More Definitions for delineate. See the full definition for delineate in the English Language Learners Dictionary. Nglish: Translation of delineate for Spanish Speakers. Britannica English: Translation of delineate for Arabic Speakers. Subscribe to America's largest dictionary and get thousands more definitions and advanced search—ad free!
Log in Sign Up. Save Word. Definition of delineate. Synonyms for delineate Synonyms define , outline , silhouette , sketch , trace Visit the Thesaurus for More. Examples of delineate in a Sentence He plants his skates millimeters outside the blue-tinted square-foot arena that delineates the crease and refuses to budge … — Michael Farber , Sports Illustrated , 21 May Screenwriter Christopher Hampton introduces a large gallery of characters, subtly delineating the unspoken class biases that will keep Robbie, for all his confidence, charm and Cambridge education, an outsider.
Although considered a core value by most citizens, it is not explicitly delineated as a protected right by the U. Cavazos et al. The characters in the story were carefully delineated.
The setting for the story is beautifully delineated in the first chapter. The definition and lessons for the word delineate were made available by the Power Vocabulary Builder. The Power Vocabulary Builder will help you develop a fuller, richer vocabulary 10 to times faster than any other program available.
Visit the the Power Vocabulary Builder site right now to discover how you can get full access to this breakthrough program today! Technical limitations of the computer's ability to work with numbers close to zero were carefully avoided by rejecting probabilities close to zero less than six decimal places. Sets of true and false quadruplets were generated from DSSP [ 8 ] output figs.
For every true quadruplet that was created, four false quadruplets were generated as shown in fig. Each quadruplet was scored using all three parameters fig. Scores for true and false quadruplets were analyzed figs. Our algorithm uses quadruplets formed from all available residues with the restriction that both covalently linked residues do not exist in any strict-helix SSET and allows a maximum overlap of one residue with a strict-helix SSET.
The quadruplets are scored similar to quadruplets obtained from DSSP [ 8 ], as described above. Based on the final score and cutoffs determined from the scores of true and false quadruplets generated from DSSP, quadruplets are placed in one of three groups. The grade 1 quadruplets are those with scores better than the best false quadruplets located from DSSP in the previous step quadruplets scoring less than c1 in fig.
The grade 2 quadruplets are those scoring in between the best false DSSP quadruplets and worst true DSSP quadruplets quadruplets scoring between c1 and c2 in figs.
Lastly, the grade 3 quadruplets are those, which passed cutoffs of distance and have non-zero probabilities for each of the three parameters fig.
Use of relaxed criteria such as those described in the previous section to determine the quality of quadruplets can lead to errors in some cases.
True quadruplets generated in the previous step from DSSP [ 8 ] output files figs. Angles were calculated for each of the common pair of residues with its pairs from both quadruplets figs. Initiation and extension of ladders of paired residues using quadruplets. Quadruplets are attached on either side to extend the arms of the ladder.
Depending on the position of the best quadruplets any number of quadruplets might be responsible for seeding a ladder. Smaller ladder fragments get joined by worse scoring quadruplets. This was used to check new residue pairings formed while adding quadruplets. Pairing and angle between pairs are checked for residues j-1 and j when worse scoring quadruplets are added.
Insertion of bulge residues is handled during joining of quadruplets. The quadruplets are simply added end to end. However, quadruplets j, j-1, k-1, k and j-2, j-3, k-2, k-1 pairing between j-2, k-1 not shown share only a single residue k As j-2, j-3, k-2, k-1 scores worse than j, j-1, k-1, k, the pairing between j-1, k-1 is retained and residue j-2 becomes a bulge with respect to residue k However, extension in the direction of hydrogen bonds poses some problems in the case of bulges.
The quadruplet extension process leads to the formation of ladders that are a sequence of paired residues. Thus, all residues on one arm of the ladder are paired with neighboring residues on the other arm of the ladder fig. Presence of a bulge is considered during ladder generation, and it is possible to have isolated residues on one arm of the ladder that do not have a pair.
Such a bulge residue is incorporated into a ladder at this step. Each grade 1 quadruplet, starting with the best scoring one, is checked for its ability to either join a previously selected better scoring quadruplet or initiate a new ladder in this single pass method. In case of a conflict with a previously chosen quadruplet, the current worse scoring quadruplet is rejected.
In every step irrespective of whether the current quadruplet is chosen or rejected, all quadruplets in the grade 1, 2 and 3 lists having scores worse than the current quadruplet and which can possibly conflict with the current quadruplet based on its constituent residues and pairing are rejected.
