Domain size distributions can predict domain boundaries

Wheelan, S. J., Marchler-Bauer, A., Bryant, S. H.·2000·Bioinformatics
DOI 10.1093/bioinformatics/16.7.613

Cited by (188)

Items 101–188 of 188

  1. Domain boundary prediction based on profile domain linker propensity index
    Qiwen Dong, Xiaolong Wang, Lei Lin, Zhiming Xu · 2006 · Computational Biology and Chemistry
  2. Identification of putative domain linkers by a neural network – application to a large sequence database
    Satoshi Miyazaki, Yutaka Kuroda, Shigeyuki Yokoyama · 2006 · BMC Bioinformatics
  3. Identifying foldable regions in protein sequence from the hydrophobic signal
    Chi Nam Ignatius Pang, K. Lin, Merridee A. Wouters, Jaap Heringa, R. A. George · 2007 · Nucleic Acids Research
  4. GP challenge: evolving energy function for protein structure prediction
    Paweł Widera, Jonathan M. Garibaldi, Natalio Krasnogor · 2009 · Genetic Programming and Evolvable Machines
  5. An Ensemble Tf-Idf Based Approach to Protein Function Prediction via Sequence Segmentation
    Ashish Ranjan, David Fernández‐Baca, Sudhakar Tripathi, Akshay Deepak · 2021 · IEEE Transactions on Computational Biology and Bioinformatics
  6. Redox-Controlled Chemical Protein Synthesis: Sundry Shades of Latency
    Vangelis Agouridas, Nathalie Ollivier, Jérôme Vicogne, Vincent Diemer, Oleg Melnyk · 2022 · Accounts of Chemical Research
  7. The role of negative selection in protein evolution revealed through the energetics of the native state ensemble
    Jordan Hoffmann, James O. Wrabl, Vincent J. Hilser · 2016 · Proteins Structure Function and Bioinformatics
  8. Prediction of protein domain boundaries from inverse covariances
    Michael I. Sadowski · 2012 · Proteins Structure Function and Bioinformatics
  9. Protein Domain Prediction
    Helgi I. Ingólfsson, Golan Yona · 2008 · Methods in molecular biology
  10. Automata Learning and Stochastic Modeling for Biosequence Analysis
    Gill Bejerano · 2003
  11. PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya
    Graham L. Cromar, Anthony Zhao, Xuejian Xiong, Lakshmipuram S. Swapna, Noeleen B. Loughran, Hongyan Song, John Parkinson · 2016 · Database
  12. Exploring Large Protein Sequence Space through Homology- and Representation-based Hierarchical Clustering
    John Z. Chen, B. Gall, S. B. Pulsford, N. Tokuriki, Colin J Jackson · 2025 · Molecular biology and evolution
  13. Characterization of the transcriptome of an ecologically important avian species, the Vinous-throated Parrotbill Paradoxornis webbianus bulomachus (Paradoxornithidae; Aves)
    Jui‐Hua Chu, Rong-Chien Lin, Chia‐Fen Yeh, Yu-Cheng Hsu, Shou‐Hsien Li · 2012 · BMC Genomics
  14. Classify a Protein Domain Using Sigmoid Support Vector Machine
    Umi Kalsum Binti Hassan, Nazri Mohd Nawi, Shahreen binti Kasim · 2014 · International Conference on Information Science and Applications
  15. SAXSDom: Modeling multidomain protein structures using small‐angle X‐ray scattering data
    Jie Hou, Badri Adhikari, John J. Tanner, Jianlin Jack Cheng · 2019 · Proteins Structure Function and Bioinformatics
  16. A Historical Perspective and Overview of Protein Structure Prediction
    John Wooley, Yuzhen Ye · 2007 · Springer eBooks
  17. LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins
    Anastasia A. Gulyaeva, Andrey I. Sigorskikh, Elena S Ocheredko, Dmitry V. Samborskiy, Alexander E. Gorbalenya · 2020 · Bioinformatics
  18. Local protein unfolding and pathogenesis of polyglutamine‐expansion diseases
    Yu Wai Chen · 2003 · Proteins Structure Function and Bioinformatics
  19. Characteristics and Prediction of RNA Structure
    Hengwu Li, Daming Zhu, Caiming Zhang, Huijian Han, Keith A. Crandall · 2014 · BioMed Research International
  20. Protein Domains: Structure, Function, and Methods
    David A. Korasick, Joseph M. Jez · 2015 · Elsevier eBooks
