Aart J. Nederveen

RECOORD: A Recalculated Coordinate Database of 500 Proteins from the PDB Using Restraints from the BioMagResBank

State‐of‐the‐art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user‐ and software‐dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure‐based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord. Proteins 2005.

Measurements and clinical consequences of prostate motion during a radiotherapy fraction.

PURPOSEnHere we study the magnitude of prostate motion during the delivery of a radiotherapy fraction. These motions have clinical consequences for on-line position verification and the choice of margins around the target volume.nnnMETHODS AND MATERIALSnWe studied the motion of the prostate for 10 patients during 251 radiotherapy treatment fractions by assessing the position of implanted gold markers. Gold markers of 1 mm diameter and 5 mm length were implanted in the prostate before the start of the radiotherapy. We obtained movies during each fraction using an a-Si flat-panel imager. The markers could be detected in separate frames using a marker extraction kernel.nnnRESULTSnMarker displacements as large as 9.5 mm were detected in one fraction. The motion of the prostate is greatest in the caudal-cranial and the anterior-posterior directions. Within a time window of 2 to 3 min, deviations from the initial marker position, averaged over all patients, are 0.3 +/- 0.5 mm and -0.4 +/- 0.7 mm in the anterior-posterior and caudal-cranial directions, respectively.nnnCONCLUSIONSnIt appeared that on average, the intrafraction prostate motions did not result in margins larger than 1 mm, provided that the position verification is performed at time intervals of 2 to 3 min. Only for some patients performing more frequent position verification or adding extra margins of 2 to 3 mm is required to account for intrafraction prostate motions.

Comparison of megavoltage position verification for prostate irradiation based on bony anatomy and implanted fiducials.

PURPOSEnThe patient position during radiotherapy treatment of prostate cancer can be verified with the help of portal images acquired during treatment. In this study we quantify the clinical consequences of the use of image-based verification based on the bony anatomy and the prostate target itself.nnnPATIENTS AND METHODSnWe analysed 2025 portal images and 23 computed tomography (CT) scans from 23 patients with prostate cancer. In all patients gold markers were implanted prior to CT scanning. Statistical data for both random and systematic errors were calculated for displacements of bones and markers and we investigated the effectiveness of an off-line correction protocol.nnnRESULTSnStandard deviations for systematic marker displacement are 2.4 mm in the lateral (LR) direction, 4.4 mm in the anterior-posterior (AP) direction and 3.7 mm in the caudal-cranial direction (CC). Application of off-line position verification based on the marker positions results in a shrinkage of the systematic error to well below 1 mm. Position verification based on the bony anatomy reduces the systematic target uncertainty to 50% in the AP direction and in the LR direction. No reduction was observed in the CC direction. For six out of 23 patients we found an increase of the systematic error after application of bony anatomy-based position verification.nnnCONCLUSIONSnWe show that even if correction based on the bony anatomy is applied, considerable margins have to be set to account for organ motion. Our study highlights that for individual patients the systematic error can increase after application of bony anatomy-based position verification, whereas the population standard deviation will decrease. Off-line target-based position verification effectively reduces the systematic error to well below 1 mm, thus enabling significant margin reduction.

DRESS: a database of refined solution NMR structures

Several studies have shown that biomolecular NMR structures are often of lower quality when compared to crystal structures, and consequently they are often excluded from structural analyses. We present a publicly available database of re‐refined NMR structures, exhibiting significantly improved quality. This database (available at http://www.cmbi.kun.nl/dress/) presents a uniformly refined and validated set of structural models that improves the value of these NMR structures as input for experimental and theoretical studies in many fields of research. Proteins 2004.

DETECTION OF FIDUCIAL GOLD MARKERS FOR AUTOMATIC ON-LINE MEGAVOLTAGE POSITION VERIFICATION USING A MARKER EXTRACTION KERNEL (MEK)

PURPOSEnIn this study automatic detection of implanted gold markers in megavoltage portal images for on-line position verification was investigated.nnnMETHODS AND MATERIALSnA detection method for fiducial gold markers, consisting of a marker extraction kernel (MEK), was developed. The detection success rate was determined for different markers using this MEK. The localization accuracy was investigated by measuring distances between markers, which were fixed on a perspex template. In order to generate images comparable to images of patients with implanted markers, this template was placed on the skin of patients before the start of the treatment. Portal images were taken of lateral prostate fields at 18 MV within 1-2 monitor units (MU).nnnRESULTSnThe detection success rates for markers of 5 mm length and 1.2 and 1.4 mm diameter were 0.95 and 0.99 respectively when placed at the beam entry and 0.39 and 0.86 when placed at the beam exit. The localization accuracy appears to be better than 0.6 mm for all markers.nnnCONCLUSIONnAutomatic marker detection with an acceptable accuracy at the start of a radiotherapy fraction is feasible. Further minimization of marker diameters may be achieved with the help of an a-Si flat panel imager and may increase the clinical acceptance of this technique.

