Jürgen Sühnel Jürgen Sühnel [email protected][email protected]Supplementary Material: http://www.fli-leibniz.de/www_bi Structures of Biological Macromolecul Structures of Biological Macromolecul Part 5: Protein Structure Prediction Part 5: Protein Structure Prediction Leibniz Institute for Age Research, Fritz Lipmann Institute, Leibniz Institute for Age Research, Fritz Lipmann Institute, Jena Centre for Bioinformatics Jena Centre for Bioinformatics Jena / Germany Jena / Germany
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Jürgen Sühnel [email protected] Supplementary Material: 3D Structures of Biological Macromolecules Part 5:
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3D Structures of Biological Macromolecules3D Structures of Biological MacromoleculesPart 5: Protein Structure Prediction Part 5: Protein Structure Prediction
Leibniz Institute for Age Research, Fritz Lipmann Institute,Leibniz Institute for Age Research, Fritz Lipmann Institute,Jena Centre for BioinformaticsJena Centre for Bioinformatics
Jena / GermanyJena / Germany
PDB Content GrowthPDB Content Growth
1993: 698 = 1588 structures (~ 2 structures per day)2003: 4187 = 23674 structures (~ 11 structures per day)2005: 5421 = 34325 structures (~ 15 structures per day)2008: 7069 = 55063 structures (~ 19 structures per day) (experimental structures only)
Structural genomics consists in the determination of the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography, NMR spectroscopy or computational approaches such as homology modelling.
As opposed to traditional structural biology, the determination of a protein structure through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. This raises new challenges in structural bioinformatics, i.e. determining protein function from its 3D structure.
One of the important aspects of structural genomics is the emphasis on high throughput determination of protein structures. This is performed in dedicated centers of structural genomics.
While most structural biologists pursue structures of individual proteins or protein groups, specialists in structural genomics pursue structures of proteins on a genome wide scale. This implies large scale cloning, expression and purification. One main advantage of this approach is economy of scale. On the other hand, the scientific value of some resultant structures is at times questioned.
• Assign all of the residues in the peptide the appropriate set of parameters. • Scan through the peptide and identify regions where 4 out of 6 contiguous residues have P(a-helix) > 100. • That region is declared an alpha-helix. Extend the helix in both directions until a set of four contiguous
residues that have an average P(a-helix) < 100 is reached. That is declared the end of the helix. If the segment defined by this procedure is longer than 5 residues and the average P(a-helix) > P(b-sheet) for that segment, the segment can be assigned as a helix.
• Repeat this procedure to locate all of the helical regions in the sequence. • Scan through the peptide and identify a region where 3 out of 5 of the residues have a value of
P(b-sheet) > 100. That region is declared as a beta-sheet. Extend the sheet in both directions until a set of four contiguous residues that have an average P(b-sheet) < 100 is reached. That is declared the end of the beta-sheet. Any segment of the region located by this procedure is assigned as a beta-sheet if the average P(b-sheet) > 105 and the average P(b-sheet) > P(a-helix) for that region.
• Any region containing overlapping alpha-helical and beta-sheet assignments are taken to be helical if the average P(a-helix) > P(b-sheet) for that region. It is a beta sheet if the average P(b-sheet) > P(a-helix) for that region.
•To identify a bend at residue number j, calculate the following value p(t) = f(j)f(j+1)f(j+2)f(j+3) where the f(j+1) value for the j+1 residue is used, the f(j+2) value for the j+2 residue is used and the f(j+3) value for the j+3 residue is used. If: (1) p(t) > 0.000075; (2) the average value for P(turn) > 1.00 in the tetrapeptide; and (3) the averages for the tetrapeptide obey the inequality P(a-helix) < P(turn) > P(b-sheet), then a beta-turn is predicted at that location.
