[The correlation and mechanism between chronic kidney disease and periodontitis based on cross-sectional data].

Objective: To explore the correlation between periodontitis (PD) and chronic kidney disease (CKD) in adults, as well as the potential mechanisms involved. Methods: Data on PD and CKD from the National Health and Nutrition Examination Survey (NHANES) database between 1999 and 2014 were downloaded. Weighted univariate and multivariate logistic regression analyses were conducted to investigate the risk factors associated with PD and CKD, considering demographic and clinical indicators. Using publicly available genome-wide association study (GWAS) summary datasets for kidney disease and periodontal disease as outcome variables, as well as 731 immune cell phenotypes and 91 inflammatory proteins as exposure factors from the OPEN GWAS database, a two-sample Mendelian randomization (TSMR) analysis was performed using the inverse-variance weighted (IVW) method. Results: Seven demographic indicators including gender, age, race, education level, marital status, income, and health are related to the incidence of CKD and PD. Among them, the elderly (≥60 years old), poverty (poverty-income ratio <1.3), divorce or widowhood, and male ratio in the comorbidity group of CKD and PD [67.12% (833/1 241), 36.83% (457/1 241), 34.41% (427/1 241), and 57.78% (717/1 241) respectively] were significantly higher than those in the control group [23.71% (4 179/17 623), 29.17% (5 141/17 623), 18.16% (3 200/17 623), and 48.73% (8 587/17 623) respectively] (all P<0.001). Those with high educational level (university and above) and self-rated excellent health accounted for a relatively small proportion in the comorbidity group [14.10% (175/1 241) and 8.22% (102/1 241) respectively]. The prevalence of PD increased among individuals with abnormal renal function indices, including glomerular filtration rate, urine protein/creatinine ratio, serum creatinine, serum uric acid, and blood urea nitrogen. Univariate logistic regression analysis showed a positive correlation between the incidence of PD and CKD (OR=2.14, 95%CI: 1.90-2.42, P<0.001). Multivariate logistic regression analysis also indicated that PD and CKD were potential risk factors for each other (PD for CKD: OR=1.22, 95%CI: 1.07-1.40, P=0.004; CKD for PD: OR=1.19, 95%CI: 1.04-1.37, P=0.012). Furthermore, after adjusting the model based on demographic indicators, there was still a significant correlation between PD and CKD (P=0.01). Mechanistically, the results of the TSMR analysis support the existence of a common risk factor mediated by immune cells between CKD and PD, namely the expression of CD64 on multiple innate immune cells mediates the occurrence of CKD and PD. The absolute count of CD64+ monocytes is associated with an increased risk for both CKD (HR=1.11) and PD (HR=1.07), while same tendency showed in the absolute count of CD64+ neutrophils for CKD (HR=1.22) and PD (HR=1.23). Conclusions: There is a positive correlation between CKD and PD, particularly moderate to severe PD, and the shared pathogenesis involves CD64+ monocytes in the circulatory system. Targeted interventions focusing on CD64 molecules or monocyte subsets may be beneficial.

[Incidence and prognosis of olfactory and gustatory dysfunctions related to infection of SARS-CoV-2 Omicron strain: a national multi-center survey of 35 566 population].