Feasibility of automatic marker detection with an a-Si flat-panel imager

Here we study automatic detection of implanted gold markers relative to the field boundary in portal images for on-line position verification. Portal images containing 1-2 MU were taken with an amorphous silicon flat-panel imager. The images were obtained with lateral field at 18 MV. Both the detection success rate and the localization accuracy of markers of 1.0 and 1.2 mm diameter were determined with the help of a marker detection method based on a marker extraction kernel. A method for determining a fiducial reference point related to the field boundary was developed. Detection success rates were 0.99, 0.90 and 0.95 for markers of 1.2 mm diameter and 5 mm length, 1.0 mm diameter and 5 mm length and 1.0 mm diameter and 10 mm length respectively. The localization accuracy appeared to be better than 0.3 mm. The reference point could be reproduced with an accuracy equal to 1 pixel (0.5 mm at isocentre) within one fraction. During the first few seconds of a treatment fraction the field edge was not stable, which appeared to be an effect of the motion of the radiation source. Thanks to the use an a-Si flat-panel imager, on-line position verification using implanted gold markers becomes clinically feasible. We can use a clinically acceptable marker diameter as small as 1.0 mm. These markers can be automatically detected in portal images obtained with 1-2 MU relative to a stable reference point related to the field boundary.

NMR Relaxation and Internal Dynamics of Ubiquitin from a 0.2 μs MD Simulation.

A 0.2 μs molecular dynamics simulation of ubiquitin in water is presented, which allows us to assess both the global tumbling in solution and the internal dynamics. The latter reveals slow motions outside the classical NMR timewindow, in agreement with recent RDC and cross-correlation measurements. Analysis of back-calculated relaxation rates using the classical NMR model-free approach reproduces the amplitudes of internal motions expressed in the order parameter, while it severely underestimates the corresponding time scales present in the simulation.

Partial boosting of prostate tumours

BACKGROUND AND PURPOSEnIn this planning study we propose a class solution for partial boosting of prostate tumours. Treatment margins and rectum dose are similar to that of the conventional treatment and are supposed to have no direct link to the level of dose escalation. We also study the robustness of our class solution in the presence of geometrical deviations.nnnMETHODS AND MATERIALSnTo study the specifications of the class solution ten patients with histologically confirmed prostate cancer were replanned. Besides a conventional plan for each patient, different partial boost plans were produced with an inverse treatment-planning tool. We also simulated treatment geometrical deviations to estimate their effect on partial boost plans.nnnRESULTSnIn our class solution we use three contours in our inverse treatment planning, which are based on the classical CTV. A three beam arrangement appeared to produce a dose distribution, which is comparable to that of a five or seven beam geometry. Comparison of partial boost plans and conventional plans indicated that all conditions for a partial boost plan could be satisfied with the proposed class solution. Simulation of treatment geometrical deviations showed that large random deviations have a minor effect on the overall dose distributions, while systematic deviations may decrease the boost dose and increase the rectal dose.nnnCONCLUSIONSnWe presented a class solution for partial boosting of prostate tumours in which the level of dose escalation is dealt with separately from the margin size and the nominal rectum dose. The framework put forward in this study allows practical introduction of intensity modulated radiotherapy in routine clinical practice using current standards of imaging and position verification.

Prediction of protein loop geometries in solution.

The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the ability to reproduce protein loop geometries in experimentally derived solution structures. Predictions were run on loops drawn from (1)NMR entries in the Protein Databank (PDB), and from (2) the RECOORD database in which NMR entries from the PDB have been standardized and re‐refined in explicit solvent. The predicted structures are validated by comparison with experimental distance restraints, a test of structural quality as defined by the WHAT IF structure validation program, root mean square deviation (RMSD) of the predicted loops to the original structural models, and comparison of precision of the original and predicted ensembles. Results show that for the RECOORD ensembles, the predicted loops are consistent with an average of 95%, 91%, and 87% of experimental restraints for the short, medium and long loops respectively. Prediction accuracy is strongly affected by the quality of the original models, with increases in the percentage of experimental restraints violated of 2% for the short loops, and 9% for both the medium and long loops in the PDB derived ensembles. We anticipate the application of our protocol to theoretical modeling of protein structures, such as fold recognition methods; as well as to experimental determination of protein structures, or segments, for which only sparse NMR restraint data is available. Proteins 2007.

Patient position verification using small IMRT fields

A commonly used approach to quantify and minimize patient setup errors is by using electronic portal imaging devices (EPIDs). The position of the tumor can be verified indirectly by matching the bony anatomy to a reference image containing the same structures. In this paper we present two off-line methods for detecting the position of the bony anatomy automatically, even if every single portal image of each segment of an IMRT treatment beam contains insufficient matching information. Extra position verification fields will no longer be necessary, which reduces the total dose to the patient. The first method, the stack matching method (SMM), stacks the portal image of each segment of a beam to a three dimensional (3D) volume, and this volume is subsequently used during the matching phase. The second method [the averaged projection matching method (APMM)], is a simplification of the first one, since the initially created volume is reduced again to a 2D artificial image, which speeds up the matching procedure considerably, without a significant loss of accuracy. Matching is based on normalized mutual information. We demonstrate our methods by comparing them to existing matching routines, such as matching based on the largest segment. Both phantom and patient experiments show that our methods are comparable with the results obtained from standard position verification methods. The matches are verified by means of visual inspection. Furthermore, we show that when a distinct area of 40-60 cm2 of the EPID is exposed during one treatment beam, both SMM and APMM are able to deliver a good matching result.