TargetDB: a target registration database for structural genomics projects

Chen, Li, Oughtred, Rose, Berman, Helen M., Westbrook, John·2004·Bioinformatics
DOI 10.1093/bioinformatics/bth300

Cited by (176)

Items 101–176 of 176

  1. Genome Pool Strategy for Structural Coverage of Protein Families
    Lukasz Jaroszewski, Lukasz Slabinski, John Wooley, Ashley M. Deacon, Scott A. Lesley, Ian A. Wilson, Adam Godzik · 2008 · Structure
  2. The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory
    Chris A. Morris, Anne Pajon, Susanne L. Griffiths, Edward Daniel, Marc Savitsky, Bill Lin, Jonathan M. Diprose, Alan Sousa da Silva, Katya Pilicheva, Peter V Troshin et al. · 2011 · Acta Crystallographica Section D Biological Crystallography
  3. TOPSAN: a collaborative annotation environment for structural genomics
    Dana Weekes, Sanjeev Krishna, Constantina Bakolitsa, Ian A. Wilson, Adam Godzik, John Wooley · 2010 · BMC Bioinformatics
  4. Drug discovery and the use of computational approaches for infectious diseases.
    Richard J. Marhöfer, Frank Oellien, P. Selzer · 2011 · Future Medicinal Chemistry
  5. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role
    Sanjeev Krishna, Lakshminarayanan Aravind, Constantina Bakolitsa, Jonathan M. Caruthers, Dennis D. Carlton, Mitchell D. Miller, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Hsiu‐Ju Chiu et al. · 2010 · Acta Crystallographica Section F Structural Biology and Crystallization Communications
  6. TSTMP: target selection for structural genomics of human transmembrane proteins
    Julia K. Varga, László Dobson, István Reményi, Gábor Tusnády · 2016 · Nucleic Acids Research
  7. Computational crystallization
    Irem Altan, Patrick Charbonneau, Edward H. Snell · 2016 · Archives of Biochemistry and Biophysics
  8. A fast SCOP fold classification system using content-based E-Predict algorithm
    Pin-Hao Chi, Chi‐Ren Shyu, Dong He Xu · 2006 · BMC Bioinformatics
  9. The Use of the Escherichia coli Cell‐Free Protein Synthesis for Structural Biology and Structural Proteomics
    T. Kigawa, Makoto Inoue, Masaaki Aoki, Takayoshi Matsuda, Takashi Yabuki, Eiko Seki, T. Harada, Satoru Watanabe, Shigeyuki Yokoyama · 2007
  10. Camps 2.0: Exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
    Sindy Neumann, Holger Hartmann, Antonio J. Martín-Galiano, Angelika Fuchs, Dmitrij Frishman · 2011 · Proteins Structure Function and Bioinformatics
  11. Efficient Approaches for Retrieving Protein Tertiary Structures
    Georgina Mirceva, Ivana Cingovska, Zoran Dimov, Danco P. Davcev · 2011 · IEEE Transactions on Computational Biology and Bioinformatics
  12. StrBioLib: a Java library for development of custom computational structural biology applications
    John‐Marc Chandonia · 2007 · Bioinformatics
  13. A graph-based meta-model for heterogeneous data management
    Ernesto Damiani, Barbara Oliboni, Elisa Quintarelli, Letizia Tanca · 2018 · Knowledge and Information Systems
  14. TMCrys: predict propensity of success for transmembrane protein crystallization
    Julia K. Varga, Gábor Tusnády · 2018 · Bioinformatics
  15. Survey of Predictors of Propensity for Protein Production and Crystallization with Application to Predict Resolution of Crystal Structures
    Jianzhao Gao, Zhonghua Wu, Gang Hu, Kui Wang, Jiangning Song, A. Joachimiak, Lukasz Kurgan · 2017 · Current Protein and Peptide Science
  16. Structural proteomics of minimal organisms: Conservation of protein fold usage and evolutionary implications
    John‐Marc Chandonia, Sung‐Hou Kim · 2006 · BMC Structural Biology
  17. Predicting protein crystallization using a simple scoring card method
