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Using SEQUEST with theoretically complete sequence databases.

Journal of the American Society for Mass Spectrometry

Sadygov RG.
PMID: 26238326
J Am Soc Mass Spectrom. 2015 Nov;26(11):1858-64. doi: 10.1007/s13361-015-1228-5. Epub 2015 Aug 04.

SEQUEST has long been used to identify peptides/proteins from their tandem mass spectra and protein sequence databases. The algorithm has proven to be hugely successful for its sensitivity and specificity in identifying peptides/proteins, the sequences of which are present...

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Sadygov RG. Using SEQUEST with theoretically complete sequence databases. J Am Soc Mass Spectrom. 2015;26(11):1858-64doi: 10.1007/s13361-015-1228-5.
Sadygov, R. G. (2015). Using SEQUEST with theoretically complete sequence databases. Journal of the American Society for Mass Spectrometry, 26(11), 1858-64. https://doi.org/10.1007/s13361-015-1228-5
Sadygov, Rovshan G. "Using SEQUEST with theoretically complete sequence databases." Journal of the American Society for Mass Spectrometry vol. 26,11 (2015): 1858-64. doi: https://doi.org/10.1007/s13361-015-1228-5
Sadygov RG. Using SEQUEST with theoretically complete sequence databases. J Am Soc Mass Spectrom. 2015 Nov;26(11):1858-64. doi: 10.1007/s13361-015-1228-5. Epub 2015 Aug 04. PMID: 26238326; PMCID: PMC4607654.
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Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together.

Nucleic acids research

Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV.
PMID: 17130145
Nucleic Acids Res. 2007 Jan;35:D566-71. doi: 10.1093/nar/gkl859. Epub 2006 Nov 27.

Protein interaction data exists in a number of repositories. Each repository has its own data format, molecule identifier and supplementary information. Michigan Molecular Interactions (MiMI) assists scientists searching through this overwhelming amount of protein interaction data. MiMI gathers data...

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Jayapandian M, Chapman A, Tarcea VG, et al. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2006;35:D566-71doi: 10.1093/nar/gkl859.
Jayapandian, M., Chapman, A., Tarcea, V. G., Yu, C., Elkiss, A., Ianni, A., Liu, B., Nandi, A., Santos, C., Andrews, P., Athey, B., States, D., & Jagadish, H. V. (2007). Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic acids research, 35D566-71. https://doi.org/10.1093/nar/gkl859
Jayapandian, Magesh, et al. "Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together." Nucleic acids research vol. 35 (2007): D566-71. doi: https://doi.org/10.1093/nar/gkl859
Jayapandian M, Chapman A, Tarcea VG, Yu C, Elkiss A, Ianni A, Liu B, Nandi A, Santos C, Andrews P, Athey B, States D, Jagadish HV. Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res. 2007 Jan;35:D566-71. doi: 10.1093/nar/gkl859. Epub 2006 Nov 27. PMID: 17130145; PMCID: PMC1716720.
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PRIDE and "Database on Demand" as valuable tools for computational proteomics.

Methods in molecular biology (Clifton, N.J.)

Vizcaíno JA, Reisinger F, Côté R, Martens L.
PMID: 21063943
Methods Mol Biol. 2011;696:93-105. doi: 10.1007/978-1-60761-987-1_6.

The Proteomics Identifications Database (PRIDE, http://www.ebi.ac.uk/pride ) provides users with the ability to explore and compare mass spectrometry-based proteomics experiments that reveal details of the protein expression found in a broad range of taxonomic groups, tissues, and disease states....