Objective: This cross-sectional investigation aimed to determine the incidence, clinical characteristics, prognosis, and related risk factors of olfactory and gustatory dysfunctions related to infection with the SARS-CoV-2 Omicron strain in mainland China. Methods: Data of patients with SARS-CoV-2 from December 28, 2022, to February 21, 2023, were collected through online and offline questionnaires from 45 tertiary hospitals and one center for disease control and prevention in mainland China. The questionnaire included demographic information, previous health history, smoking and alcohol drinking, SARS-CoV-2 vaccination, olfactory and gustatory function before and after infection, other symptoms after infection, as well as the duration and improvement of olfactory and gustatory dysfunction. The self-reported olfactory and gustatory functions of patients were evaluated using the Olfactory VAS scale and Gustatory VAS scale. Results: A total of 35 566 valid questionnaires were obtained, revealing a high incidence of olfactory and taste dysfunctions related to infection with the SARS-CoV-2 Omicron strain (67.75%). Females(χ2=367.013, P<0.001) and young people(χ2=120.210, P<0.001) were more likely to develop these dysfunctions. Gender(OR=1.564, 95%CI: 1.487-1.645), SARS-CoV-2 vaccination status (OR=1.334, 95%CI: 1.164-1.530), oral health status (OR=0.881, 95%CI: 0.839-0.926), smoking history (OR=1.152, 95%CI=1.080-1.229), and drinking history (OR=0.854, 95%CI: 0.785-0.928) were correlated with the occurrence of olfactory and taste dysfunctions related to SARS-CoV-2(above P<0.001). 44.62% (4 391/9 840) of the patients who had not recovered their sense of smell and taste also suffered from nasal congestion, runny nose, and 32.62% (3 210/9 840) suffered from dry mouth and sore throat. The improvement of olfactory and taste functions was correlated with the persistence of accompanying symptoms(χ2=10.873, P=0.001). The average score of olfactory and taste VAS scale was 8.41 and 8.51 respectively before SARS-CoV-2 infection, but decreased to3.69 and 4.29 respectively after SARS-CoV-2 infection, and recovered to 5.83and 6.55 respectively at the time of the survey. The median duration of olfactory and gustatory dysfunctions was 15 days and 12 days, respectively, with 0.5% (121/24 096) of patients experiencing these dysfunctions for more than 28 days. The overall self-reported improvement rate of smell and taste dysfunctions was 59.16% (14 256/24 096). Gender(OR=0.893, 95%CI: 0.839-0.951), SARS-CoV-2 vaccination status (OR=1.334, 95%CI: 1.164-1.530), history of head and facial trauma(OR=1.180, 95%CI: 1.036-1.344, P=0.013), nose (OR=1.104, 95%CI: 1.042-1.171, P=0.001) and oral (OR=1.162, 95%CI: 1.096-1.233) health status, smoking history(OR=0.765, 95%CI: 0.709-0.825), and the persistence of accompanying symptoms (OR=0.359, 95%CI: 0.332-0.388) were correlated with the recovery of olfactory and taste dysfunctions related to SARS-CoV-2 (above P<0.001 except for the indicated values). Conclusion: The incidence of olfactory and taste dysfunctions related to infection with the SARS-CoV-2 Omicron strain is high in mainland China, with females and young people more likely to develop these dysfunctions. Active and effective intervention measures may be required for cases that persist for a long time. The recovery of olfactory and taste functions is influenced by several factors, including gender, SARS-CoV-2 vaccination status, history of head and facial trauma, nasal and oral health status, smoking history, and persistence of accompanying symptoms.

[Impact of individual and combined assessment of age- and sex-specific brachial-ankle pulse wave velocity and pulse pressure on all-cause mortality].

Objective: To evaluate the impact of individual and combined assessment of age- and sex-specific brachial-ankle pulse wave velocity (baPWV) and pulse pressure (PP) on all-cause mortality. Methods: This study is a prospective cohort study. Individuals participated in the Kailuan Study and completed baPWV measurements between 2010 and 2016 were included in this study. After stratifying by sex, 75th percentile baPWV and PP values for different age group were calculated at five years interval. BaPWV and PP values below the 75th percentile were defined as normal, and those above or equal to the 75th percentile were defined as increased. The participants were allocated to four groups according to their PP and baPWV status: normal baPWV/PP group, high baPWV/normal PP group, normal baPWV/high PP group and high baPWV/PP group. The primary outcome was all-cause mortality during the follow-up period. Cox proportional hazards models were used to explore the impact of individual and combined assessment of baPWV and PP on all-cause mortality events. Results: A total of 39 339 participants were enrolled in this study, aged (49.3±12.8) years, of which 28 731 (73.03%) were males. There were 23 268, 6 025, 6 210 and 3 836 cases in the normal baPWV/PP group, high baPWV/normal PP group, normal baPWV/high PP group and high baPWV/PP group, respectively. The average follow-up duration was (4.98±2.53) years. During the follow-up period, all-cause mortality occurred in 998 individuals. Multivariate Cox regression analysis showed increased risk of all-cause mortality in the high baPWV/normal PP group (HR=1.27, 95%CI 1.07-1.50), and in the high baPWV/PP group (HR=1.33, 95%CI 1.08-1.65) compared to the normal baPWV/PP group. Increased pulse pressure alone had no impcat on all-cause death (HR=1.06, 95%CI 0.87-1.29). Conclusions: The risk of all-cause mortality significantly increases with increased age-and sex-specific baPWV and PP values. BaPWV may be a better predictor of all-cause mortality than PP in this cohort.

