Ab initio folding

ES Huang, P Koehl, M Levitt, RV Pappu, JW Ponder. Accuracy of side-chain prediction upon near-native protein backbones generated by ab initio folding methods. Proteins 33 204-217, 1998. 

Fig. 3.8 Dehydronic field averaged over all backbone hydrogen bonds formed at time t for the protein G variant along the ab initio folding trajectory described in Figs. 3.3, 3.2,3.3,3.4, 3.5,3.6, and 3.7...

Skolnick-Kolinski group Threading tools, ab initio folding tools, FEE hbrary http //bioinformatics. danforthcenter.oig... 

B. Results of Ab Initio Folding on 28 Test Proteins Compatibility of Reduced and Atomic Models... 

Identification of Active Sites in Experimental Structures Requirements of Sequence-Structure-Function Prediction Methods Use of Predicted Structures from Ab Initio Folding Use of Threaded Structures to Predict Biochemical Function Use of Low-Resolution Structures for Ligand Identification Outlook for the Future... 

A similar methodology, but one based on a completely different protein representation [139,140] (that are discussed in Sections V and VI), was employed by Kolinski and co-workers with a similar fraction of correctly predicted stmctures [133]. An important advantage of this method was its computational speed and nicer scaling of computational cost against protein chain length. Thus, the prediction of stmctures of larger proteins via ab initio folding became possible. 

Predicted Contact Accuracy from Threading for 28 Proteins Used in an Ab Initio Folding Test"... 

A recently proposed method is described in the next sections that attempt to address this problem. The idea is to perform a kind of ab initio folding in the... 

The method for ab initio folding of smaD globular proteins employs the same modeling tools as in generalized comparative modeling. There are, however, some differences. Of course, now there is no template to restrict the... 

Unfortunately, such methods require the exact placement of atoms within protein side chains and are inapplicable to the inexact, low-resolution predicted structures generated by the state-of-the-art ab initio folding and threading algorithms (see Sections IV-VI). These methods are required when the sequence identity of the sequence of interest to solved structures is too low to use comparative modeling. To address this need, Skolnick and Fetrow have recently developed fuzzy, inexact descriptors of protein functional sites [8]. They are applicable to both high-resolution, experimental structures and low-resolution (backbone RMSD 4—6 A from native) structures. These descriptors are a-carbon-based, fuzzy functional forms (FFFs). Initially, they created FFFs for the disulfide oxidoreductase [8,10] and a/p-hydrolase catalytic active sites [11] (an additional 198 have now been bmlt, with comparable results [234]). 

Turning to issues associated with ab initio folding and, to a lesser extent, generalized comparative modeling, some elements of the force field of the lattice model are not yet satisfactory. The scaling of various contributions to the... 

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