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Showing 1 to 12 of 84 entries
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A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

Advances and applications in bioinformatics and chemistry : AABC

Omagari K, Mitomo D, Kubota S, Nakamura H, Fukunishi Y.
PMID: 21918604
Adv Appl Bioinform Chem. 2008;1:19-28. doi: 10.2147/aabc.s3767. Epub 2008 Aug 12.

We examined the procedures to combine two different in silico drug-screening results to achieve a high hit ratio. When the 3D structure of the target protein and some active compounds are known, both structure-based and ligand-based in silico screening...

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Omagari K, Mitomo D, Kubota S, et al. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Adv Appl Bioinform Chem. 2008;1:19-28doi: 10.2147/aabc.s3767.
Omagari, K., Mitomo, D., Kubota, S., Nakamura, H., & Fukunishi, Y. (2008). A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Advances and applications in bioinformatics and chemistry : AABC, 119-28. https://doi.org/10.2147/aabc.s3767
Omagari, Katsumi, et al. "A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 19-28. doi: https://doi.org/10.2147/aabc.s3767
Omagari K, Mitomo D, Kubota S, Nakamura H, Fukunishi Y. A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening. Adv Appl Bioinform Chem. 2008;1:19-28. doi: 10.2147/aabc.s3767. Epub 2008 Aug 12. PMID: 21918604; PMCID: PMC3169939.
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Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms.

Advances and applications in bioinformatics and chemistry : AABC

Kim HO, Snyder GP, Blazey TM, Race RE, Chesebro B, Skinner PJ.
PMID: 21918605
Adv Appl Bioinform Chem. 2008;1:29-50. doi: 10.2147/aabc.s3411. Epub 2008 Sep 07.

Prion diseases are fatal neurodegenerative disorders that affect animals and humans. There is a need to gain understanding of prion disease pathogenesis and to develop diagnostic assays to detect prion diseases prior to the onset of clinical symptoms. The...

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Kim HO, Snyder GP, Blazey TM, et al. Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms. Adv Appl Bioinform Chem. 2008;1:29-50doi: 10.2147/aabc.s3411.
Kim, H. O., Snyder, G. P., Blazey, T. M., Race, R. E., Chesebro, B., & Skinner, P. J. (2008). Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms. Advances and applications in bioinformatics and chemistry : AABC, 129-50. https://doi.org/10.2147/aabc.s3411
Kim, Hyeon O, et al. "Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 29-50. doi: https://doi.org/10.2147/aabc.s3411
Kim HO, Snyder GP, Blazey TM, Race RE, Chesebro B, Skinner PJ. Prion disease induced alterations in gene expression in spleen and brain prior to clinical symptoms. Adv Appl Bioinform Chem. 2008;1:29-50. doi: 10.2147/aabc.s3411. Epub 2008 Sep 07. PMID: 21918605; PMCID: PMC3169940.
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A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells.

Advances and applications in bioinformatics and chemistry : AABC

Ohyashiki JH, Hamamura R, Kobayashi C, Zhang Y, Ohyashiki K.
PMID: 21918608
Adv Appl Bioinform Chem. 2008;1:85-98. doi: 10.2147/aabc.s4133. Epub 2008 Oct 30.

There is a need to identify the regulatory gene interaction of anticancer drugs on target cancer cells. Whole genome expression profiling offers promise in this regard, but can be complicated by the challenge of identifying the genes affected by...

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Ohyashiki JH, Hamamura R, Kobayashi C, et al. A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells. Adv Appl Bioinform Chem. 2008;1:85-98doi: 10.2147/aabc.s4133.
Ohyashiki, J. H., Hamamura, R., Kobayashi, C., Zhang, Y., & Ohyashiki, K. (2008). A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells. Advances and applications in bioinformatics and chemistry : AABC, 185-98. https://doi.org/10.2147/aabc.s4133
Ohyashiki, Junko H, et al. "A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 85-98. doi: https://doi.org/10.2147/aabc.s4133
Ohyashiki JH, Hamamura R, Kobayashi C, Zhang Y, Ohyashiki K. A network biology approach evaluating the anticancer effects of bortezomib identifies SPARC as a therapeutic target in adult T-cell leukemia cells. Adv Appl Bioinform Chem. 2008;1:85-98. doi: 10.2147/aabc.s4133. Epub 2008 Oct 30. PMID: 21918608; PMCID: PMC3169936.
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Discrimination between biological interfaces and crystal-packing contacts.