[Nasal acinar cell carcinoma：a case report].

Acinar cell carcinoma is a rare type of low-grade malignant tumor of the parotid gland epithelium. The progression of the disease is slow, and its tissue type and cell morphology are diverse. The diagnosis of tumor is difficult so that it is easy to cause missed diagnosis and misdiagnosis. A 72-year-old patient, without the history of surgery and trauma, complained of nasal congestion, bloody sputum, and loss of olfactory. CT and MRI suggested that the nasal cavity and sinuses were occupied with soft tissue. An endoscopic nasal cavity and sinus mass resection was performed under general anesthesia. No recurrence was observed after 1 year of follow-up. The nasal symptoms disappeared and the recovery effect was good.

[The curative effect analysis of 164 tinnitus patients with different types of hearing curve].

Objective:To investigate the difference of therapeutic effect of tinnitus patients with different types of hearing curve.Method:Patients with the inclusion and exclusion criteria for the treatment were studied retrospectively.Use the SPSS 20.0 Chinese version of the software to collect data and analysis.The difference was statistically significant when P<0.05.Result:A total of 164 patients were collected, and the most of the hearing curve types was high frequency hearing loss; according to the TEQ scoring and grading method, most tinnitus patients were in the middle severity; The chi-square test showed that there was no significant difference among the patients with different hearing curve types when the first visit,the severity among the groups was evenly distributed. After treatment,there was no significant difference in the effect of last visit and the follow-up between the patients with different hearing curve types.Conclusion：Unlike the sudden deafness, there was no statistically significant difference in the prognosis of tinnitus patients with different types of hearing curve. We can not choose the treatment program or even predict the curative effect according to the hearing curve type.

[Imaging analysis of respiratory epithelial adenomatoid hamartoma of olfactory clefts].

Objective:Analyze the imaging features of respiratory epithelial adenomatoid hamartoma(REAH) of olfactory clefts，to provide the basis for clinical diagnosis and treatment. Method:A retrospective study of 54 cases of nasal REAH of bilateral olfactory clefts confirmed by pathology were collected，analyze their imaging information. Result:All the lesions of 54 cases are located in olfactory cleft，sinus CT and MR show soft tissue shadows in olfactory cleft which grows expansive，extruding bilateral middle turbinate to the lateral sides，and it's like "the head of mushroom".All the cases are with different degree of sinusitis and nasal polyps. Conclusion:This kind of REAH has special imaging performance，and it's different from nasal polyp．So if clinical doctors can fully recognize this disease and completely resect the lesion of olfactory cleft in operation，we can increase the probability of treatment，and reduce the probability of postoperative recurrence.

[Causes and management of frontal sinusitis after transfrontal craniotomy].

Objective:The aim of this study is to investigate the causes and the strategy of frontal sinusitis after transfrontal craniotomy by endoscopic frontal sinus surgery and traditional surgery with facial incision. Method:A total of thirty-four patients with frontal sinusitis after transfrontal craniotomy were admitted, with the symptom of purulence stuff, headache and upper eyelid discharging. The onset time was 2.6 years on average. The frontal sinus CT and MRI images showed frontal sinusitis. Twenty-seven patients were treated with endoscopic frontal sinus surgery, and seven patient was treated with combined endoscopic and traditional frontal sinus surgery. In the revision surgery, the bone wax and inflammatory granulation tissue were cleaned out in both operational methods. The cure standard was that the postoperative frontal sinus inflammation disappeared and the drainage of the volume recess was unobstructed. Result:Thirty-four patients had a history of transfrontal craniotomy, and there was a record of bone wax packing in every operation. Among twenty-seven patients with endoscopic frontal sinus surgery, Twenty-five cases cured and two cases were operated twice. Seven patients were cured with combined endoscopic and traditional frontal sinus surgery. Conclusion:The frontal sinusitis after transfrontal craniotomy may be related to the inadequate sinus management, especially bone wax to be addressed to the frontal sinus ramming leading to frontal sinus mucosa secretion obstruction and poor drainage. Endoscopic frontal sinus surgery is a way of minimally invasive surgery. The satisfying curative effect can be obtained by endoscopic removal of bone wax, inflammatory granulation tissue, and the enlargement of frontal sinus aperture after exposure to the frontal sinus, and some cases was treated with both operation method.

