𝔖 Bobbio Scriptorium
✦   LIBER   ✦

CASP9 assessment of free modeling target predictions

✍ Scribed by Lisa Kinch; Shuo Yong Shi; Qian Cong; Hua Cheng; Yuxing Liao; Nick V. Grishin

Book ID
105358328
Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
914 KB
Volume
79
Category
Article
ISSN
0887-3585

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

We present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) “Template free modeling” category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the “winner” of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as “meta predictors” by correctly selecting among models produced by the top‐performing automated servers. The details of evaluation are available at http://prodata.swmed.edu/CASP9/. © Proteins 2011; © 2011 Wiley‐Liss, Inc.

📜 SIMILAR VOLUMES

Assessment of ligand-binding residue pre
Assessment of ligand-binding residue predictions in CASP9
✍ Tobias Schmidt; Jürgen Haas; Tiziano Gallo Cassarino; Torsten Schwede 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 741 KB

## Abstract Interactions between proteins and their ligands play central roles in many physiological processes. The structural details for most of these interactions, however, have not yet been characterized experientially. Therefore, various computational tools have been developed to predict the l

Analysis of comparative modeling predict
Analysis of comparative modeling predictions for CASP2 targets 1, 3, 9, and 17
✍ Robert W. Harrison; Charles C. Reed; Irene T. Weber 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 228 KB 👁 2 views

Comparative modeling targets 1, 3, 9, and 17 were predicted by alignment of multiple sequences and structures, when available, followed by minimization using the program AMMP. The minimization used improved potentials, and distance restraints for regions of common structure. New prediction procedure

Evaluation of residue–residue contact pr
Evaluation of residue–residue contact predictions in CASP9
✍ Bohdan Monastyrskyy; Krzysztof Fidelis; Anna Tramontano; Andriy Kryshtafovych 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 546 KB

## Abstract This work presents the results of the assessment of the intramolecular residue–residue contact predictions submitted to CASP9. The methodology for the assessment does not differ from that used in previous CASPs, with two basic evaluation measures being the precision in recognizing conta

Assessment of comparative modeling in CA
Assessment of comparative modeling in CASP2
✍ Martin, Andrew C. R.; MacArthur, Malcolm W.; Thornton, Janet M. 📂 Article 📅 1997 🏛 John Wiley and Sons 🌐 English ⚖ 285 KB 👁 2 views

An assessment is presented for all submissions to the comparative modeling challenge in the 1996 Critical Assessment of Structure Prediction (CASP2). Of the original 12 target structures, 9 were solved prior to the meeting: 8 by X-ray crystallography and 1 by NMR spectroscopy. These targets varied o

Structure classification-based assessmen
Structure classification-based assessment of CASP3 predictions for the fold recognition targets
✍ Alexey G. Murzin 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 252 KB 👁 2 views

The sequences of at least 23 of the 43 CASP3 targets showed no significant similarity to the sequences of known structures. The experimental structures of all but three of these 23 targets revealed substantial similarities to known structures, with at least eleven of the target structures likely bei