Crystal structure of the unliganded retinoblastoma protein pocket domain.
Published in Proteins
Model quality assessment using distance constraints from alignments.
Published in Proteins
Given a set of alternative models for a specific protein sequence, the model quality assessment (MQA) problem asks for an assignment of scores to each model in the set. A good MQA program assigns these scores such that they correlate well with real quality of the models, ideally scoring best that model which is closest to the true structure. In thi...
Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performe...
Published in Proteins
A correct alignment is an essential requirement in homology modeling. Yet in order to bridge the structural gap between template and target, which may not only involve loop rearrangements, but also shifts of secondary structure elements and repacking of core residues, high-resolution refinement methods with full atomic details are needed. Here, we ...
Applying Undertaker to quality assessment.
Published in Proteins
Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM-T08-MQAO), a function which added other single-model terms to the distance constraints (SAM-T08-MQAU), and a function which used both single-model and consensus terms (SAM-T08-MQAC). We analyzed the functions bo...
Structural characterization of the neurabin sterile alpha motif domain.
Published in Proteins Structure Function and Bioinformatics
Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go ...
Published in Proteins Structure Function and Bioinformatics
Discretization of protein conformational space and fragment assembly methods simplify the search of native structures. These methods, mostly of Monte Carlo and genetic-type, do not exploit, however, the fact that short fragments describing consecutive parts of proteins are conformation-dependent. Yet, this information should be useful in improving ...
Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets
Published in Proteins Structure Function and Bioinformatics
Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets
Published in Proteins Structure Function and Bioinformatics
Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets
Published in Proteins Structure Function and Bioinformatics
Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets
Published in Proteins Structure Function and Bioinformatics