  21. DomHR: Accurately Identifying Domain Boundaries in Proteins Using a Hinge Region Strategy
    Xiaoyan Zhang, Long-jian Lu, Qi Song, Qianqian Yang, Da-peng Li, Jiangming Sun, Tong-hua Li, Peisheng Cong · 2013 · PLoS ONE
  22. Sequence‐based protein domain boundary prediction using BP neural network with various property profiles
    Lei Ye, Ting Liu, Zhaohui Wu, Ruhong Zhou · 2007 · Proteins Structure Function and Bioinformatics
  23. Extending Protein Domain Boundary Predictors to Detect Discontinuous Domains
    Zhidong Xue, Richard Jang, Brandon Govindarajoo, Yichu Huang, Yan Wang · 2015 · PLoS ONE
  24. Initial large-scale exploration of protein-protein interactions in human brain
    Jake Y. Chen, Andrey Sivachenko, Russell N. Bell, Cornelia Kurschner, Irene M. Ota, Sudhir R. Sahasrabudhe · 2004 · IEEE Computational Systems Bioinformatics Conference (CSB)
  25. A modular kernel approach for integrative analysis of protein domain boundaries
    Paul D. Yoo, Bing Bing Zhou, Albert Y. Zomaya · 2009 · BMC Genomics
  26. Domain selection combined with improved cloning strategy for high throughput expression of higher eukaryotic proteins
    Yunjia Chen, Shihong Qiu, Chi-Hao Luan, Ming Luo · 2007 · BMC Biotechnology
  27. SAFE Software and FED Database to Uncover Protein-Protein Interactions using Gene Fusion Analysis
    Dimosthenis Tsagrasoulis, Vasilis Danos, Maria Kissa, Philip Trimpalis, Vassiliki Lila Koumandou, Amalia D. Karagouni, Athanasios Tsakalidis, Σοφία Κοσσίδα · 2011 · Evolutionary Bioinformatics
  28. A novel phylogenetic tree based on the presence of protein domains in selected actinobacteria
    Indrani Sarkar, Maher Gtari, Louis S. Tisa, Arnab Sen · 2018 · Antonie van Leeuwenhoek
  29. From Jabberwocky to Genome: Lewis Carroll and Computational Biology
    David B. Searls · 2001 · Journal of Computational Biology
  30. Spectral Analysis of Distributions: Finding Periodic Components in Eukaryotic Enzyme Length Data
    Eugene Kolker, Brian C. Tjaden, Robert M. Hubley, Edward N. Trifonov, Andrew F. Siegel · 2002 · OMICS A Journal of Integrative Biology
  31. Mathematical model for empirically optimizing large scale production of soluble protein domains
    Eisuke Chikayama, Atsushi Kurotani, Takanori Tanaka, Takashi Yabuki, Satoshi Miyazaki, Shigeyuki Yokoyama, Yutaka Kuroda · 2010 · BMC Bioinformatics
  32. Segmented Genome: Elementary Units of Genome Structure
    E. N. Trifonov · 2002 · Russian Journal of Genetics
  33. Protein Structural Domains: Definition and Prediction
    Iakes Ezkurdia, Michael L. Tress · 2011 · Current Protocols in Protein Science
  34. Prediction of protein domain boundaries from statistics of appearance of amino acid residues
    Oxana V. Galzitskaya, Nikita V. Dovidchenko, Mikhail Yu. Lobanov, Sergiy O. Garbuzynskiy · 2006 · Molecular Biology
  35. Food Proteins–Peptides
    Arvind Kannan, NAVAM S. HETTIARACHCHY, Maurice R. Marshall · 2012 · CRC Press eBooks
  36. Minor deviations from randomness have huge repercussions on the functional structuring of sequence space
    Laura Weidmann, Tjeerd M. H. Dijkstra, Oliver Kohlbacher, Andrei N. Lupas · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  37. Classify a Protein Domain Using SVM Sigmoid Kernel
    Ummi Kalsum Hassan, Nazri Mohd Nawi, Shahreen binti Kasim, Azizul Azhar Ramli, Mohd Farhan Md Fudzee, Mohamad Aizi Salamat · 2014 · Advances in intelligent systems and computing
  38. Bayesian data mining of protein domains gives an efficient predictive algorithm and new insight
    Rajani R. Joshi, Vivekanand V. Samant · 2006 · Journal of Molecular Modeling
  39. Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea
    Philipp F. Popp, Vadim M. Gumerov, Ekaterina P. Andrianova, Lisa Bewersdorf, Thorsten Mascher, Igor B. Zhulin, Diana Wolf · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Positions of cysteine residues reveal local clusters and hidden relationships to Sequons and Transmembrane domains in Human proteins