    Watshara Shoombuatong, Huiling Huang, Jeerayut Chaijaruwanich, Phasit Charoenkwan, Hua-Chin Lee, Shinn‐Ying Ho · 2013 · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)
  18. Sequence-Based Classification Using Discriminatory Motif Feature Selection
    Hao Xiong, Daniel Capurso, Śaunak Sen, Mark Robert Segal · 2011 · PLoS ONE
  19. Crystals of TELSAM–target protein fusions that exhibit minimal crystal contacts and lack direct inter-TELSAM contacts
    Supeshala Nawarathnage, Sara Soleimani, Moriah H. Mathis, Braydan D. Bezzant, Diana Tamara Ramírez, Parag L. Gajjar, Derick R. Bunn, Cameron Stewart, Tobin Smith, Maria Jose Pedroza Romo et al. · 2022 · Open Biology
  20. Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments
    Pin-Hao Chi, Bin Pang, Dmitry Korkin, Chi‐Ren Shyu · 2009 · Bioinformatics
  21. Integrating Omics Data to Prioritize Target Genes in Pathogenic Bacteria
    Marisa Nicolás, Maiana de Oliveira Cerqueira e Costa, Pablo Ivan Pereira Ramos, Marcelo Trindade dos Santos, Ernesto Pérez‐Rueda, Marcelo Adrian Marti, Darío Fernández Do Porto, Adrian Gustavo Turjanski · 2020 · Computational biology
  22. Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures
    Dominik Gront, Marek Grabowski, Matthew D. Zimmerman, John W. Raynor, Karolina L. Tkaczuk, Wladek Minor · 2012 · Journal of Structural and Functional Genomics
  23. Computational approaches to selecting and optimising targets for structural biology
    Ian M. Overton, Geoffrey J. Barton · 2011 · Methods
  24. Establishing synthesis pathway‐host compatibility via enzyme solubility
    Sara Adel Amin, Venkatesh Endalur Gopinarayanan, Nikhil U. Nair, Soha Hassoun · 2019 · Biotechnology and Bioengineering
  25. Protein Crystallizability
    Pawel Smialowski, Philip Wong · 2016 · Methods in molecular biology
  26. Predicting experimental properties of integral membrane proteins by a naive Bayes approach
    Antonio J. Martín-Galiano, Pawel Smialowski, Dmitrij Frishman · 2007 · Proteins Structure Function and Bioinformatics
  27. Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome
    James E. Bray · 2012 · Journal of Structural and Functional Genomics
  28. Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni
    Heping Zheng, Ekaterina V. Filippova, Karolina L. Tkaczuk, Piotr Dworzyński, M. Chruszcz, Przemyslaw Jerzy Porebski, Zdzislaw Wawrzak, Olena Onopriyenko, Marina Kudritska, S. Grimshaw et al. · 2012 · Journal of Structural and Functional Genomics
  29. Possible Random Mechanism in Crystallization Evidenced in Proteins from Plasmodium falciparum
    Shaomin Yan, Guang Wu · 2011 · Crystal Growth & Design
  30. Protein Crystallizability
    Pawel Smialowski, Dmitrij Frishman · 2009 · Methods in molecular biology
  31. Harnessing Knowledge from Structural Genomics
    Helen Miriam Berman · 2008 · Structure
  32. Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system
    Nathan Philip Cowieson, Pawel Listwan, Mareike Kurz, Anna Aagaard, Timothy Ravasi, Christine Anne Wells, Thomas Huber, David Arthur Hume, Boštjan Kobe, Jennifer L. Martin · 2005 · Journal of Structural and Functional Genomics
  33. Protein yield is tunable by synonymous codon changes of translation initiation sites
    Bikash Kumar Bhandari, Chun Shen Lim, Daniela M. Remus, Augustine Chen, Craig J. van Dolleweerd, Paul P. Gardner · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  34. PLMC: Language Model of Protein Sequences Enhances Protein Crystallization Prediction
    Dapeng Xiong, U Kaicheng, Jianfeng Sun, Adam P. Cribbs · 2024 · Interdisciplinary Sciences Computational Life Sciences
  35. ProSol-multi: Protein solubility prediction via amino acids multi-level correlation and discriminative distribution
    Hina Ghafoor, Muhammad Nabeel Asim, Muhammad Ali Ibrahim, Andreas Dengel · 2024 · Heliyon
