An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences
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Summary
This paper reviews the recent advances in computational template-based structural modelling and proposes the subclustering of protein domain superfamilies to guide the template-selection process.
- Type
- review
- Published
- 2017-07-28
- Cited by
- 52
- References
- 149
- Access
- Open access
- OpenAlex
- https://openalex.org/W2740279634
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:9647311
Keywords
Computer science, Domain (mathematical analysis), Computational biology, Selection (genetic algorithm), Process (computing)
References
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- Protein interactions and ligand binding: From protein subfamilies to functional specificity
- Modeling, Docking, and Fitting of Atomic Structures to 3D Maps from Cryo-electron Microscopy
- Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data
- Introduction to Protein Structure Prediction
- Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.
- Protein structure modeling for CASP10 by multiple layers of global optimization
- Enzyme nomenclature 1992. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes.
- Detecting folding motifs and similarities in protein structures.
- Protein Structure Prediction Using Residue- and Fragment-Environment Potentials in CASP11
- The Phyre2 web portal for protein modelling, prediction and analysis
- Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop
- Improving accuracy of protein contact prediction using balanced network deconvolution
- Effective protein model structure refinement by loop modeling and overall relaxation
- MRFalign: Protein Homology Detection through Alignment of Markov Random Fields
- Assessment of template based protein structure predictions in CASP10
- Interactome3D: adding structural details to protein networks
- Can correct protein models be identified?
- Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns
- Fundamentals of Homology Modeling Steps and Comparison among Important Bioinformatics Tools: An Overview
Cited by
- Energetic Materials: From Cradle to Grave
- Protein structure and function analyses to understand the implication of mutually exclusive splicing
- Choosing the Best Enzyme Complex Structure Made Easy.
- Combined approaches from physics, statistics, and computer science for ab initio protein structure prediction: ex unitate vires (unity is strength)?
- Molecular modelling of ATP-gated P2X receptor ion channels
- Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics
- VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes
- A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations
- SCOP-Aided Fragment Assembly Protein Structure Prediction
- Structure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections
- DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data
- Exploring Novel Biophysical Mechanisms in Evolved Optical Systems
- Development of a comprehensive 3D structural database of human pan-proteomic interaction with the most valuable sold drugs
- Assessing Protein Function Through Structural Similarities with CATH.
- Integrative/Hybrid Modeling Approaches for Studying Biomolecules.
- Can exascale computing and explainable artificial intelligence applied to plant biology deliver on the United Nations sustainable development goals?
- Structural Biology in the Multi-Omics Era
- Enhanced Rosetta-based Protein Structure Prediction For non-Beta Sheet Dominated Targets
- Rosetta and the Journey to Predict Proteins’ Structures, 20 Years on
- Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network
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