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Vizcaíno JA, Reisinger F, Côté R, et al. PRIDE and "Database on Demand" as valuable tools for computational proteomics. Methods Mol Biol. 2011;696:93-105doi: 10.1007/978-1-60761-987-1_6.
Vizcaíno, J. A., Reisinger, F., Côté, R., & Martens, L. (2011). PRIDE and "Database on Demand" as valuable tools for computational proteomics. Methods in molecular biology (Clifton, N.J.), 69693-105. https://doi.org/10.1007/978-1-60761-987-1_6
Vizcaíno, Juan Antonio, et al. "PRIDE and "Database on Demand" as valuable tools for computational proteomics." Methods in molecular biology (Clifton, N.J.) vol. 696 (2011): 93-105. doi: https://doi.org/10.1007/978-1-60761-987-1_6
Vizcaíno JA, Reisinger F, Côté R, Martens L. PRIDE and "Database on Demand" as valuable tools for computational proteomics. Methods Mol Biol. 2011;696:93-105. doi: 10.1007/978-1-60761-987-1_6. PMID: 21063943.
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A reliability measure of protein-protein interactions and a reliability measure-based search engine.

Computer methods in biomechanics and biomedical engineering

Park B, Han K.
PMID: 19657800
Comput Methods Biomech Biomed Engin. 2010 Feb;13(1):97-104. doi: 10.1080/10255842.2010.494039.

Many methods developed for estimating the reliability of protein-protein interactions are based on the topology of protein-protein interaction networks. This paper describes a new reliability measure for protein-protein interactions, which does not rely on the topology of protein interaction...

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Park B, Han K. A reliability measure of protein-protein interactions and a reliability measure-based search engine. Comput Methods Biomech Biomed Engin. 2010;13(1):97-104doi: 10.1080/10255842.2010.494039.
Park, B., & Han, K. (2010). A reliability measure of protein-protein interactions and a reliability measure-based search engine. Computer methods in biomechanics and biomedical engineering, 13(1), 97-104. https://doi.org/10.1080/10255842.2010.494039
Park, Byungkyu, and Han, Kyungsook. "A reliability measure of protein-protein interactions and a reliability measure-based search engine." Computer methods in biomechanics and biomedical engineering vol. 13,1 (2010): 97-104. doi: https://doi.org/10.1080/10255842.2010.494039
Park B, Han K. A reliability measure of protein-protein interactions and a reliability measure-based search engine. Comput Methods Biomech Biomed Engin. 2010 Feb;13(1):97-104. doi: 10.1080/10255842.2010.494039. PMID: 19657800.
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HAPPI: an online database of comprehensive human annotated and predicted protein interactions.

BMC genomics

Chen JY, Mamidipalli S, Huan T.
PMID: 19594875
BMC Genomics. 2009 Jul 07;10:S16. doi: 10.1186/1471-2164-10-S1-S16.

BACKGROUND: Human protein-protein interaction (PPIs) data are the foundation for understanding molecular signalling networks and the functional roles of biomolecules. Several human PPI databases have become available; however, comparisons of these datasets have suggested limited data coverage and poor...

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Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics. 2009;10:S16doi: 10.1186/1471-2164-10-S1-S16.
Chen, J. Y., Mamidipalli, S., & Huan, T. (2009). HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC genomics, 10S16. https://doi.org/10.1186/1471-2164-10-S1-S16
Chen, Jake Yue, et al. "HAPPI: an online database of comprehensive human annotated and predicted protein interactions." BMC genomics vol. 10 (2009): S16. doi: https://doi.org/10.1186/1471-2164-10-S1-S16
Chen JY, Mamidipalli S, Huan T. HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics. 2009 Jul 07;10:S16. doi: 10.1186/1471-2164-10-S1-S16. PMID: 19594875; PMCID: PMC2709259.
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Current progress in computational metabolomics.

Briefings in bioinformatics

Wishart DS.
PMID: 17626065
Brief Bioinform. 2007 Sep;8(5):279-93. doi: 10.1093/bib/bbm030. Epub 2007 Jul 11.

Being a relatively new addition to the 'omics' field, metabolomics is still evolving its own computational infrastructure and assessing its own computational needs. Due to its strong emphasis on chemical information and because of the importance of linking that...

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Wishart DS. Current progress in computational metabolomics. Brief Bioinform. 2007;8(5):279-93doi: 10.1093/bib/bbm030.
Wishart, D. S. (2007). Current progress in computational metabolomics. Briefings in bioinformatics, 8(5), 279-93. https://doi.org/10.1093/bib/bbm030
Wishart, David S. "Current progress in computational metabolomics." Briefings in bioinformatics vol. 8,5 (2007): 279-93. doi: https://doi.org/10.1093/bib/bbm030
Wishart DS. Current progress in computational metabolomics. Brief Bioinform. 2007 Sep;8(5):279-93. doi: 10.1093/bib/bbm030. Epub 2007 Jul 11. PMID: 17626065.
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Unified data resource for cryo-EM.

