Comparative protein structure modeling of genes and genomes.

By Marc A. Martí-Renom, A. C. Stuart, András Fiser, R. Sánchez, Francisco Melo, Andrej S̆ali. 2000

1,530 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Andrej Sali
2. Yang Zhang
3. Ben M. Webb
4. Torsten Schwede
5. Jinbo Xu
6. Sheng Wang
7. Jianlin Cheng
8. Andriy Kryshtafovych

In Molecular Biology

1. Yang Zhang
2. Andrej Sali
3. Torsten Schwede
4. Ben M. Webb
5. Jinbo Xu
6. Sheng Wang
7. Jianlin Cheng
8. David Baker

Citations in the corpus

• Outcome of a Workshop on Applications of Protein Models in Biomedical Research (2009, background): “…library of known folds (Godzik, 2003); atomic models of a protein can be calculated on the basis of known template structures by homology modeling (Marti-Renom et al., 2000; Petrey and Honig, 2005; Schwede et al., 2003); and atomicandreducedrepresentation modelsofproteincomplexes with small…”
• Template-based protein structure modeling using the RaptorX web server (2012, methodology): “Methods in the former group include comparative modeling methods 6 , which, given a target sequence, identify evolutionarily related templates with solved structure by sequence or sequence-profile comparison (e.g., BLAST and HHpred 7 ) and construct structure models based on the scaffold provided…”
• How well can the accuracy of comparative protein structure models be predicted? (2008, methodology): “Comparative modeling is the most widely used and generally most accurate class of protein structure prediction approaches (Marti-Renom et al. 2000; Tramontano et al. 2001; Eswar et al. 2007).”
• Protein structure modeling with MODELLER. (2014, methodology): “Comparative modeling relies on structural information from related proteins to guide the modeling procedure(6-8).”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “As stated earlier, comparative modeling consists of four main steps: fold assignment, target-template alignment, model building, and model evaluation (Marti-Renom et al., 2000; Fig.”
• Using multiple templates to improve quality of homology models in automated homology modeling (2008, background): “It was one of the first fully automated programs and it is also relatively fast, making it suitable, e.g., for whole-genome modeling ( Marti-Renom et al. 2000; Pieper et al. 2004).”
• Accurate and efficient loop selections by the DFIRE‐based all‐atom statistical potential (2004, background): “Loop-structure prediction is a nontrivial miniprotein folding problem, especially if the loop length is longer than eight residues (Mart-Renom et al. 2000; Schonbrun et al. 2002).”
• GalaxyRefine2: simultaneous refinement of inaccurate local regions and overall protein structure (2019, methodology): “Template-based protein structure prediction methods can generate accurate protein models when sufficiently similar structural templates are available (1).”
• Comparative protein structure modeling by iterative alignment, model building and model assessment. (2003, background): “protein (target) that is related to at least one known protein structure (template) (3,4).”
• Outcome of a workshop on archiving structural models of biological macromolecules. (2006, background): “Introduction Types of Theoretical Models and Current Resources Protein structure prediction methods include many types (Baker and Sali, 2001; Marti-Renom et al., 2000; Petrey and Honig, 2005) that differ in terms of the input information used and the aspects of protein structure predicted.”
• HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm (2018, methodology): “With the selected template, the 3D structure of the protein is built using MODELLER (32), in which the sequence alignment is conducted by ClustalW (30,31).”
• Reconstruction of Protein Backbones from the BriX Collection of Canonical Protein Fragments (2008, methodology): “this coverage using related proteins with known structures to build a model [2–5].”
• Local Protein Structures (2007, methodology): “The number of related protein sequences has led to the generalization of homology modeling with softwares like Modeller [291-293] or Composer [294].”
• Tools for comparative protein structure modeling and analysis (2003, methodology): “MODWEB relies on MODPIPE, a completely automated software pipeline for comparative protein structure modeling, which can calculate comparative models for a large number of protein sequences, using many different template structures and sequence–structure alignments (7,12,22) (Fig.”
• MultiSeq: unifying sequence and structure data for evolutionary analysis (2006, background): “Modeller [44] allows structural features to be built using sequences and structures of homologous proteins and nucleic acids.”