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PubMed2002

ConsDock: A new program for the consensus analysis of protein-ligand interactions.

Protein-based virtual screening of chemical libraries is a powerful technique for identifying new molecules that may interact with a macromolecular target of interest. Because of docking and scoring limitations, it is more difficult to apply as a lead optimization method because it requires that the docking/scoring tool is able to propose as few solutions as possible and all of them with a very good accuracy for both the protein-bound orientation and the conformation of the ligand. In the present study, we present a consensus docking approach (ConsDock) that takes advantage of three widely used docking tools (Dock, FlexX, and Gold). The consensus analysis of all possible poses generated by several docking tools is performed sequentially in four steps: (i) hierarchical clustering of all poses generated by a docking tool into families represented by a leader; (ii) definition of all consensus pairs from leaders generated by different docking programs; (iii) clustering of consensus pairs into classes, represented by a mean structure; and (iv) ranking the different means starting from the most populated class of consensus pairs. When applied to a test set of 100 protein-ligand complexes from the Protein Data Bank, ConsDock significantly outperforms single docking with respect to the docking accuracy of the top-ranked pose. In 60% of the cases investigated here, ConsDock was able to rank as top solution a pose within 2 A RMSD of the X-ray structure. It can be applied as a postprocessing filter to either single- or multiple-docking programs to prioritize three-dimensional guided lead optimization from the most likely docking solution.

Animals↗
PubMed1995

Consensus preferred hydration sites in six FKBP12-drug complexes.

A set of consensus hydration sites for the FK506-FKBP12 complex are derived by comparing six FKBP12-drug complexes. These hydration sites include a subset of the observed water molecules plus some sites that are occupied by neighboring protein atoms in the FK506-FKBP12 crystal structure. Two hydration prediction algorithms, AUTO-SOL and AQUARIUS2, showed significant increases in apparent efficacy using these consensus water sites, suggesting that our proposed set of consensus hydration sites is truly a better representation of the hydration properties of FKBP12 in solution. Predictably, the consensus hydration sites include all buried water molecules. Otherwise, the features of solvation sites included in the consensus list versus those discarded reveal no distinctive features that would allow them to be selected unambiguously without reference to multiple crystal forms. We suggest that analyses such as this one are a crucial prelude to any theoretical analysis aimed at understanding hydration properties.

Algorithms↗
PubMed1999

Total evidence, consensus, and bat phylogeny: A distance-based approach.

Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for combining trees, and (3) indifference to aspects of trees other than their topologies. We demonstrate a uniform, distance-based approach which allows for comparability among the results of character- and taxonomic-congruence studies, whether or not an identical suite of taxa has been included in all contributing data sets. Our results indicate that total-evidence and consensus trees differ little in topology if branch lengths are taken into account when combining two or more trees. In addition, when character-state data are converted to distances, our method permits their combination with information produced by techniques which generate distances directly. Moreover, treating all data sets or trees as distance matrices avoids the problem that different numbers of characters in contributing studies may confound the conclusions of a total-evidence or consensus analysis. Our protocol is illustrated with an example involving bats, in which the three component studies based on serology, DNA hybridization, and anatomy imply distinct phylogenies. However, the total-evidence and consensus trees support a fourth, somewhat different, topology resolved at all but one node and which conforms closely to the currently accepted higher category classification of Chiroptera.

Animals↗
PubMed1995

Protein kinase C consensus sites and the regulation of renal Na/Pi-cotransport (NaPi-2) expressed in XENOPUS laevis oocytes.

Renal brush border membrane sodium/phosphate (Na/Pi)-cotransport activity is inhibited by hormonal mechanisms involving activation of protein kinases A and C. The recently cloned rat renal Na/Pi-cotransporter (NaPi-2) contains several protein kinase C but no protein kinase A consensus sites [17, 20]. In the present study we have expressed wild type and polymutant (protein kinase C consensus sites removed) NaPi-2-transporters in Xenopus laevis oocytes. The expression of transport function as well as the basic transport properties were unaffected by the removal of the consensus sites. Pharmacological activation of protein kinase C with phorbol 12,13-didecanoate (PDD) led to a time-dependent inhibition of expressed wild type Na/Pi-cotransport function; simultaneous exposure to staurosporine (0.3) prevented the PDD induced (50 nM) inhibition. The kinase-C-mediated inhibition was not prevented by the removal of the protein kinase C consensus sites. Pharmacological activation of protein kinase A (dibutyryl adenosine 3':5':cyclic monophosphate (cAMP)/forskolin) had no effect on wild type NaPi-2-induced oocyte Na/Pi-cotransport. It is concluded that the protein-kinase-C-mediated regulation of expressed Na/Pi-cotransport does not involve the predicted consensus sites. The involvement of "cryptic" phosphorylation sites and/or of a phosphorylated "regulatory" protein is discussed.

