33,653 research outputs found
Improving the Physical Realism and Structural Accuracy of Protein Models by a Two-Step Atomic-Level Energy Minimization
AbstractMost protein structural prediction algorithms assemble structures as reduced models that represent amino acids by a reduced number of atoms to speed up the conformational search. Building accurate full-atom models from these reduced models is a necessary step toward a detailed function analysis. However, it is difficult to ensure that the atomic models retain the desired global topology while maintaining a sound local atomic geometry because the reduced models often have unphysical local distortions. To address this issue, we developed a new program, called ModRefiner, to construct and refine protein structures from CĪ± traces based on a two-step, atomic-level energy minimization. The main-chain structures are first constructed from initial CĪ± traces and the side-chain rotamers are then refined together with the backbone atoms with the use of a composite physics- and knowledge-based force field. We tested the method by performing an atomic structure refinement of 261 proteins with the initial models constructed from both ab initio and template-based structure assemblies. Compared with other state-of-art programs, ModRefiner shows improvements in both global and local structures, which have more accurate side-chain positions, better hydrogen-bonding networks, and fewer atomic overlaps. ModRefiner is freely available at http://zhanglab.ccmb.med.umich.edu/ModRefiner
Ab initio protein structure assembly using continuous structure fragments and optimized knowledgeābased force field
Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for templateāfree protein structure prediction. Query sequences are first broken into fragments of 1ā20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Fullālength structure models are then assembled from fragments using replicaāexchange Monte Carlo simulations, which are guided by a composite knowledgeābased force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in oneāthird cases of short proteins up to 100 residues. In the ninth communityāwide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z āscore of global distance testātotal scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Proteins 2012; Ā© 2012 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/91314/1/24065_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/91314/2/PROT_24065_sm_SuppInfo.pd
An Alarm System For Segmentation Algorithm Based On Shape Model
It is usually hard for a learning system to predict correctly on rare events
that never occur in the training data, and there is no exception for
segmentation algorithms. Meanwhile, manual inspection of each case to locate
the failures becomes infeasible due to the trend of large data scale and
limited human resource. Therefore, we build an alarm system that will set off
alerts when the segmentation result is possibly unsatisfactory, assuming no
corresponding ground truth mask is provided. One plausible solution is to
project the segmentation results into a low dimensional feature space; then
learn classifiers/regressors to predict their qualities. Motivated by this, in
this paper, we learn a feature space using the shape information which is a
strong prior shared among different datasets and robust to the appearance
variation of input data.The shape feature is captured using a Variational
Auto-Encoder (VAE) network that trained with only the ground truth masks.
During testing, the segmentation results with bad shapes shall not fit the
shape prior well, resulting in large loss values. Thus, the VAE is able to
evaluate the quality of segmentation result on unseen data, without using
ground truth. Finally, we learn a regressor in the one-dimensional feature
space to predict the qualities of segmentation results. Our alarm system is
evaluated on several recent state-of-art segmentation algorithms for 3D medical
segmentation tasks. Compared with other standard quality assessment methods,
our system consistently provides more reliable prediction on the qualities of
segmentation results.Comment: Accepted to ICCV 2019 (10 pages, 4 figures
Toward optimal fragment generations for ab initio protein structure assembly
Fragment assembly using structural motifs excised from other solved proteins has shown to be an efficient method for ab initio proteināstructure prediction. However, how to construct accurate fragments, how to derive optimal restraints from fragments, and what the best fragment length is are the basic issues yet to be systematically examined. In this work, we developed a gaplessāthreading method to generate positionāspecific structure fragments. Distance profiles and torsion angle pairs are then derived from the fragments by statistical consistency analysis, which achieved comparable accuracy with the machineālearningābased methods although the fragments were taken from unrelated proteins. When measured by both accuracies of the derived distance profiles and torsion angle pairs, we come to a consistent conclusion that the optimal fragment length for structural assembly is around 10, and at least 100 fragments at each location are needed to achieve optimal structure assembly. The distant profiles and torsion angle pairs as derived by the fragments have been successfully used in QUARK for ab initio protein structure assembly and are provided by the QUARK online server at http://zhanglab.ccmb. med.umich.edu/QUARK/ . Proteins 2013. Ā© 2012 Wiley Periodicals, Inc.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/96355/1/24179_ftp.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/96355/2/PROT_24179_sm_SuppInfo.pd
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