Protein structure prediction
Building a better fragment library for de novo protein structure prediction.
... novo protein structure predic- ...for structure fragment library generation and its application in fragment-based de novo protein structure ...novo protein structure ...
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Potentials of mean force for protein structure prediction vindicated, formalized and generalized.
... in protein structure prediction are thus not statistically rigorous, because they do not make use of a proper joint probability distribution over the pairwise distances, which are strongly ...
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Protein structural model selection by combining consensus and single scoring methods.
... Quality assessment (QA) for predicted protein structural models is an important and challenging research problem in protein structure prediction. Consensus Global Distance Test (CGDT) methods ...
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PredPPCrys: accurate prediction of sequence cloning, protein production, purification and crystallization propensity from protein sequences using multi-step heterogeneous feature fusion and selection.
... As a result of the SG efforts, an increasing number of previously unknown proteins have been structurally solved using X-ray crystallography, NMR spectroscopy and electron microscopy [11]. However, despite the ...
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A linear model for transcription factor binding affinity prediction in protein binding microarrays.
... We have presented a linear model for uncovering TF binding specificity based on PBM measurements. While we only tested our model using data and metrics from the DREAM5 transcription factor/DNA motif recognition ...
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J. Bras. Patol. Med. Lab. vol.52 número5
... used protein sequence analysis tool available in the public domain ...or protein sequence, referred to as a query and nucleotide sequences against other database of nucleotide, referred to as subject ...
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Cupin: A candidate molecular structure for the Nep1-like protein family
... a prediction for the 3d-structure of the β -strand rich portion (positions 90– 220 in Figure 1) which presented stability for 3nS under molecular ...This structure presents the classical signature of ...
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PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites.
... silico prediction tools for protease cleavage sites, they have certain limitations, principally their prediction performance, which varies consider- ...secondary structure, solvent accessibility and ...
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Effects of NMR spectral resolution on protein structure calculation.
... calculated protein structures are high. Structure calculations work well above resolutions obtained at around 200 points for different protein sizes and RMSD groups, beyond which there is nearly no ...
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Heparan sulfate proteoglycans: structure, protein interactions and cell signaling
... It is well established that fibroblast growth factors and their receptors are dependent on binding to hep- aran sulfate, and this interaction is an absolute require- ment for full signaling. However most of the studies ...
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Dissertation presented at Faculdade de Ciências e Tecnologia of Universidade Nova de Lisboa to obtain the Degree of Master in Biotecnology Supervisor: Rita Abranches, PhD, ITQB-UNL Co-supervisor: Ana Sofia Pires, PhD, ITQB-UNL LISBOA
... the protein deposition, three microscopes were used: Leica DMRB Fluorescence Microscope, Leica DM600B Fluorescence Microscope and Leica SP5 Confocal Microscope, ...
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Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework.
... the structure of a neuronal network affects its functionality has gained a lot of attention in ...on structure-dynamics relationships consider few types of network structures and assess limited numbers of ...
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Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes.
... epitope prediction using homology models of class II MHC allotypes without available X-ray structures in the ...to structure-base prediction results for a series of all possible single residue ...
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Mammalian microRNA prediction through a support vector machine model of sequence and structure.
... hairpin structure that contains one or two mature miRNAs in either or both of its ...target prediction in mammals indicates that ,10– 30% of protein-coding genes may be under control of currently ...
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Mutational robustness of gene regulatory networks.
... effect of evolutionary tinkering with network structure via changes in the sequences of the underlying components has received less attention [18,19,20,21,22]. This is true in general, but in particular for ...
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FP Silva-Jr, FZ Veyl, J Clos, S Giovanni De Simone
... domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are ...this protein ...
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Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.
... ESAT-6 secretion pathway in S. gallolyticus. The ESAT-6 secretion system (Ess) pathway was first identified in Mycobacterium tuberculosis where important etiological agents of human tuberculosis (TB), ESAT-6 and CFP-10, ...
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Position-specific analysis and prediction for protein lysine acetylation based on multiple features.
... et al. [18] proposed a novel predicted method called Ensemble- Pail, which encodes sequences based on improved position weight matrices (PWMs) and then implements an ensemble of support vector machine (SVM) classifiers ...
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Random field model reveals structure of the protein recombinational landscape.
... With the random field model, we can now explore how key recombination parameters, such as parent sequence identity or the number of sequence crossovers, influence the shape of the recombination curve shown in Figure 2A. ...
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SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
... of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional tran- sitions in ...
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