    Manthan Desai, Bingyun Sun · 2024 · Scientific Reports
  41. Terpinen-4-ol from Trachyspermum ammi is a potential and safer candidate molecule for fungicide development against Alternaria solani
    Qudsia Yousafi, Muhammad Sohail Shahzad, Saleem Shahzad, Muhammad Sajid, Abrar Hussain, Asim Mehmood, Allah Ditta Abid, Amina Qandeel, Anum Shahid, Muhammad Saad Khan et al. · 2021 · Journal of King Saud University - Science
  42. Bioinformatic and literature assessment of toxicity and allergenicity of a CRISPR-Cas9 engineered gene drive to control Anopheles gambiae the mosquito vector of human malaria
    Alima Qureshi, John B. Connolly · 2023 · Malaria Journal
  43. Prediction of Protein Interdomain Linker Regions by a Nonstationary Hidden Markov Model
    Kyounghwa Bae, Bani K. Mallick, Christine G. Elsik · 2008 · Journal of the American Statistical Association
  44. A multi-expert system for the automatic detection of protein domains from sequence information
    Niranjan Nagarajan, Golan Yona · 2003 · Research in Computational Molecular Biology
  45. SPOT-1D-LM: Reaching Alignment-profile-based Accuracy in Predicting Protein Secondary and Tertiary Structural Properties without Alignment
    Jaspreet Singh, Kuldip K. Paliwal, Jaswinder Singh, Yaoqi Zhou · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  46. Fast prediction of protein domain boundaries using conserved local patterns
    Rajani R. Joshi, Vivekanand V. Samant · 2006 · Journal of Molecular Modeling
  47. Gene Fusion Analysis in the Battle against the African Endemic Sleeping Sickness
    Philip Trimpalis, Vassiliki Lila Koumandou, Evangelia Pliakou, Nicholas P. Anagnou, Σοφία Κοσσίδα · 2013 · PLoS ONE
  48. Computing motif correlations in proteins
    Jorng‐Tzong Horng, Hsien‐Da Huang, Shih‐Hsien Wang, Ming‐You Chen, Shir‐Ly Huang, Jenn‐Kang Hwang · 2003 · Journal of Computational Chemistry
  49. Magnitude and spatial orientation of the hydrophobic moments of multi-domain proteins
    Ruhong Zhou, Ajay K. Royyuru, Prasanna Athma, Frank Suits, B. D. Silverman · 2006 · International Journal of Bioinformatics Research and Applications
  50. Random Gene Dissection: A Tool for the Investigation of Protein Structural Organization
    Rimantas Sapranauskas, Arvydas Lubys · 2005 · BioTechniques
  51. Finding Protein Domain Boundaries: An Automated, Non-Homology-Based Method
    Brian M. Gurbaxani, Parag Mallick · 2005 · IEEE Intelligent Systems
  52. Detection, Characterization and Evolution of Internal Repeats in Chitinases of Known 3-D Structure
    Manigandan Sivaji, Vinoth Sadasivam, Narayanasamy Jayabalan, Selvaraj Samuel, Chuanzhu Fan · 2014 · PLoS ONE
  53. Identification and Correction of Erroneous Protein Sequences in Public Databases
    László Patthy · 2016 · Methods in molecular biology
  54. Learning Proteome Domain Folding Using LSTMs in an Empirical Kernel Space
    Da Kuang, Dina Issakova, Junhyong Kim · 2022 · Journal of Molecular Biology
  55. Protein Structure and Conformational Dynamics
    Volkhard Helms · 2022 · Protein Interactions
  56. Inferring Boundary Information of Discontinuous-Domain Proteins
    Abdur Rahman Sikder, Albert Y. Zomaya · 2008 · IEEE Transactions on NanoBioscience
  57. Statistical techniques for biological motif discovery
    Uri Keich, Niranjan Nagarajan · 2007
  58. Protein Domain Boundary Prediction
    Paul D. Yoo, Bing Bing Zhou, Albert Y. Zomaya · 2010 · Wiley eBooks
  59. Automated Sequence‐Based Approaches for Identifying Domain Families
    Liisa Holm, Andreas Heger · 2013
  60. Predicting Simplified Features of Protein Structure
    Dariusz Przybylski, Burkhard Rost · 2007
  61. Correct assignment of homology is crucial when genomics meets molecular evolution
    Mohamed Zouine, Quentin Sculo, Bernard Labedan · 2002 · Comparative and Functional Genomics
