Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
نویسندگان
چکیده
منابع مشابه
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement.
A combination of sequence comparison, threading, lattice, and off-lattice Monte Carlo (MC) simulations and clustering of MC trajectories was used to predict the structure of all (but one) targets of the CASP4 experiment on protein structure prediction. Although this method is automated and is operationally the same regardless of the level of uniqueness of the query proteins, here we focus on th...
متن کاملAb Initio Protein Structure Prediction
Predicting protein 3D structures from the amino acid sequence still remains as an unsolved problem after five decades of efforts. If the target protein has a homologue already solved, the task is relatively easy and high-resolution models can be built by copying the framework of the solved structure. However, such a modelling procedure does not help answer the question of how and why a protein ...
متن کاملGeneralized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement.
An improved generalized comparative modeling method, GENECOMP, for the refinement of threading models is developed and validated on the Fischer database of 68 probe-template pairs, a standard benchmark used to evaluate threading approaches. The basic idea is to perform ab initio folding using a lattice protein model, SICHO, near the template provided by the new threading algorithm PROSPECTOR. P...
متن کاملTOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints.
The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are deriv...
متن کاملAb initio protein structure prediction using a combined hierarchical approach.
As part of the third Critical Assessment of Structure Prediction meeting (CASP3), we predict the three-dimensional structures for 13 proteins using a hierarchical approach. First, all possible compact conformations of a protein sequence are enumerated using a highly simplified tetrahedral lattice model. We select a large subset of these conformations using a lattice-based scoring function and b...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Genetics
سال: 2001
ISSN: 0887-3585,1097-0134
DOI: 10.1002/prot.1172