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Literature DB >> 18071927

The evaluation of protein structure prediction results.

Domenico Cozzetto¹, Alejandro Giorgetti, Domenico Raimondo, Anna Tramontano.

Abstract

Methods for protein structure prediction are flourishing and becoming widely available to both experimentalists and computational biologists. However, how good are they? What is their range of applicability and how can we know which method is better suited for the task at hand? These are the questions that this review tries to address, by describing the worldwide Critical Assessment of techniques for protein Structure Prediction (CASP) initiative and focusing on the specific problems of assessing the quality of a protein 3D model.

Entities: Gene

Mesh：

Substances：
Proteins

Year: 2007 PMID： 18071927 DOI： 10.1007/s12033-007-9023-6

Source DB: PubMed Journal: Mol Biotechnol ISSN： 1073-6085 Impact factor: 2.695

33 in total

1. Ab initio protein structure prediction of CASP III targets using ROSETTA.

Authors: K T Simons; R Bonneau; I Ruczinski; D Baker
Journal: Proteins Date: 1999

2. LiveBench-1: continuous benchmarking of protein structure prediction servers.

Authors: J M Bujnicki; A Elofsson; D Fischer; L Rychlewski
Journal: Protein Sci Date: 2001-02 Impact factor: 6.725

3. Relationship between multiple sequence alignments and quality of protein comparative models.

Authors: Domenico Cozzetto; Anna Tramontano
Journal: Proteins Date: 2005-01-01

4. Prediction of global and local model quality in CASP7 using Pcons and ProQ.

Authors: Björn Wallner; Arne Elofsson
Journal: Proteins Date: 2007

5. Assessment of predictions in the model quality assessment category.

Authors: Domenico Cozzetto; Andriy Kryshtafovych; Michele Ceriani; Anna Tramontano
Journal: Proteins Date: 2007

6. A large-scale experiment to assess protein structure prediction methods.

Authors: J Moult; J T Pedersen; R Judson; K Fidelis
Journal: Proteins Date: 1995-11

7. Profile analysis: detection of distantly related proteins.

Authors: M Gribskov; A D McLachlan; D Eisenberg
Journal: Proc Natl Acad Sci U S A Date: 1987-07 Impact factor: 11.205

8. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2.

Authors: D Fischer; A Elofsson; L Rychlewski
Journal: Protein Eng Date: 2000-10

The evaluation of protein structure prediction results.

1. Ab initio protein structure prediction of CASP III targets using ROSETTA.

2. LiveBench-1: continuous benchmarking of protein structure prediction servers.

3. Relationship between multiple sequence alignments and quality of protein comparative models.

4. Prediction of global and local model quality in CASP7 using Pcons and ProQ.

5. Assessment of predictions in the model quality assessment category.

6. A large-scale experiment to assess protein structure prediction methods.

7. Profile analysis: detection of distantly related proteins.

8. The 2000 Olympic Games of protein structure prediction; fully automated programs are being evaluated vis-à-vis human teams in the protein structure prediction experiment CAFASP2.

9. RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions.

10. High-resolution structure prediction and the crystallographic phase problem.

Review 1. Protein structure prediction and model quality assessment.

2. Genome-wide Membrane Protein Structure Prediction.

3. ModeRNA: a tool for comparative modeling of RNA 3D structure.