Amino Acid Sequence↗
PubMed2004

Computer-assisted detection of pulmonary nodules: performance evaluation of an expert knowledge-based detection system in consensus reading with experienced and inexperienced chest radiologists.

To evaluate the performance of experienced versus inexperienced radiologists in comparison and in consensus with an interactive computer-aided detection (CAD) system for detection of pulmonary nodules. Eighteen consecutive patients (mean age: 62.2 years; range 29-83 years) prospectively underwent routine 16-row multislice computed tomography (MSCT). Four blinded radiologists (experienced: readers 1, 2; inexperienced: readers 3, 4) assessed image data against CAD for pulmonary nodules. Thereafter, consensus readings of readers 1+3, reader 1+CAD and reader 3+CAD were performed. Data were compared against an independent gold standard. Statistical tests used to calculate interobserver agreement, reader performance and nodule size were Kappa, ROC and Mann-Whitney U. CAD and experienced readers outperformed inexperienced readers (Az=0.72, 0.71, 0.73, 0.49 and 0.50 for CAD, readers 1-4, respectively; P<0.05). Performance of reader 1+CAD was superior to single reader and reader 1+3 performances (Az=0.93, 0.72 for reader 1+CAD and reader 1+3 consensus, respectively, P<0.05). Reader 3+CAD did not perform superiorly to experienced readers or CAD (Az=0.79 for reader 3+CAD; P>0.05). Consensus of reader 1+CAD significantly outperformed all other readings, demonstrating a benefit in using CAD as an inexperienced reader replacement. It is questionable whether inexperienced readers can be regarded as adequate for interpretation of pulmonary nodules in consensus with CAD, replacing an experienced radiologist.

Adult↗
PubMed1993

Determinants of heart-lung transplantation outcomes: results of a consensus survey.

Substantial progress has been made in clinical heart-lung transplantation. Although outcomes vary across centers, 1-year patient survival is now 59%. This study was an attempt to assess consensus among transplant program directors regarding the major determinants of patient outcome. In the National Cooperative Transplantation Study we evaluated consensus through a survey of all heart-lung transplant programs active in 1988. Of the eligible programs, 23 (85%) returned completed surveys. Data on the medical and surgical determinants of outcome were analyzed. There was considerable consensus among program directors as to the importance of several factors. The three most critical predictors of favorable outcomes were periodic pulmonary function tests to detect rejection (85.7%), avoidance of use of prednisone during the first 14 days after transplantation (76.2%), and annual left and right heart catheterization with coronary arteriography (76.2%). Several approaches were considered undesirable or unnecessary. These included electrocardiogram as standard rejection monitoring technique (71.4%), cytoimmunological monitoring as standard rejection monitoring technique (66.7%), and routine steroid discontinuation after transplantation (66.7%). On various other treatment approaches there was little evidence of consensus. These included prophylaxis with acyclovir and severe bronchiolitis as a criterion for retransplantation. Although controversial, consensus conferences are one means by which to evaluate technological innovations. Based on their results, practice guidelines can be developed to better inform third-party payers on issues related to transplantation.

Data Collection↗
PubMed1991

Identification and purification of a protein that binds the yeast ARS consensus sequence.