This ensures that conflicting quadruplets do not initiate ladders on their own. Attempts are made to join quadruplets end to end in one of two ways. A check is first made if both edge residues fig. This allows two consecutive quadruplets to be joined end to end to extend the ladder by a pair of residues. Upon failure to join a quadruplet by this method, the second method is applied. If only one corner of a quadruplet has the same residue as a corner of the other quadruplet, and the pairs to that corner residue in the different quadruplets are consecutive, the quadruplets are joined end to end to extend the ladder by one pair of residues.
The pair for the common corner in the new quadruplet is designated as a bulge with respect to the common corner residue.
This method of generating bulges also ensures that bulges arise from the worse scoring quadruplet. We have found such an assignment to be correct by manual inspection. In case no suitable existing quadruplet is located at either edge of any preformed ladder, the current quadruplet is designated as a ladder by itself and can be extended by quadruplets scoring lower than it.
Joining of quadruplets is attempted for both edges of a quadruplet. Thus, a quadruplet can potentially join with the edge quadruplets from two different ladders, with its own two edges. This joins the two existing ladders to form a single longer ladder of quadruplets.
These ladders of paired residues are checked for errors before further processing. It is possible to obtain quadruplets with both residues on its diagonal as bulges. All such quadruplets are removed after breaking the links at their edges with neighboring quadruplets. Quadruplets are selectively removed even if a single common residue belonging to a pair of neighboring quadruplets fails to pass the cutoff angle for wrong residue pairing as described in step 4 fig.
Cases where residues have two and three pairing residues are treated differently. A single residue, pairing with more than three other residues was not observed, thus showing that quadruplet parameters are able to distinguish between gross errors in geometry. A residue having only two pairs indicates two neighboring quadruplets. If the residues involved fail to pass the cutoff scores for the angle, the worse scoring quadruplet is rejected. A residue pairing with three other residues indicates three neighboring quadruplets having at least one common residue.
It is possible for a set of three residues at this location to pass cutoff scores for angle, in real structures, so we choose and eliminate the wrong quadruplet at this location. Two distinct cases are handled. A quadruplet is removed if it does not pass the angle cutoff with another neighboring quadruplet.
If two quadruplets do not pass cutoff within themselves, but both pass cutoffs with a third quadruplet, we keep only one of the first two. This is chosen based on the length of the ladder of paired residues which the quadruplet takes part in. The quadruplet from the longer ladder is retained while the other one is rejected, consistently with the goal of obtaining longer elements.
We define a helix as being a minimum of five residues, as this could suitably represent a single turn of a helix. We consider a maximum overlap of two residues between elements, so all helices of eight residues or longer always pass this criterion.
Thus for this step, all helices up to seven residues long are considered for removal. Quadruplets with grade two scores are used to extend ladders formed from at least two grade 1 quadruplets. All ladders therefore have a core region of grade 1 quadruplets, which are then extended to the regions that are more distorted. Extension is very similar to the initiation step using grade 1 quadruplets, except that more checks are put in place when each quadruplet is added, to prevent unreasonably distorted regions from being joined.
Our algorithm attempts to approximate elements as linear vectors at every step of the process. We incorporated steps to geometrically define the end of a ladder of paired residues to prevent generating ladders that span more than a single linear element. Quadruplets are not added if these criteria are violated. Extension is attempted on a list of ladders sorted by length. This ensures that longer elements have a better chance of ending due to geometric criteria rather than due to an extension quadruplet already being allocated to a shorter ladder.
A pair of residues are added to the ladder only if neither of the new residues already have two other residue pairs each. Thus, ladder extension depends both on ladder length as well as on quadruplet grade. Extension of a ladder is also terminated if this causes residue overlap with residues already participating in a strict-helix SSET.
Only residues that are a part of a loose-strand SSET are used in the extension step. No residues are added if the pair about to be added does not fall within the distance cutoffs of 3. Grade 3 quadruplets are used next, to extend only single grade 1 quadruplets that have not been extended by any of the above methods.
As grade three quadruplets are the worst scoring quadruplets that are used, two important constraints are utilized to prevent spurious extensions of lone grade 1 quadruplets. This constraint alone was able to eliminate most cases of chance interaction between pairs of residues.
However, in highly distorted regions that are too twisted to represent linear elements, more than a pair of consecutive residues seem to form isolated ladders. We decided not to include them as well. These ladders are joined with a single bulge residue if consecutive pairing arms on the other side share a common residue and restrictions imposed during ladder extension are not violated. Our method of ladder generation also makes it possible to obtain overlapping ladders such that one arm of one ladder overlaps with the arm of a different ladder.
Thus, we join all ladder arms that are formed from consecutive stretches of residues or with common residues between them. In order to approximate these elements by vectors suitable for motif search, we decided to split these helices into linear elements while considering overlap between them.