  36. Update on the Pfam5000 Strategy for Selection of Structural Genomics Targets
    John‐Marc Chandonia, Steven E. Brenner · 2005 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  37. Selecting Targets from Eukaryotic Parasites for Structural Genomics and Drug Discovery
    Isabelle Q. Phan, Robin Stacy, Peter John Myler · 2014 · Methods in molecular biology
  38. Correlating dynamic amino acid properties with success rate of crystallization of proteins from Bacteroides vulgatus
    Shaomin Yan, Guang Wu · 2012 · Crystal Research and Technology
  39. Structure based virtual screening, molecular dynamic simulation to identify the oxadiazole derivatives as inhibitors of Enterococcus D-Ala-D-Ser ligase for combating vancomycin resistance
    Sneha B. Paymal, Sagar S. Barale, Shirishkumar Vishnu Supanekar, Kailas Dasharath Sonawane · 2023 · Computers in Biology and Medicine
  40. The TMCrys server for supporting crystallization of transmembrane proteins
    Julia K. Varga, Gábor Tusnády · 2019 · Bioinformatics
  41. A graphical approach to tracking and reporting target status in structural genomics
    Xiaokang Pan, Gary E. Wesenberg, John L. Markley, Brian G. Fox, George N. Phillips, C.A. Bingman · 2007 · Journal of Structural and Functional Genomics
  42. Association of combined features of amino acid and protein withcrystallization propensity of proteins fromCytophaga Hutchinsonii
    Shaomin Yan, Guang Wu · 2013 · Zeitschrift für Kristallographie - Crystalline Materials
  43. Recording information on protein complexes in an information management system
    Marc Savitsky, Jonathan M. Diprose, Chris A. Morris, Susanne L. Griffiths, Edward Daniel, Bill Lin, Susan Daenke, B. Bishop, Christian Siebold, Keith S. Wilson et al. · 2011 · Journal of Structural Biology
  44. Predicting Crystallization Propensity of Proteins from Arabidopsis Thaliana
    Shaomin Yan, Guang Wu · 2015 · Biological Procedures Online
  45. Protein Structure Annotation Resources
    Margaret J. Gabanyi, Helen Miriam Berman · 2014 · Methods in molecular biology
  46. Molecular Modeling for Protein Aggregation and Formulation
    Dorota Roberts, Jim Warwicker, Robin Curtis · 2015 · Wiley eBooks
  47. Structural Genomics of Minimal Organisms: Pipeline and Results
    Sung‐Hou Kim, Dong-Hae Shin, Rosalind Kim, Paul D. Adams, John‐Marc Chandonia · 2008 · Methods in molecular biology
  48. Correlation of Combined Characters of Amino Acid and Whole Protein with Success Rate of Crystallization of Lactobacillus Proteins
    Shaomin Yan, Guang Wu · 2019 · Journal of Biomedical Science and Engineering
  49. Target Selection in Structural Genomics Projects to Increase Knowledge of Protein Structure and Function Space
    Phil Carter, David Lee, Christine Anne Orengo · 2008 · Advances in protein chemistry and structural biology
  50. Disease Risk of Missense Mutations Using Structural Inference from Predicted Function
    Jeremy A. Horst, Kai Wang, Orapin V. Horst, Michael L. Cunningham, Ram Samudrala · 2010 · Current Protein and Peptide Science
  51. Target Selection for Structural Genomics of Infectious Diseases
    Corin Yeats, Benoît H. Dessailly, Elizabeth M. Glass, Daved H. Fremont, Christine Anne Orengo · 2014 · Methods in molecular biology
  52. Distance-based indexing of residue contacts for protein structure retrieval and alignment
    Ahmet Saçan, İsmail Hakkı Toroslu, Hakan Ferhatosmanoğlu · 2008 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
  53. Quantification of the impact of PSI:Biology according to the annotations of the determined structures
    Paul DePietro, Elchin S. Julfayev, William A. McLaughlin · 2013 · BMC Structural Biology