We have identified a yeast protein that binds specifically to the ARS consensus sequence. By two-step chromatography we have purified the factor to apparent homogeneity as a single polypeptide of 67 kd. The purified ARS consensus-binding protein (ACBP) recognizes the ARS consensus of the four genomic ARS elements tested, binding preferentially to the T-rich single strand. Point mutations in the consensus significantly reduce the affinity of the single-strand binding. At the histone H4 ARS, ACBP recognizes both the perfect ARS consensus and a 9/11 match 3' of it. These two binding sites correlate with the boundaries of the minimal functional H4 ARS element. A similar configuration of binding sites is found at ARS1. We propose a model implicating this factor in an early step of the initiation of DNA replication.

Base Sequence↗
PubMed2006

The contribution of consensus within staff and client groups as well as concordance between staff and clients to treatment engagement.

Two nonspecific organizational factors-consensus, defined as agreement within staff and client groups, and concordance, defined as agreement between staff and client groups-were shown to influence client engagement in treatment in a national sample of 80 residential substance abuse treatment programs including 595 staff and 3,732 clients. Agreement was tested using a combined therapeutic community, cognitive-behavioral therapy, and 12-step treatment scale completed by staff and clients. Treatment engagement was measured by the combined scores on the three scales completed by the clients, including engagement, rapport with the counseling process, and confidence in treatment. Within-group consensus was measured by the standard deviations of the mean scores, whereas between-groups concordance was measured by the standard error of the difference between staff and client mean scores. Regression analyses showed that staff consensus was a significant independent predictor of client treatment engagement (p < .05), whereas client consensus approached significance (p < .10). Concordance was also a significant predictor of client engagement (p < .002) after controlling for staff and client consensus. The potential contribution of the findings to a better understanding of program quality and effectiveness of programmatic interventions is discussed.

Adult↗
PubMed2005

Consensus decision making in animals.

Individual animals routinely face decisions that are crucial to their fitness. In social species, however, many of these decisions need to be made jointly with other group members because the group will split apart unless a consensus is reached. Here, we review empirical and theoretical studies of consensus decision making, and place them in a coherent framework. In particular, we classify consensus decisions according to the degree to which they involve conflict of interest between group members, and whether they involve either local or global communication; we ask, for different categories of consensus decision, who makes the decision, what are the underlying mechanisms, and what are the functional consequences. We conclude that consensus decision making is common in non-human animals, and that cooperation between group members in the decision-making process is likely to be the norm, even when the decision involves significant conflict of interest.

Journal Article↗
PubMed2003

A randomized trial of consensus interferon in combination with ribavirin as initial treatment for chronic hepatitis C.

BACKGROUND/AIMS: The aim of the present, open-labeled, randomized study was to determine the efficacy and safety of different doses of consensus interferon plus ribavirin in the initial treatment of chronic hepatitis C. METHODS: One hundred and one genotype 2/3 patients were randomized to receive 9 mcg (group A, n=48) or 18 mcg (group B, n=53) of consensus interferon thrice weekly plus ribavirin (1000/1200 mg/daily) for 24 weeks and 92 genotype 1 patients to receive 9 mcg (group C, n=47) or 18 mcg (group D, n=45) of consensus interferon plus ribavirin for 48 weeks. RESULTS: In an intention-to-treat analysis, the sustained virologic response at 24-week follow-up was 69% and 66% for group A and B (P=0.77) and 40% and 36% for group C and D (P=0.63). The overall sustained response was 67% and 38% in patients with genotype 2/3 and 1, respectively. Among genotype 1 patients the sustained virologic response was 39% and 41% for high or low baseline viremia levels. CONCLUSIONS: Higher consensus interferon dose does not increase sustained virologic response. Naive genotype 1 patients may achieve significant response rate of approximately 40% if treated with 9 mcg of consensus interferon plus ribavirin for 48 weeks.

Adult↗
PubMed2001

Chemical disease-free survival in localized carcinoma of prostate treated with external beam irradiation: comparison of American Society of Therapeutic Radiology and Oncology Consensus or 1 ng/mL as endpoint.