Advances and applications in bioinformatics and chemistry : AABC

Tsuchiya Y, Nakamura H, Kinoshita K.
PMID: 21918609
Adv Appl Bioinform Chem. 2008;1:99-113. doi: 10.2147/aabc.s4255. Epub 2008 Nov 02.

A discrimination method between biologically relevant interfaces and artificial crystal-packing contacts in crystal structures was constructed. The method evaluates protein-protein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most...

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Tsuchiya Y, Nakamura H, Kinoshita K. Discrimination between biological interfaces and crystal-packing contacts. Adv Appl Bioinform Chem. 2008;1:99-113doi: 10.2147/aabc.s4255.
Tsuchiya, Y., Nakamura, H., & Kinoshita, K. (2008). Discrimination between biological interfaces and crystal-packing contacts. Advances and applications in bioinformatics and chemistry : AABC, 199-113. https://doi.org/10.2147/aabc.s4255
Tsuchiya, Yuko, et al. "Discrimination between biological interfaces and crystal-packing contacts." Advances and applications in bioinformatics and chemistry : AABC vol. 1 (2008): 99-113. doi: https://doi.org/10.2147/aabc.s4255
Tsuchiya Y, Nakamura H, Kinoshita K. Discrimination between biological interfaces and crystal-packing contacts. Adv Appl Bioinform Chem. 2008;1:99-113. doi: 10.2147/aabc.s4255. Epub 2008 Nov 02. PMID: 21918609; PMCID: PMC3169932.
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An online conserved SSR discovery through cross-species comparison.

Advances and applications in bioinformatics and chemistry : AABC

Pai TW, Chen CM, Hsiao MC, Cheng R, Tzou WS, Hu CH.
PMID: 21918613
Adv Appl Bioinform Chem. 2009;2:23-35. doi: 10.2147/aabc.s4744. Epub 2009 Feb 08.

Simple sequence repeats (SSRs) play important roles in gene regulation and genome evolution. Although there exist several online resources for SSR mining, most of them only extract general SSR patterns without providing functional information. Here, an online search tool,...

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Pai TW, Chen CM, Hsiao MC, et al. An online conserved SSR discovery through cross-species comparison. Adv Appl Bioinform Chem. 2009;2:23-35doi: 10.2147/aabc.s4744.
Pai, T. W., Chen, C. M., Hsiao, M. C., Cheng, R., Tzou, W. S., & Hu, C. H. (2009). An online conserved SSR discovery through cross-species comparison. Advances and applications in bioinformatics and chemistry : AABC, 223-35. https://doi.org/10.2147/aabc.s4744
Pai, Tun-Wen, et al. "An online conserved SSR discovery through cross-species comparison." Advances and applications in bioinformatics and chemistry : AABC vol. 2 (2009): 23-35. doi: https://doi.org/10.2147/aabc.s4744
Pai TW, Chen CM, Hsiao MC, Cheng R, Tzou WS, Hu CH. An online conserved SSR discovery through cross-species comparison. Adv Appl Bioinform Chem. 2009;2:23-35. doi: 10.2147/aabc.s4744. Epub 2009 Feb 08. PMID: 21918613; PMCID: PMC3169944.
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Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies.

Advances and applications in bioinformatics and chemistry : AABC

Poltz R, Franke R, Schweitzer K, Klamt S, Gilles ED, Naumann M.
PMID: 21918620
Adv Appl Bioinform Chem. 2009;2:125-38. doi: 10.2147/aabc.s8211. Epub 2009 Dec 03.

Genotoxic stress is induced by a broad range of DNA-damaging agents and could lead to a variety of human diseases including cancer. DNA damage is also therapeutically induced for cancer treatment with the aim to eliminate tumor cells. However,...

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Poltz R, Franke R, Schweitzer K, et al. Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Adv Appl Bioinform Chem. 2009;2:125-38doi: 10.2147/aabc.s8211.
Poltz, R., Franke, R., Schweitzer, K., Klamt, S., Gilles, E. D., & Naumann, M. (2009). Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Advances and applications in bioinformatics and chemistry : AABC, 2125-38. https://doi.org/10.2147/aabc.s8211
Poltz, Rainer, et al. "Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies." Advances and applications in bioinformatics and chemistry : AABC vol. 2 (2009): 125-38. doi: https://doi.org/10.2147/aabc.s8211
Poltz R, Franke R, Schweitzer K, Klamt S, Gilles ED, Naumann M. Logical network of genotoxic stress-induced NF-κB signal transduction predicts putative target structures for therapeutic intervention strategies. Adv Appl Bioinform Chem. 2009;2:125-38. doi: 10.2147/aabc.s8211. Epub 2009 Dec 03. PMID: 21918620; PMCID: PMC3169943.
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Computer applications for prediction of protein-protein interactions and rational drug design.