Rel_sec reliability index for PROF_sec prediction (0=low to 9=high) SUB_sec subset of the PROFsec prediction, for all residues with an expected average accuracy > 82% (tables in header)
NOTE: for this subset the following symbols are used:L: is loop (for which above ' ' is used).: means that no prediction is made for this residue, as the reliability is: Rel < 5
O3_acc observed relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%. P3_acc PROF predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.Rel_acc reliability index for PROFacc prediction (0=low to 9=high) SUB_acc subset of the PROFacc prediction, for all residues with an expected average correlation > 0.69 (tables in header)
NOTE: for this subset the following symbols are used:I: is intermediate (for which above ' ' is used).: means that no prediction is made for this residue, as the reliability is: Rel < 4
• Perform BLAST search to find local alignments• Remove alignments that are “too close”• Perform multiple alignments of sequences• Construct a profile (PSSM) of amino-acid frequencies at each residue• Use this profile as input to the neural network• A second network performs “smoothing”• The third level computes jury decision of several different instantiations of
PSIPRED is a simple and reliable secondary structure prediction method, incorporating two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST (Position Specific Iterated - BLAST).
Version 2.0 of PSIPRED includes a new algorithm which averages the output from up to 4 separate neural networks in the prediction process to further increase prediction accuracy.
Using a very stringent cross validation method to evaluate the method's performance, PSIPRED 2.0 is capable of achieving an average Q3 score of nearly 78%. Predictions produced by PSIPRED were also submitted to the CASP4 server and assessed during the CASP4 meeting, which took place in December 2000 at Asilomar.PSIPRED 2.0 achieved an average Q3 score of 80.6% across all 40 submitted target domains with no obvious sequence similarity to structures present in PDB, which placed PSIPRED in first place out of 20 evaluated methods (an earlier version of PSIPRED was also ranked first in CASP3 held in 1998).
PSI-BLAST PSI-BLAST
Position specific iterative BLAST (PSI-BLAST) refers to a feature of BLAST 2.0 in which a profile (or position specific scoring matrix, PSSM) is constructed (automatically) from a multiple alignment of the highest scoring hits in an initial BLAST search.
The PSSM is generated by calculating position-specific scores for each position in the alignment. Highly conserved positions receive high scores and weakly conserved positions receive scores near zero.
The profile is used to perform a second (etc.) BLAST search and the results of each "iteration" are used to refine the profile.
This iterative searching strategy results in increased sensitivity.
Modeling by Homology (Comparative Modeling) Modeling by Homology (Comparative Modeling)
http://swissmodel.expasy.org/
Modeling by Homology (Comparative Modeling) Modeling by Homology (Comparative Modeling)
http://salilab.org/modeller/
Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates).
The prediction process consists of
• fold assignment, • target template alignment, • model building, and • model evaluation and refinement.
The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software.
Further advances are necessary in recognizing weak sequence structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences.
Methods of protein fold recognition attempt to detect similarities between protein 3D structure that are not accompanied by any significant sequence similarity.
The unifying theme of these appraoches is to try and find folds that are compatible with a particular sequence. Unlike sequence-only comparison, these methods take advantage of the extra information made available by 3D structure information.
Rather than predicting how a sequence will fold, they predict how well a fold will fit a sequence.
• Secondary structure is more conserved than primary structure
• Tertiary structure is more conserved than secondary structure
• Therefore very remote relationships can be better detected through 2o or 3o structural homology instead of sequence homology
Clusters are made up of dedicated components and all components in a cluster are exclusively owned and managed as part of the cluster. All resources are known, fixed and usually uniform in configuration. It is a static environment.
Grids differ from clusters because grids share resources from and among independent system owners. Grids are configured from computer systems that are individually managed and used both as independent systems and as part of the grid. Thus, individual components are not 'fixed' in the grid and the overall configuration of the grid changes over time. This results in a dynamic system that continually assesses and optimises its utilisation of resources.
Cluster vs. Grid Computing Cluster vs. Grid Computing
EUROGRID - BioGRID EUROGRID - BioGRID
www.eurogrid.org/wp1.html
Simulation of Protein FoldingSimulation of Protein Folding
Simulation of Protein FoldingSimulation of Protein Folding
Thousand trillon FLOPs
~ 65.000 processors
teraflop – a trillion floating point operations per second
IBM Blue Gene Project | System-on-a-Chip ApproachIBM Blue Gene Project | System-on-a-Chip Approach