Interleukin-33 promotes the inflammatory reaction in chronic rhinosinusitis with nasal polyps by NF-κB signaling pathway.

OBJECTIVE: Interleukin (IL)-33 promotes T helper (Th2) immune response and may be involved in the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP). Using murine and human specimens, we evaluated the role of IL-33 in CRSwNP. MATERIALS AND METHODS: To establish CRSwNP, Balb/c mice were sensitized with house dust mite, followed up by intranasal exposure to Staphylococcus aureus to stimulate the inflammatory response of nasal mucosa. The hematoxylin-eosin staining and total serum IgE were used to the successful construction of CRSwNP model. For mechanistic studies, we blocked mice with IL-33 and the Th2 cells counts in tissue were detected. Th2 cytokine expression of IL-4, IL-5, IL-13, IL-22, CCL-11, and CCL-24 in control group, CRSwNP group and IL-33 blockade group at 12 weeks after CRSwNP model establishment, were analyzed by qRT-PCR. Meanwhile, the relative mRNA and protein expression levels of NF-κB, MyD88 and TLR7 were detected after IL-33 blockade. To document the inflammatory response in patients with CRSwNP, The relative mRNA expression of IL-4, IL-5, IL-13, IL-22, CCL-11, and CCL-24 in control individuals and patients with CRSwNP (chronic rhinosinusitis with nasal polyps) were analyzed by qRT-PCR. RESULTS: The CRSwNP model was successfully constructed. After IL-33 blocked, the relative expression of IL-33 and Th2 cells counts were reduced significantly. CRSwNP mice showed overproduction of IL-4, IL-5, IL-13, IL-22, CCL-11, and CCL-24 and IL-33 blockade inhibited the expression of IL-4, IL-5, IL-13, IL-22, CCL-11, and CCL-24. Furthermore, IL-33 blockade decreased the mRNA levels of NF-κB, MyD88 and TLR7, and also restrained the protein expression of them. On the other hand, patients' specimens with CRSwNP showed high levels of Th2 cytokines including IL-33, IL-4, IL-5, IL-13, IL-22, CCL-11, and CCL-24. CONCLUSIONS: CRSwNP is associated with overexpression of IL-33, with subsequent activation of Th2 immune response by NF-κB signaling pathway.

[Complete endoscopic resection of septonasal chondrosarcoma by coblation: two cases report].

Septonasal chondrosarcoma is extremely rare, though chondrosarcoma ranks the third in bone malignant tumors. Typical symptoms can be lack duing to elusive anatomical structure of the nasal sinuses, which easily leads to misdiagnosis. Here we reported two cases of low-grade chondrosarcoma deriving from nasal septom removed by intranasal endoscope using coblation. MRI and CT scan revealed typical ring-and-arc appearance. Treatment with septonasal chondrosarcoma varied from neoplasm staging and surgical approcaches had been reported long disease-free survival.

[Thirty-two cases of nasal lymphoma CT and MRI analysis].