PURPOSE: To compare postirradiation biochemical disease-free survival using the American Society of Therapeutic Radiology and Oncology (ASTRO) Consensus or elevation of postirradiation prostate-specific antigen (PSA) level beyond 1 ng/mL as an endpoint and correlate chemical failure with subsequent appearance of clinically detected local recurrence or distant metastasis. METHODS AND MATERIALS: Records of 466 patients with histologically confirmed adenocarcinoma of the prostate treated with irradiation alone between January 1987 and December 1995 were analyzed; 339 patients were treated with bilateral 120 degrees arc rotation and, starting in 1992, 117 with three-dimensional conformal irradiation. Doses were 68--77 Gy in 1.8 to 2 Gy daily fractions. Minimum follow-up is 4 years (mean, 5.5 years; maximum, 9.6 years). A chemical failure was recorded using the ASTRO Consensus or when postirradiation PSA level exceeded 1 ng/mL at any time. Clinical failures were determined by rectal examination, radiographic studies, and, when clinically indicated, biopsy. RESULTS: Six-year chemical disease-free survival rates using the ASTRO Consensus according to pretreatment PSA level for T1 tumors were: < or = 4 ng/mL, 100%; 4.1--20 ng/mL, 80%; and > 20 ng/mL, 50%. For T2 tumors the rates were: < or = 4 ng/mL, 91%; 4.1--10 ng/mL, 81%; 10.1--20 ng/mL, 55%; 20.1--40 ng/mL, 63%; and > 40 ng/mL, 46%. When postirradiation PSA levels higher than 1 ng/mL were used, the corresponding 6-year chemical disease-free survival rates for T1 tumors were 92% for pretreatment PSA levels of < or = 4 ng/mL, 58--60% for levels of 4.1--20 ng/mL, and 30% for levels > 20 ng/mL. For T2 tumors, the 6-year chemical disease-free survival rates were 78% in patients with pretreatment PSA levels of 4--10 ng/mL, 45% for 10.1--40 ng/mL, and 25% for > 40 ng/mL. Of 167 patients with T1 tumors, 30 (18%) developed a chemical failure, 97% within 5 years from completion of radiation therapy; no patient has developed a local recurrence or distant metastasis. In patients with T2 tumors, overall 45 of 236 (19%) had chemical failure, 94% within 5 years of completion of radiation therapy; 4% have developed a local recurrence, and 10%, distant metastasis. In patients with T3 tumors, overall, 24 of 65 (37%) developed a chemical failure, 100% within 3.5 years from completion of radiation therapy; 4% of these patients developed a local recurrence within 2 years, and 12% developed distant metastasis within 4 years of completion of irradiation. The average time to clinical appearance of local recurrence or distant metastasis after a chemical failure was detected was 5 years and 3 years, respectively. CONCLUSION: There was a close correlation between the postirradiation nadir PSA and subsequent development of a chemical failure. Except for patients with T1 tumors and pretreatment PSA of 4.1--20 ng/mL, there is good agreement in 6-year chemical disease-free survival using the ASTRO Consensus or PSA elevations above 1 ng/mL as an endpoint. Although the ASTRO Consensus tends to give a higher percentage of chemical disease-free survival in most groups, the differences with longer follow-up are not statistically significant (p > 0.05). It is important to follow these patients for at least 10 years to better assess the significance of and the relationship between chemical and clinical failures.

Disease-Free Survival↗
PubMed2003

Attributes of trainers for postgraduate training in general surgery--a national consensus.

BACKGROUND: The aim of this study was to obtain consensus amongst consultant surgeons on the attributes of a good surgical trainer that can be used to inform continuing professional development programmes for trainers. METHODS: good trainer attributes were generated from an intensive qualitative study using a participative inquiry process with consultant general surgeons and specialist registrars in the Tayside region. These good trainer attributes were then used as the basis of a modified Delphi study; the early rounds of the Delphi simultaneously sought participants' views concerning stated attributes and sought to generate new attributes. A final Delphi questionnaire was sent to all 180 consultant general surgeons in Scotland to identify consensus. RESULTS: The first two rounds of the Delphi process produced 45 attributes covering seven themes: interest in training, trainer as a team member, communication, receptiveness to trainee needs, trainer as a role model, reflection on practice and clinical and operative competence. The final survey identified significant consensus among surgeons. Clinical and operative competence achieved the highest consensus with 89.2% of surgeons believing it to be an essential attribute. CONCLUSIONS: The results indicate that there is consensus on the seven themes identified as essential for a trainer in general surgery. The recognition of the importance by trainers of non-surgical trainer attributes in the changed training structure is encouraging. Surgeons' level of awareness of their roles as a trainer will help inform the level and direction of trainer training and support required as part of a flexible and continuing developmental process.