Methods in enzymology

Lawson CL.
PMID: 20888470
Methods Enzymol. 2010;483:73-90. doi: 10.1016/S0076-6879(10)83004-6.

Three-dimensional (3D) cryoelectron microscopy reconstruction methods are uniquely able to reveal structures of many important macromolecules and macromolecular complexes. EMDataBank.org, a joint effort of the Protein Databank in Europe (PDBe), the Research Collaboratory for Structural Bioinformatics (RCSB), and the...

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Lawson CL. Unified data resource for cryo-EM. Methods Enzymol. 2010;483:73-90doi: 10.1016/S0076-6879(10)83004-6.
Lawson, C. L. (2010). Unified data resource for cryo-EM. Methods in enzymology, 48373-90. https://doi.org/10.1016/S0076-6879(10)83004-6
Lawson, Catherine L. "Unified data resource for cryo-EM." Methods in enzymology vol. 483 (2010): 73-90. doi: https://doi.org/10.1016/S0076-6879(10)83004-6
Lawson CL. Unified data resource for cryo-EM. Methods Enzymol. 2010;483:73-90. doi: 10.1016/S0076-6879(10)83004-6. PMID: 20888470; PMCID: PMC2966391.
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Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

PloS one

Orii N, Ganapathiraju MK.
PMID: 23209562
PLoS One. 2012;7(11):e49029. doi: 10.1371/journal.pone.0049029. Epub 2012 Nov 28.

Protein-protein interactions (PPIs) are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about...

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Orii N, Ganapathiraju MK. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PLoS One. 2012;7(11):e49029doi: 10.1371/journal.pone.0049029.
Orii, N., & Ganapathiraju, M. K. (2012). Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PloS one, 7(11), e49029. https://doi.org/10.1371/journal.pone.0049029
Orii, Naoki, and Ganapathiraju, Madhavi K. "Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function." PloS one vol. 7,11 (2012): e49029. doi: https://doi.org/10.1371/journal.pone.0049029
Orii N, Ganapathiraju MK. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PLoS One. 2012;7(11):e49029. doi: 10.1371/journal.pone.0049029. Epub 2012 Nov 28. PMID: 23209562; PMCID: PMC3509123.
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PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files.

Proteomics

Medina-Aunon JA, Carazo JM, Albar JP.
PMID: 21204261
Proteomics. 2011 Jan;11(2):334-7. doi: 10.1002/pmic.201000448. Epub 2010 Dec 17.

Current standardization initiatives have greatly contributed to share the information derived by proteomics experiments. One of these initiatives is the XML-based repository PRIDE (PRoteomics IDEntification database), although an XML-based document does not appear to present a user-friendly view at...

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Medina-Aunon JA, Carazo JM, Albar JP. PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files. Proteomics. 2010;11(2):334-7doi: 10.1002/pmic.201000448.
Medina-Aunon, J. A., Carazo, J. M., & Albar, J. P. (2011). PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files. Proteomics, 11(2), 334-7. https://doi.org/10.1002/pmic.201000448
Medina-Aunon, J Alberto, et al. "PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files." Proteomics vol. 11,2 (2011): 334-7. doi: https://doi.org/10.1002/pmic.201000448
Medina-Aunon JA, Carazo JM, Albar JP. PRIDEViewer: a novel user-friendly interface to visualize PRIDE XML files. Proteomics. 2011 Jan;11(2):334-7. doi: 10.1002/pmic.201000448. Epub 2010 Dec 17. PMID: 21204261.
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DOMINE: a comprehensive collection of known and predicted domain-domain interactions.

Nucleic acids research

Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R.
PMID: 21113022
Nucleic Acids Res. 2011 Jan;39:D730-5. doi: 10.1093/nar/gkq1229. Epub 2010 Nov 27.