Objective:Analysis of nasal lymphoma CT and MRI data, summarize imaging characteristics, provide help for clinical diagnosis. Method:Retrospectively analyzed the image manifestations of 32 cases of nasal lymphoma diagnosed by surgery and pathology. Lesion locations, tumor extension, bone destruction and its density, signal characteristics, enhancement degree, the situation of adjacent tissues were evaluated. Result:NK/T cells, T cell NHL have the characteristics: the lesions to diffuse growth, widely existed in nasal breathing zone, often involving middle and inferior turbinate, local bone slightly damaged, and no obvious bony shift. Tumor of uneven density, fuzzy boundaries, mixed signalse. The characteristics of B cell NHL: the lesion originated in the front of the nasal cavity, on the surrounding adjacent tissue compression performance, local feature is swelling growth and bone have insect damage sample sample, the dotted line change, very mild osseous shift, the tumor boundary is relatively clear, lesions density is uniform, and part of the uniform tumors had signal. Conclusion:Nasal lymphoma imaging changes have its characteristics. Image change prompts the pathological classification, providing help for clinical diagnosis.

Synergistic therapeutic actions of herbal ingredients and their mechanisms from molecular interaction and network perspectives.

Opinions about the therapeutic efficacy of medicinal herbs differ significantly. Some reported herbal efficacies at low doses of active ingredients suggest a need for investigating whether these are because of placebo or multi-ingredient synergistic effects. This review discusses the opinions, methods and outcomes of herbal synergism investigations and analyzes indications from 48 in vivo tests and 106 rigorous clinical trials. Analyses of ingredient-mediated interactions at molecular and pathway levels indicate multi-ingredient synergism in 27 of the 39 reported cases of herbal synergism with available ingredient information. Synergistic actions may be responsible for the therapeutic efficacy of a substantial number of herbal products and their mechanisms may be studied by analyzing ingredient-mediated molecular interactions and network regulation.

SEPPA: a computational server for spatial epitope prediction of protein antigens.

In recent years, a lot of efforts have been made in conformational epitope prediction as antigen proteins usually bind antibodies with an assembly of sequentially discontinuous and structurally compact surface residues. Currently, only a few methods for spatial epitope prediction are available with focus on single residue propensity scales or continual segments clustering. In the method of SEPPA, a concept of 'unit patch of residue triangle' was introduced to better describe the local spatial context in protein surface. Besides that, SEPPA incorporated clustering coefficient to describe the spatial compactness of surface residues. Validated by independent testing datasets, SEPPA gave an average AUC value over 0.742 and produced a successful pick-up rate of 96.64%. Comparing with peers, SEPPA shows significant improvement over other popular methods like CEP, DiscoTope and BEpro. In addition, the threshold scores for certain accuracy, sensitivity and specificity are provided online to give the confidence level of the spatial epitope identification. The web server can be accessed at http://lifecenter.sgst.cn/seppa/index.php. Batch query is supported.

Prediction of antibiotic resistance proteins from sequence-derived properties irrespective of sequence similarity.

Increasing antibiotic resistance has become a worldwide challenge to the clinical treatment of infectious diseases. The identification of antibiotic resistance proteins (ARPs) would be helpful in the discovery of new therapeutic targets and the design of novel drugs to control the potential spread of antibiotic resistance. In this work, a support vector machine (SVM)-based ARP prediction system was developed using 1308 ARPs and 15587 non-ARPs. Its performance was evaluated using 313 ARPs and 7156 non-ARPs. The computed prediction accuracy was 88.5% for ARPs and 99.2% for non-ARPs. A potential application of this method is the identification of ARPs non-homologous to proteins of known function. Further genome screening found that ca. 3.5% and 3.2% of proteins in Escherichia coli and Staphylococcus aureus, respectively, are potential ARPs. These results suggest the usefulness of SVMs for facilitating the identification of ARPs. The software can be accessed at SARPI (Server for Antibiotic Resistance Protein Identification).

A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor.