Education, Medical, Graduate↗
PubMed1998

Detection and diagnosis of delirium in the elderly: psychiatrist diagnosis, confusion assessment method, or consensus diagnosis?

The clinical diagnosis of delirium has traditionally been based on an assessment by one or more physicians. Because of the transient, ubiquitous, and fluctuating nature of the symptoms of delirium, however, this approach may be flawed. Therefore, we decided to compare diagnosis based on one assessment by a psychiatrist, diagnosis by a nurse clinician (using the Confusion Assessment Method [CAM] and multiple observation points), and diagnosis by consensus. The study subjects were 87 patients aged 65 and over who were admitted consecutively from the emergency department to the medical wards, and who scored 3 or more on the Short Portable Mental Status Questionnaire. All subjects were assessed independently by one of three psychiatrists (a chart review and clinical examination) and a nurse clinician (using the CAM and multiple observation points). A consensus conference, attended by the three psychiatrists and the nurse clinician, used all available information to reach a consensus diagnosis. Compared to the consensus diagnosis, the clinical diagnosis by a psychiatrist had a sensitivity of .73 (95% confidence interval [CI]: .61-.85), a specificity of .93 (95% CI: .79-1.0), and an agreement kappa coefficient of .58 (95% CI: .41-.74). The nurse clinician diagnosis had a sensitivity of .89 (95% CI: .81-.97), a specificity of 1.00, and an agreement kappa coefficient of .86 (95% CI: .75-.97). These results suggest that one clinical assessment by a psychiatrist may not be the best method for detecting and diagnosing delirium in the elderly. A consensus diagnosis or diagnosis by a trained rater (using the CAM and multiple observation points) may be more sensitive approaches.

Aged↗
PubMedDate not supplied

Different immune response of mice immunized with conjugates containing multiple copies of either consensus or mixotope versions of the V3 loop peptide from human immunodeficiency virus type 1.

The critical role that antibody responses to the V3 loop epitope play in human immunodeficiency virus type 1 (HIV-1) neutralization has caused this peptide to be used in many HIV-1 vaccine candidates. To enhance cross-reactivity toward several V3 sequences, a database of 50 peptides of the V3 region from HIV-1 subtype A was used to design both a consensus peptide and a combinatorial peptide (mixotope) library representative of these sequences. The two immunogens (consensus and mixotope) were incorporated into multiple antigen peptide (MAP) constructions, conjugated to a recombinant surface antigen from hepatitis B virus (HbsAg) carrier protein, and inoculated to mice in combination with a C4 (CD4-binding) peptide MAP construction, also conjugated to HBsAg. The respective responses and cross-reactivity to several V3 loop sequences of both types of immunogens were compared. Mice inoculated with the V3 consensus-MAP-HBsAg + C4-MAP-HBsAg mixture elicited higher antibody responses than those given the V3 mixotope-MAP-HBsAg + C4-MAP-HBsAg mixture. In addition, pooled serum from the first group of immunogens analyzed at dilution 1:100 had higher cross-reactivity against V3 peptides on cellulose membranes than those from mice given the combinatorial immunogen. Fine epitope mapping of both consensus and C4 peptide by the spot synthesis technique showed that sera of the first group strongly recognized both sequences in their entirety, whereas mice immunized with the mixotope library recognized only the N-terminal region of V3. These results seem to suggest that the V3 consensus peptide is superior to the combinatorial strategy in inducing potent and cross-reactive responses to HIV.

Amino Acid Sequence↗
PubMedDate not supplied

Effect of preinduction specific growth rate on recombinant alpha consensus interferon synthesis in Escherichia coli.