DOMINE is a comprehensive collection of known and predicted domain-domain interactions (DDIs) compiled from 15 different sources. The updated DOMINE includes 2285 new domain-domain interactions (DDIs) inferred from experimentally characterized high-resolution three-dimensional structures, and about 3500 novel predictions by...

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Yellaboina S, Tasneem A, Zaykin DV, et al. DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res. 2010;39:D730-5doi: 10.1093/nar/gkq1229.
Yellaboina, S., Tasneem, A., Zaykin, D. V., Raghavachari, B., & Jothi, R. (2011). DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic acids research, 39D730-5. https://doi.org/10.1093/nar/gkq1229
Yellaboina, Sailu, et al. "DOMINE: a comprehensive collection of known and predicted domain-domain interactions." Nucleic acids research vol. 39 (2011): D730-5. doi: https://doi.org/10.1093/nar/gkq1229
Yellaboina S, Tasneem A, Zaykin DV, Raghavachari B, Jothi R. DOMINE: a comprehensive collection of known and predicted domain-domain interactions. Nucleic Acids Res. 2011 Jan;39:D730-5. doi: 10.1093/nar/gkq1229. Epub 2010 Nov 27. PMID: 21113022; PMCID: PMC3013741.
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Prediction of intrinsic disorder in proteins using MFDp2.

Methods in molecular biology (Clifton, N.J.)

Mizianty MJ, Uversky V, Kurgan L.
PMID: 24573480
Methods Mol Biol. 2014;1137:147-62. doi: 10.1007/978-1-4939-0366-5_11.

Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant across all kingdoms of life, particularly in eukaryotes, and are implicated in numerous cellular processes. Experimental annotation...

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Mizianty MJ, Uversky V, Kurgan L. Prediction of intrinsic disorder in proteins using MFDp2. Methods Mol Biol. 2014;1137:147-62doi: 10.1007/978-1-4939-0366-5_11.
Mizianty, M. J., Uversky, V., & Kurgan, L. (2014). Prediction of intrinsic disorder in proteins using MFDp2. Methods in molecular biology (Clifton, N.J.), 1137147-62. https://doi.org/10.1007/978-1-4939-0366-5_11
Mizianty, Marcin J, et al. "Prediction of intrinsic disorder in proteins using MFDp2." Methods in molecular biology (Clifton, N.J.) vol. 1137 (2014): 147-62. doi: https://doi.org/10.1007/978-1-4939-0366-5_11
Mizianty MJ, Uversky V, Kurgan L. Prediction of intrinsic disorder in proteins using MFDp2. Methods Mol Biol. 2014;1137:147-62. doi: 10.1007/978-1-4939-0366-5_11. PMID: 24573480.
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On optimal placement of molecules in the unit cell.

Acta crystallographica. Section D, Biological crystallography

Dauter Z.
PMID: 23633598
Acta Crystallogr D Biol Crystallogr. 2013 May;69:872-8. doi: 10.1107/S0907444913002722. Epub 2013 Apr 19.

There are currently no rules for a unified, standard way of placing macromolecular structures in the crystal lattice. An analysis of all possible symmetry-equivalent representations of molecular structures in various space groups leads to the concept of the anti-Cheshire...

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Dauter Z. On optimal placement of molecules in the unit cell. Acta Crystallogr D Biol Crystallogr. 2013;69:872-8doi: 10.1107/S0907444913002722.
Dauter, Z. (2013). On optimal placement of molecules in the unit cell. Acta crystallographica. Section D, Biological crystallography, 69872-8. https://doi.org/10.1107/S0907444913002722
Dauter, Zbigniew. "On optimal placement of molecules in the unit cell." Acta crystallographica. Section D, Biological crystallography vol. 69 (2013): 872-8. doi: https://doi.org/10.1107/S0907444913002722
Dauter Z. On optimal placement of molecules in the unit cell. Acta Crystallogr D Biol Crystallogr. 2013 May;69:872-8. doi: 10.1107/S0907444913002722. Epub 2013 Apr 19. PMID: 23633598; PMCID: PMC4005360.
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Showing 1 to 12 of 218 entries