Some helix SSETs are found to overlap with parts of ladders generated and extended in the previous step. The helices are again checked for the presence of at least five residues before being accepted for processing by this step. Manual judgment of the results at this point indicated that our program's delineation of helices were acceptable in terms of residue coverage.
Presence of bent helices was noticed in the checkset described previously and we decided to split them into linear elements without loss of constituent residues.
We used helices defined by our program for calculation of parameters for breaking helices. Using data from helices defined by our program, enabled us to implement a system that could properly handle loosely defined helices and not to break them more frequently than needed. The results were visually inspected for errors. The helix breaking method relies on an analysis of the RMSD of helix residues around the helix axis.
Two different methods were used to generate the helix axis. Only one of the methods was finally adopted fig. The first method calculates the principal moment of the helix residues and used the eigenvector corresponding to the largest eigenvalue as the helix axis.
This method thus depends only on the spread of the residues in space and does not take into account the linear connectivity of the helix residues.
Due to the spread of residues being more on the diametrical plane of these helices, the axis found using the eigenvector method lay closer to the plane of the diameter instead of being normal to it. This method gave good results for longer helices. Helix endpoints redefined based on RMSD and angle between their axial vectors. The green arrow shows the rotational axis obtained when the helix that is shifted by one residue, is aligned to the original helix. Our algorithm uses the rotational-fit method described below, 8b for all helices.
RMSD of residues are calculated over this vector. Angles between vectors, calculated from residues of consecutive helices, are used to determine whether to break them so as to appropriately define the helices as linear elements. Average RMSD of unbroken helices from our algorithm varies widely. The helices were broken multiple times and the angle of break was analyzed data not shown. Average RMSD of broken helices is shown in this figure. A line was fitted using "gnuplot" [40] to approximate the RMSD of broken helices.
A Z-score of 2. Data were collected from helices broken once, twice and thrice. The normalized data are shown. All possibilities of broken pieces are assessed with respect to the RMSD of the pieces and angle of break. Based on the observations above, a rotational fit method was used to determine helix axis [ 22 , 45 ] fig.
This involves shifting the helix by one residue and aligning it with the original helix. The rotation axis corresponds to the helix axis. This was found to precisely determine the helix axis and was not dependent upon the length or under-winding of the helix.
The axis determined by this method and that determined by the eigenvector method correlate very well for helices greater than 8 residues data not shown. Our program was run on the "statset", described previously, and all helices were extracted for study. The RMSD of helix residues from the helix axis were calculated and analyzed fig.
All helices were processed using the helix-breaking method described below. Each helix was split in three ways such that case 1 gave rise to 2 pieces, case 2 gave rise to 3 pieces and case 3 gave rise to 4 pieces from the original unbroken helix.
The mode of breaking angles was calculated for every helix length data not shown. Broken helices that arose from this set were used to calculate the RMSD of broken helices around the rotational fit axis fig.
The standard deviation was calculated for every helix length and the results showing dependency of the standard deviation on the length were fitted to a straight line data not shown. The average RMSD and average standard deviation calculated above were used to obtain broken helices as described below that were analyzed manually.
Our algorithm does not break a helix showing a slight curvature in its structure, or containing a few distorted residues. For bent helices, we decided to use two cutoffs to determine breakpoints. Flexibility is represented by a Z-score representing the allowed deviation as multiples of the standard deviation of helix residues as calculated above. A sharp bend in the helix axis is measured by the angle between the axes of two neighboring helices as calculated by the rotational fit method described above.
The broken helices observed were manually inspected to determine the optimum Z-score and the break angle fig. A breaking method for helices was developed in order to determine the correct cutoffs for Z-score and angle of break. The method considers every possible breakpoint in a helix and attempts to choose the optimal result.
We define broken helices as single elements only if the piece with the highest RMSD is still acceptable fig. Multiple breaks are considered with no overlaps and with overlaps of up to two residues at every position of the helix. The minimum helix length allowed is five residues. Broken helices are considered starting from the shortest helix length 5 residues , with maximum overlap 2 residues , to the longest possible helix the unbroken helix. The helix breaking process analyses the RMSD and angle of break for every combination of helical fragments instance derived from the unbroken helix.
Thus, every "instance" is the set of broken helical fragments produced during the iterative breaking process. Every possible case of broken helices that can be formed by an unbroken helix is considered and a single helix is broken into as many long fragments as is optimal for correct representation as linear elements. RMSD along the helix axis, computed by the rotational fit method described above, is used to determine overall suitability of broken helical pieces.
For every unbroken helix, RMSD of every possible broken helical fragment is considered. For all "instances" of broken helices, the fragment with the highest RMSD is located.
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