino acids. For 61 out of these proteins, the best SSE-only models obtained have an RMSD100 below 8.0 Å and recover more than 20% of the native contacts. The algorithm assembles protein topologies with up to 215 residues and a relative contact order of 0.46. The method is tailored to be used in conjunction with low-resolution or sparse experimental data sets which often provide restraints for regions of defined secondary structure.
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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.