ABSTRACT
SUMMARY: One of the more common uses of the program FingerPrint Contigs (FPC) is to assemble random restriction digest 'fingerprints' of overlapping genomic clones into contigs. To improve the rate of assembling contigs from large fingerprint databases we have adapted FPC so that it can be run in parallel on multiple processors and servers. The current version of 'parallelized FPC' has been used in our laboratory to assemble mammalian BAC fingerprint databases, each containing more than 300000 BAC fingerprints. AVAILABILITY: This parallelized version of FPC is available under the GNU GPL licence, and can be downloaded from ftp://ftp.bcgsc.bc.ca/pub/fpcd.
Subject(s)
Algorithms , Cloning, Molecular , Computing Methodologies , Contig Mapping/methods , Databases, Genetic , Animals , Base Sequence , Contig Mapping/statistics & numerical data , DNA Fingerprinting/methods , Humans , Internet , Mice , Molecular Sequence Data , Restriction Mapping , Sensitivity and Specificity , Sequence Tagged Sites , Software , Time FactorsABSTRACT
While functioning as a general practitioner at the Camp Pendleton Marine Base, the first author treated numerous patients with recurrent genital herpes. Beginning in 1998, a number of these patients failed to return for periodic acyclovir therapy. Inquiries revealed that these patients had all commenced supplemental creatine after their last outbreak, and had experienced no further outbreaks. A literature search uncovered a report that cyclocreatine, a synthetic compound structurally and functionally homologous to creatine, inhibits the replication of cytomegalovirus, varicella-zoster, and herpes simplex types 1 and 2, in low millimolar concentrations; furthermore, dietary cyclocreatine reduces morbidity and mortality in mice infected with HSV-2. The fact that both creatine and cyclocreatine exert neuroprotective and cancer-retardant effects in rodents, encourages the speculation that creatine shares the anti-viral activity of cyclocreatine. Pilot studies to assess the impact of creatine loading on recurrence of oral and genital herpes appear warranted; the impact of creatine on shingles occurrence in high-risk patients could also be explored. Although initially conceived as an aid to athletic performance, creatine loading may prove to have broad preventive and therapeutic applications.
Subject(s)
Creatine/therapeutic use , Herpes Genitalis/prevention & control , Animals , Herpes Genitalis/drug therapy , Herpes Genitalis/physiopathology , Herpesvirus 1, Human/physiology , Herpesvirus 2, Human/physiology , Humans , Mice , Recurrence , Virus ReplicationABSTRACT
The binding positions of six small-molecule ligands in their complexes with target proteins were predicted using our Research docking program for the CASP2 challenge. Research uses a Monte Carlo procedure with pairwise energies and allows for the conformational searching of ligand torsional space. We were able to predict 2 of the 5 noncovalent complexes within 2 A root-mean-square (RMS) of the experimental structures as ranked by interaction energy or by a score calculated using our interaction evaluation program, Out-rank. In addition, for 4 of the 5 noncovalent structures we found a docking within 2 A RMS of the experimental structure within the top 20 dockings as ranked by energy. The main limitation in our approach is in the ability of the energy function and Outrank to discriminate among the lowest energy dockings. On the other hand, our success in exploring the multi-dimensional docking space of position, orientation and conformation is encouraging.