  54. Correlating Combined Features of Amino Acid and Protein with Crystallization Propensity of Proteins from Mycobacterium tuberculosis
    Shaomin Yan, Guang Wu · 2019 · Journal of Biomedical Science and Engineering
  55. Decoding sequence-level information to predict membrane protein expression
    Shyam M. Saladi, Nauman M. Javed, Axel Müller, William Clemons · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Resources and Infrastructure for Structural Bioinformatics
    Dong He Xu, Jie Liang, Ying Xu · 2007 · Biological and medical physics series
  57. Structural genomics – expanding protein structural universe
    A. Joachimiak · 2005 · Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics
  58. PROSPERO: online prediction of crystallographic success from experimental results and sequence
    Frank H. Zucker, Hae Young Kim, Ethan A. Merritt · 2012 · Journal of Applied Crystallography
  59. PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies
    Jouhyun Jeon, Roland R. Arnold, Fateh Singh, Joan Teyra, Tatjana Braun, Philip M. Kim · 2016 · BMC Bioinformatics
  60. [Progresses in predicting the crystallizability of proteins].
    Ren‐Bin Zhou, Hui‐Meng Lu, Da‐Chuan Yin · 2014 · PubMed
  61. The Impact of Structural Proteomics on Macromolecular Structure Databases
    James D. Watson, Janet M. Thornton · 2008 · WORLD SCIENTIFIC eBooks
  62. Computational support systems for prediction and characterization of protein crystallization outcomes
    Marcin J. Mizianty · 2013 · ERA: Education and Research Archive (University of Alberta)
  63. Developing a strategy to enhance protein crystallization using metal chelate complexes
    Randeniya Adikaram Mudiyanselage Subhani Samanmali Bandara · 2014
  64. Structural Genomics
    Philip E. Bourne, Adam Godzik · 2007
  65. Prediction of Crystallization Propensity of Proteins from Bacillus haloduran Using Various Amino Acid and Protein Features
    Shaomin Yan, Guang Wu · 2019 · Journal of Biomedical Science and Engineering
  66. Improving recombinant protein production using TISIGNER.com
    Bikash Kumar Bhandari, Chun Shen Lim, Paul P. Gardner · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  67. TELSAM polymers accelerate crystallization of fused target proteins by stabilizing minimal crystal contacts and in the absence of direct inter-TELSAM contacts
    Supeshala Nawarathnage, Sara Soleimani, Moriah H. Mathis, Braydan D. Bezzant, Diana Tamara Ramírez, Parag L. Gajjar, Derick R. Bunn, Cameron Stewart, Tobin Smith, Maria Jose Pedroza Romo et al. · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  68. Current awareness on comparative and functional genomics
    2005 · Comparative and Functional Genomics
  69. Information sharing
    Katrin Legg · 2010 · PSI Structural Genomics Knowledgebase
  70. Servers and databases
    2010 · PSI Structural Genomics Knowledgebase
  71. Additional file 3 of Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE
    Chao Wang, Quan Zou · 2023 · Figshare
  72. A Medium-Throughput Structural Proteomics Approach Applied to the Genome of E. coli
    Allan Matte, Irena H. Ekiel, Zongchao Jia, Kalle Gehring, Mirosław Cygler · 2009 · Springer eBooks
  73. Additional file 2 of Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE
    Wang, Chao, Zou, Quan · 2023 · Figshare
  74. Additional file 4 of Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE
    Wang, Chao, Zou, Quan · 2023 · Figshare
  75. Additional file 1 of Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE
    Wang, Chao, Zou, Quan · 2023 · Figshare
  76. Additional file 5 of Prediction of protein solubility based on sequence physicochemical patterns and distributed representation information with DeepSoluE
    Wang, Chao, Zou, Quan · 2023 · Figshare