Alignment algorithm for homology modeling and threading
نویسندگان
چکیده
منابع مشابه
FINDSITELHM: A Threading-Based Approach to Ligand Homology Modeling
Ligand virtual screening is a widely used tool to assist in new pharmaceutical discovery. In practice, virtual screening approaches have a number of limitations, and the development of new methodologies is required. Previously, we showed that remotely related proteins identified by threading often share a common binding site occupied by chemically similar ligands. Here, we demonstrate that acro...
متن کاملLow-homology protein threading
MOTIVATION The challenge of template-based modeling lies in the recognition of correct templates and generation of accurate sequence-template alignments. Homologous information has proved to be very powerful in detecting remote homologs, as demonstrated by the state-of-the-art profile-based method HHpred. However, HHpred does not fare well when proteins under consideration are low-homology. A p...
متن کاملConsensus alignment for reliable framework prediction in homology modeling
MOTIVATION Even the best sequence alignment methods frequently fail to correctly identify the framework regions for which backbones can be copied from the template into the target structure. Since the underprediction and, more significantly, the overprediction of these regions reduces the quality of the final model, it is of prime importance to attain as much as possible of the true structural ...
متن کاملImproving threading algorithms for remote homology modeling by combining fragment and template comparisons.
In this work, we develop a method called fragment comparison and the template comparison (FTCOM) for assessing the global quality of protein structural models for targets of medium and hard difficulty (remote homology) produced by structure prediction approaches such as threading or ab initio structure prediction. FTCOM requires the C(alpha) coordinates of full length models and assesses model ...
متن کاملProtein threading using context-specific alignment potential
MOTIVATION Template-based modeling, including homology modeling and protein threading, is the most reliable method for protein 3D structure prediction. However, alignment errors and template selection are still the main bottleneck for current template-base modeling methods, especially when proteins under consideration are distantly related. RESULTS We present a novel context-specific alignmen...
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ژورنال
عنوان ژورنال: Protein Science
سال: 1998
ISSN: 0961-8368
DOI: 10.1002/pro.5560070204