The effect of preinduction specific growth rate on the yield of recombinant alpha consensus interferon in Escherichia coli K-12 was investigated. The cells used in the investigation contain a temperature-sensitive, walkaway plasmid bearing an insert that codes for alpha consensus interferon. Transcription of the recombinant gene is controlled by a lambda repressor/pL promoter system. The lambda promoter is regulated by the temperature-sensitive gene cI857 at 30 degrees C, but at 42 degrees C the promoter is derepressed. The cells were grown under glucose-limited conditions in a chemostat at pH 7 and 30 degrees C. Once steady state was achieved, the vessel temperature was raised to 42 degrees C and a fed-batch mode was initiated. Six dilution rates ranging from 0.025/h to 0.2/h were investigated. Cell dry weight, alpha consensus interferon content, glucose concentration, acetate concentration, and plasmid stability were measured. At each dilution rate, the expression level of alpha consensus interferon (g/g of cell dry wt) reached its maximum value approximately 3 h after induction. In addition, the expression level of alpha consensus interferon increases 4-fold as the dilution rate prior to induction is increased from 0.025/h to 0.2/h. Consequently, the expression of recombinant protein produced by E. coli is dependent on the preinduction specific growth rate.

Acetates↗
PubMedDate not supplied

How does consensus scoring work for virtual library screening? An idealized computer experiment.

It has been reported recently that consensus scoring, which combines multiple scoring functions in binding affinity estimation, leads to higher hit-rates in virtual library screening studies. This method seems quite independent to the target receptor, the docking program, or even the scoring functions under investigation. Here we present an idealized computer experiment to explore how consensus scoring works. A hypothetical set of 5000 compounds is used to represent a chemical library under screening. The binding affinities of all its member compounds are assigned by mimicking a real situation. Based on the assumption that the error of a scoring function is a random number in a normal distribution, the predicted binding affinities were generated by adding such a random number to the "observed" binding affinities. The relationship between the hit-rates and the number of scoring functions employed in scoring was then investigated. The performance of several typical ranking strategies for a consensus scoring procedure was also explored. Our results demonstrate that consensus scoring outperforms any single scoring for a simple statistical reason: the mean value of repeated samplings tends to be closer to the true value. Our results also suggest that a moderate number of scoring functions, three or four, are sufficient for the purpose of consensus scoring. As for the ranking strategy, both the rank-by-number and the rank-by-rank strategy work more effectively than the rank-by-vote strategy.

Computer Simulation↗
PubMed1987

In search of the false-uniqueness phenomenon: fear and estimates of social consensus.

An examination of the social perception literature yields little evidence for the false-uniqueness phenomenon (Valins & Nisbett, 1972), the perception that one's attributes are more unique than is the case. In contrast, the tendency for individuals to project their own characteristics onto other people and assume that more people are like themselves is a robust phenomenon. One reason researchers may not have found false uniqueness is that they have not looked at the accuracy of consensus estimates. A close look at the results of Tabachnik, Crocker, and Alloy (1983) and Sanders and Mullen (1983), who did assess accuracy, suggests that people possessing undesirable attributes over-estimate consensus, whereas people holding desirable attributes underestimate consensus. The latter pattern is a form of false uniqueness. In this study we looked at the accuracy of social consensus estimates in the context of psychological fears. A sample of subjects filled out an abbreviated version of a fear survey and made estimates of consensus. The results showed that both high- and low-fear respondents overestimated the incidence of high fear among their peers, but high-fear subjects were more inaccurate in their estimates. A false-uniqueness effect was found on the part of low-fear subjects, as they tended to underestimate the incidence of low fear among their peers. These findings are consistent with a motivational interpretation that emphasizes the individual's need to justify or normalize stigmatized behavior and to bolster perceived self-competence.

Adolescent↗
PubMed1994

The truly false consensus effect: an ineradicable and egocentric bias in social perception.

Consensus bias is the overuse of self-related knowledge in estimating the prevalence of attributes in a population. The bias seems statistically appropriate (Dawes, 1989), but according to the egocentrism hypothesis, it merely mimics normative inductive reasoning. In Experiment 1, Ss made population estimates for agreement with each of 40 personality inventory statements. Even Ss who had been educated about the consensus bias, or had received feedback about actual consensus, or both showed the bias. In Experiment 2, Ss attributed bias to another person, but their own consensus estimates were more affected by their own response to the item than by the other person's response. In Experiment 3, there was bias even in the presence of unanimous information from 20 randomly chosen others. In all 3 experiments, Ss continued to show consensus bias despite the availability of other statistical information.

Analysis of Variance↗