Support vector machines (SVM) and other machine-learning (ML) methods have been explored as ligand-based virtual screening (VS) tools for facilitating lead discovery. While exhibiting good hit selection performance, in screening large compound libraries, these methods tend to produce lower hit-rate than those of the best performing VS tools, partly because their training-sets contain limited spectrum of inactive compounds. We tested whether the performance of SVM can be improved by using training-sets of diverse inactive compounds. In retrospective database screening of active compounds of single mechanism (HIV protease inhibitors, DHFR inhibitors, dopamine antagonists) and multiple mechanisms (CNS active agents) from large libraries of 2.986 million compounds, the yields, hit-rates, and enrichment factors of our SVM models are 52.4-78.0%, 4.7-73.8%, and 214-10,543, respectively, compared to those of 62-95%, 0.65-35%, and 20-1200 by structure-based VS and 55-81%, 0.2-0.7%, and 110-795 by other ligand-based VS tools in screening libraries of >or=1 million compounds. The hit-rates are comparable and the enrichment factors are substantially better than the best results of other VS tools. 24.3-87.6% of the predicted hits are outside the known hit families. SVM appears to be potentially useful for facilitating lead discovery in VS of large compound libraries.

Computer prediction of cardiovascular and hematological agents by statistical learning methods.

Computational methods have been explored for predicting agents that produce therapeutic or adverse effects in cardiovascular and hematological systems. The quantitative structure-activity relationship (QSAR) method is the first statistical learning methods successfully used for predicting various classes of cardiovascular and hematological agents. In recent years, more sophisticated statistical learning methods have been explored for predicting cardiovascular and hematological agents particularly those of diverse structures that might not be straightforwardly modelled by single QSAR models. These methods include partial least squares, multiple linear regressions, linear discriminant analysis, k-nearest neighbour, artificial neural networks and support vector machines. Their application potential has been exhibited in the prediction of various classes of cardiovascular and hematological agents including 1, 4-dihydropyridine calcium channel antagonists, angiotensin converting enzyme inhibitors, thrombin inhibitors, AchE inhibitors, HERG potassium channel inhibitors and blockers, potassium channel openers, platelet aggregation inhibitors, protein kinase inhibitors, dopamine antagonists and torsade de pointes causing agents. This article reviews the strategies, current progresses and problems in using statistical learning methods for predicting cardiovascular and hematological agents. It also evaluates algorithms for properly representing and extracting the structural and physicochemical properties of compounds relevant to the prediction of cardiovascular and hematological agents.

Prediction of MHC-binding peptides of flexible lengths from sequence-derived structural and physicochemical properties.

Peptide binding to MHC is critical for antigen recognition by T-cells. To facilitate vaccine design, computational methods have been developed for predicting MHC-binding peptides, which achieve impressive prediction accuracies of 70-90% for binders and 40-80% for non-binders. These methods have been developed for peptides of fixed lengths, for a limited number of alleles, trained from small number of non-binders, and in some cases based straightforwardly on sequence. These limit prediction coverage and accuracy particularly for non-binders. It is desirable to explore methods that predict binders of flexible lengths from sequence-derived physicochemical properties and trained from diverse sets of non-binders. This work explores support vector machines (SVM) as such a method for developing prediction systems of 18 MHC class I and 12 class II alleles by using 4208-3252 binders and 234,333-168,793 non-binders, and evaluated by an independent set of 545-476 binders and 110,564-84,430 non-binders. Binder accuracies are 86-99% for 25 and 70-80% for 5 alleles, non-binder accuracies are 96-99% for 30 alleles. Binder accuracies are comparable and non-binder accuracies substantially improved against other results. Our method correctly predicts 73.3% of the 15 newly-published epitopes in the last 4 months of 2005. Of the 251 recently-published HLA-A*0201 non-epitopes predicted as binders by other methods, 63 are predicted as binders by our method. Screening of HIV-1 genome shows that, compared to other methods, a comparable percentage (75-100%) of its known epitopes is correctly predicted, while a lower percentage (0.01-5% for 24 and 5-8% for 6 alleles) of its constituent peptides are predicted as binders. Our software can be accessed at .

Database of traditional Chinese medicine and its application to studies of mechanism and to prescription validation.