  62. Exact algorithms for pairwise protein structure alignment
    Inken Wohlers · 2012 · Data Archiving and Networked Services (DANS)
  63. Beyond gene length: Exon-intron architecture and isoform potential in the evolution of eukaryotic complexity
    Senbao Lu, Yue Bao, Gloria Sheynkman, Dmitry Korkin · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
  64. Quality control of gene predictions
    Alinda Nagy, Hédi Hegyi, Krisztina Farkas, Hedvig Tordai, Evelin Kozma, László Bányai, László Patthy · 2008 · Springer eBooks
  65. Comparative Genomics of Microbial Chemoreceptor Sequence, Structure, and Function
    Aaron D. Fleetwood · 2014
  66. Prediction of Protein Domains from Sequence Information Using Support Vector Machines
    Shuxue Zou, Yanxin Huang, Yan Wang, Chunguang Zhou · 2006 · Lecture notes in computer science
  67. New Methods for the Prediction and Classification of Protein Domains
    Jan E. Gewehr · 2007
  68. A Mixture of Experts Method for Predicting Domain Boundaries in Proteins
    Ian M. MacDonald, George Berg · 2007 · IEEE International Conference on Bioinformatics and Bioengineering (BIBE)
  69. LENGTH SCALE EFFECTS OF SMALL MODEL PROTEIN FOLDING
    Linsen Zhang, MING ZHANG, Changjun Chen, Yi Xiao · 2005 · International Journal of Modern Physics C
  70. Characteristics of equipartition for RNA structure
    Hengwu Li, Daming Zhu, Caiming Zhang, Huijian Han, Keith A. Crandall · 2014 · BMC Proceedings
  71. Origin of genes with unresolved ancestry Analysis of orphan genes in H.sapiens, D.melanogaster and S.cerevisiae
    Adrián César‐Razquin · 2013
  72. Analysis and prediction of protein domains
    Russell L. Marsden · 2003 · OpenGrey (Institut de l'Information Scientifique et Technique)
  73. Regulation of G Protein Signaling by GoLoco Motif Containing Proteins
    Peishen Zhao · 2011 · Scholarship@Western (Western University)
  74. Current Awareness
    2001 · Comparative and Functional Genomics
  75. Protein Domains: Structure, Function, and Methods
    David A. Korasick, Joseph M. Jez · 2022 · Elsevier eBooks
  76. Faculty Opinions recommendation of Complex evolutionary footprints revealed in an analysis of reused protein segments of diverse lengths.
    Patrice Koehl · 2017 · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature
  77. Sub-region analysis of DMD gene in cases with idiopathic generalized epilepsy
    Zhi-Jian Lin, Bixia Huang, Li-Fang Su, Sheng-Yin Zhu, Junwei He, Guozhang Chen, Peng-Xing Lin · 2023 · Neurogenetics
  78. The Protein World
    Michael Lynch · 2024 · Oxford University Press eBooks
  79. Additional file 6 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  80. Additional file 3 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  81. Additional file 5 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  82. Additional file 7 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  83. Additional file 4 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  84. Additional file 1 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Natasha Glover, Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  85. Compression of protein secondary structures enables ultra-fast and accurate structure searching
    Runfeng Lin, Sebastian E. Ahnert · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  86. DomDiff: protein family and domain annotation via diffusion model and ESM2 embedding
    Chao Zhang, Haopeng Xia, Yin Peng · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  87. Additional file 2 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Glover, Natasha M., Christophe Dessimoz, Odile Lecompte · 2023 · Figshare
  88. Additional file 8 of Protein length distribution is remarkably uniform across the tree of life
    Yannis Nevers, Glover, Natasha M., Christophe Dessimoz, Odile Lecompte · 2023 · Figshare