Advances and applications in bioinformatics and chemistry : AABC

Grosdidier S, Totrov M, Fernández-Recio J.
PMID: 21918619
Adv Appl Bioinform Chem. 2009;2:101-23. Epub 2009 Nov 10.

In recent years, protein-protein interactions are becoming the object of increasing attention in many different fields, such as structural biology, molecular biology, systems biology, and drug discovery. From a structural biology perspective, it would be desirable to integrate current...

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Grosdidier S, Totrov M, Fernández-Recio J. Computer applications for prediction of protein-protein interactions and rational drug design. Adv Appl Bioinform Chem. 2009;2:101-23
Grosdidier, S., Totrov, M., & Fernández-Recio, J. (2009). Computer applications for prediction of protein-protein interactions and rational drug design. Advances and applications in bioinformatics and chemistry : AABC, 2101-23.
Grosdidier, Solène, et al. "Computer applications for prediction of protein-protein interactions and rational drug design." Advances and applications in bioinformatics and chemistry : AABC vol. 2 (2009): 101-23.
Grosdidier S, Totrov M, Fernández-Recio J. Computer applications for prediction of protein-protein interactions and rational drug design. Adv Appl Bioinform Chem. 2009;2:101-23. Epub 2009 Nov 10. PMID: 21918619; PMCID: PMC3169948.
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Construction of random perfect phylogeny matrix.

Advances and applications in bioinformatics and chemistry : AABC

Sadeghi M, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM.
PMID: 21918630
Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16.

PURPOSE: Interest in developing methods appropriate for mapping increasing amounts of genome-wide molecular data are increasing rapidly. There is also an increasing need for methods that are able to efficiently simulate such data.PATIENTS AND METHODS: In this article, we...

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Sadeghi M, Pezeshk H, Eslahchi C, et al. Construction of random perfect phylogeny matrix. Adv Appl Bioinform Chem. 2010;3:89-96doi: 10.2147/AABC.S13397.
Sadeghi, M., Pezeshk, H., Eslahchi, C., Ahmadian, S., & Abadi, S. M. (2010). Construction of random perfect phylogeny matrix. Advances and applications in bioinformatics and chemistry : AABC, 389-96. https://doi.org/10.2147/AABC.S13397
Sadeghi, Mehdi, et al. "Construction of random perfect phylogeny matrix." Advances and applications in bioinformatics and chemistry : AABC vol. 3 (2010): 89-96. doi: https://doi.org/10.2147/AABC.S13397
Sadeghi M, Pezeshk H, Eslahchi C, Ahmadian S, Abadi SM. Construction of random perfect phylogeny matrix. Adv Appl Bioinform Chem. 2010;3:89-96. doi: 10.2147/AABC.S13397. Epub 2010 Nov 16. PMID: 21918630; PMCID: PMC3170006.
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SNP analysis of follistatin gene associated with polycystic ovarian syndrome.

Advances and applications in bioinformatics and chemistry : AABC

Panneerselvam P, Sivakumari K, Jayaprakash P, Srikanth R.
PMID: 21918632
Adv Appl Bioinform Chem. 2010;3:111-9. doi: 10.2147/AABC.S11013. Epub 2010 Dec 13.

Follistatin has been reported as a candidate gene for polycystic ovarian syndrome (PCOS) based on linkage and association studies. In this study, investigation of polymorphisms in the FST gene was done to determine if genetic variation is associated with...

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Panneerselvam P, Sivakumari K, Jayaprakash P, et al. SNP analysis of follistatin gene associated with polycystic ovarian syndrome. Adv Appl Bioinform Chem. 2010;3:111-9doi: 10.2147/AABC.S11013.
Panneerselvam, P., Sivakumari, K., Jayaprakash, P., & Srikanth, R. (2010). SNP analysis of follistatin gene associated with polycystic ovarian syndrome. Advances and applications in bioinformatics and chemistry : AABC, 3111-9. https://doi.org/10.2147/AABC.S11013
Panneerselvam, Palanisamy, et al. "SNP analysis of follistatin gene associated with polycystic ovarian syndrome." Advances and applications in bioinformatics and chemistry : AABC vol. 3 (2010): 111-9. doi: https://doi.org/10.2147/AABC.S11013
Panneerselvam P, Sivakumari K, Jayaprakash P, Srikanth R. SNP analysis of follistatin gene associated with polycystic ovarian syndrome. Adv Appl Bioinform Chem. 2010;3:111-9. doi: 10.2147/AABC.S11013. Epub 2010 Dec 13. PMID: 21918632; PMCID: PMC3170008.
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Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study.

