DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories.

This work describes a fast implementation of a software algorithm associated with determination of protein secondary structure based on the Define Secondary Structure of Proteins (DSSP) algorithm. This implementation is fully compatible with the DSSP v.4 and DSSP v.2 algorithms and implemented as a native GROMACS trajectory analysis module, which allows us to analyze molecular dynamics trajectories without any restrictions of the original DSSP implementation. This implementation works much faster than the original DSSP v.4 and DSSP v.2 algorithms.

Could the sextant prostate biopsy be replaced by transurethral resection?

AIM OF THE STUDY: We studied patients with elevated serum levels of prostate specific antigen (PSA) and low urinary tract symptoms (LUTS) aiming to determine whether histological examination after transurethral resection of the prostate (TURP) could detect prostate cancer (PC) missed by previous routine transrectal ultrasound (TRUS) guided sextant prostate biopsies. MATERIALS AND METHODS: We considered 98 consecutive men with serum tPSA level from 4 to 12 ng/mL who were submitted to TRUS-guided sextant biopsies. RESULTS: PC was detected in 28 (28.6%) cases at first biopsy. Of the 70 patients who were not proven to have PC, 49 underwent TURP for severe LUTS. The median volume of resected tissue was 14.2 g (11.0-19.4 g). PC was detected in 12 (24.5%) specimens of resected tissue after TURPF PC lesions diagnosed after TURP were located mainly in the TZ, with cancer volume not more than 0.108 cm3. In 21 patients with negative first biopsy who did not underwent TURP was prescribed a conservative treatment and follow-up. In 7 of those patients elevated serum PSA levels were revealed during the follow-up. A second sextant TRUS-guided biopsy demonstrated PC in 4 patients. The remaining patients showed no significant increase in their serum PSA level and are still observed in present days. CONCLUSIONS: The sensitivity of routine sextant TRUS-guided biopsy of the prostate is not high enough and the detection of cancer is not warranted using this standard procedure. TURP can detect cancers in TZ of the prostate, when performed for treating LUTS in patients with negative prostate biopsy. In patients who did not need TURP: only in 4 out of 21 patients with a negative first biopsy a repeat biopsy demonstrated PC. In conclusion TURP is recommended for all the patients with enlarged prostate, negative prostate biopsy and severe LUTS after unsuccessful conservative treatment.