BACKGROUND AND PURPOSE: Traditional Chinese Medicine (TCM) is widely practised and is viewed as an attractive alternative to conventional medicine. Quantitative information about TCM prescriptions, constituent herbs and herbal ingredients is necessary for studying and exploring TCM. EXPERIMENTAL APPROACH: We manually collected information on TCM in books and other printed sources in Medline. The Traditional Chinese Medicine Information Database TCM-ID, at http://tcm.cz3.nus.edu.sg/group/tcm-id/tcmid.asp, was introduced for providing comprehensive information about all aspects of TCM including prescriptions, constituent herbs, herbal ingredients, molecular structure and functional properties of active ingredients, therapeutic and side effects, clinical indication and application and related matters. RESULTS: TCM-ID currently contains information for 1,588 prescriptions, 1,313 herbs, 5,669 herbal ingredients, and the 3D structure of 3,725 herbal ingredients. The value of the data in TCM-ID was illustrated by using some of the data for an in-silico study of molecular mechanism of the therapeutic effects of herbal ingredients and for developing a computer program to validate TCM multi-herb preparations. CONCLUSIONS AND IMPLICATIONS: The development of systems biology has led to a new design principle for therapeutic intervention strategy, the concept of 'magic shrapnel' (rather than the 'magic bullet'), involving many drugs against multiple targets, administered in a single treatment. TCM offers an extensive source of examples of this concept in which several active ingredients in one prescription are aimed at numerous targets and work together to provide therapeutic benefit. The database and its mining applications described here represent early efforts toward exploring TCM for new theories in drug discovery.

Therapeutic targets: progress of their exploration and investigation of their characteristics.

Modern drug discovery is primarily based on the search and subsequent testing of drug candidates acting on a preselected therapeutic target. Progress in genomics, protein structure, proteomics, and disease mechanisms has led to a growing interest in and effort for finding new targets and more effective exploration of existing targets. The number of reported targets of marketed and investigational drugs has significantly increased in the past 8 years. There are 1535 targets collected in the therapeutic target database compared with approximately 500 targets reported in a 1996 review. Knowledge of these targets is helpful for molecular dissection of the mechanism of action of drugs and for predicting features that guide new drug design and the search for new targets. This article summarizes the progress of target exploration and investigates the characteristics of the currently explored targets to analyze their sequence, structure, family representation, pathway association, tissue distribution, and genome location features for finding clues useful for searching for new targets. Possible "rules" to guide the search for druggable proteins and the feasibility of using a statistical learning method for predicting druggable proteins directly from their sequences are discussed.

Prediction of compounds with specific pharmacodynamic, pharmacokinetic or toxicological property by statistical learning methods.

Computational methods for predicting compounds of specific pharmacodynamic, pharmacokinetic, or toxicological property are useful for facilitating drug discovery and drug safety evaluation. The quantitative structure-activity relationship (QSAR) and quantitative structure-property relationship (QSPR) methods are the most successfully used statistical learning methods for predicting compounds of specific property. More recently, other statistical learning methods such as neural networks and support vector machines have been explored for predicting compounds of higher structural diversity than those covered by QSAR and QSPR. These methods have shown promising potential in a number of studies. This article is intended to review the strategies, current progresses and underlying difficulties in using statistical learning methods for predicting compounds of specific property. It also evaluates algorithms commonly used for representing structural and physicochemical properties of compounds.

PEARLS: program for energetic analysis of receptor-ligand system.

Analysis of the energetics of small molecule ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions facilitates the quantitative understanding of molecular interactions that regulate the function and conformation of proteins. It has also been extensively used for ranking potential new ligands in virtual drug screening. We developed a Web-based software, PEARLS (Program for Energetic Analysis of Ligand-Receptor Systems), for computing interaction energies of ligand-protein, ligand-nucleic acid, protein-nucleic acid, and ligand-protein-nucleic acid complexes from their 3D structures. AMBER molecular force field, Morse potential, and empirical energy functions are used to compute the van der Waals, electrostatic, hydrogen bond, metal-ligand bonding, and water-mediated hydrogen bond energies between the binding molecules. The change in the solvation free energy of molecular binding is estimated by using an empirical solvation free energy model. Contribution from ligand conformational entropy change is also estimated by a simple model. The computed free energy for a number of PDB ligand-receptor complexes were studied and compared to experimental binding affinity. A substantial degree of correlation between the computed free energy and experimental binding affinity was found, which suggests that PEARLS may be useful in facilitating energetic analysis of ligand-protein, ligand-nucleic acid, and protein-nucleic acid interactions. PEARLS can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/rune.pl.