Advances and applications in bioinformatics and chemistry : AABC

Hasan TN, B LG, Masoodi TA, Shafi G, Alshatwi AA, Sivashanmugham P.
PMID: 21918635
Adv Appl Bioinform Chem. 2011;4:29-36. doi: 10.2147/AABC.S17371. Epub 2011 Mar 08.

BACKGROUND: The human progesterone receptor (hPR) belongs to the steroid receptor family. It may be found as monomers (A and B) and or as a dimer (AB). hPR is regarded as the prognostic biomarker for breast cancer. In a...

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Hasan TN, B LG, Masoodi TA, et al. Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study. Adv Appl Bioinform Chem. 2011;4:29-36doi: 10.2147/AABC.S17371.
Hasan, T. N., B, L. G., Masoodi, T. A., Shafi, G., Alshatwi, A. A., & Sivashanmugham, P. (2011). Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study. Advances and applications in bioinformatics and chemistry : AABC, 429-36. https://doi.org/10.2147/AABC.S17371
Hasan, Tarique N, et al. "Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study." Advances and applications in bioinformatics and chemistry : AABC vol. 4 (2011): 29-36. doi: https://doi.org/10.2147/AABC.S17371
Hasan TN, B LG, Masoodi TA, Shafi G, Alshatwi AA, Sivashanmugham P. Affinity of estrogens for human progesterone receptor A and B monomers and risk of breast cancer: a comparative molecular modeling study. Adv Appl Bioinform Chem. 2011;4:29-36. doi: 10.2147/AABC.S17371. Epub 2011 Mar 08. PMID: 21918635; PMCID: PMC3169952.
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Parallel computing in genomic research: advances and applications.

Advances and applications in bioinformatics and chemistry : AABC

Ocaña K, de Oliveira D.
PMID: 26604801
Adv Appl Bioinform Chem. 2015 Nov 13;8:23-35. doi: 10.2147/AABC.S64482. eCollection 2015.

Today's genomic experiments have to process the so-called "biological big data" that is now reaching the size of Terabytes and Petabytes. To process this huge amount of data, scientists may require weeks or months if they use their own...

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Ocaña K, de Oliveira D. Parallel computing in genomic research: advances and applications. Adv Appl Bioinform Chem. 2015;8:23-35doi: 10.2147/AABC.S64482.
Ocaña, K., & de Oliveira, D. (2015). Parallel computing in genomic research: advances and applications. Advances and applications in bioinformatics and chemistry : AABC, 823-35. https://doi.org/10.2147/AABC.S64482
Ocaña, Kary, and de Oliveira, Daniel. "Parallel computing in genomic research: advances and applications." Advances and applications in bioinformatics and chemistry : AABC vol. 8 (2015): 23-35. doi: https://doi.org/10.2147/AABC.S64482
Ocaña K, de Oliveira D. Parallel computing in genomic research: advances and applications. Adv Appl Bioinform Chem. 2015 Nov 13;8:23-35. doi: 10.2147/AABC.S64482. eCollection 2015. PMID: 26604801; PMCID: PMC4655901.
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Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.

Advances and applications in bioinformatics and chemistry : AABC

Suravajhala P, Benso A.
PMID: 28652783
Adv Appl Bioinform Chem. 2017 Jun 12;10:57-64. doi: 10.2147/AABC.S123604. eCollection 2017.

Next-generation sequencing technology has provided resources to easily explore and identify candidate single-nucleotide polymorphisms (SNPs) and variants. However, there remains a challenge in identifying and inferring the causal SNPs from sequence data. A problem with different methods that predict...

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Suravajhala P, Benso A. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Adv Appl Bioinform Chem. 2017;10:57-64doi: 10.2147/AABC.S123604.
Suravajhala, P., & Benso, A. (2017). Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Advances and applications in bioinformatics and chemistry : AABC, 1057-64. https://doi.org/10.2147/AABC.S123604
Suravajhala, Prashanth, and Benso, Alfredo. "Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis." Advances and applications in bioinformatics and chemistry : AABC vol. 10 (2017): 57-64. doi: https://doi.org/10.2147/AABC.S123604
Suravajhala P, Benso A. Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis. Adv Appl Bioinform Chem. 2017 Jun 12;10:57-64. doi: 10.2147/AABC.S123604. eCollection 2017. PMID: 28652783; PMCID: PMC5473491.
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Showing 1 to 12 of 84 entries