Comparative modeling for protein structure prediction

Ginalski, Krzysztof·2006·Current Opinion in Structural Biology
DOI 10.1016/j.sbi.2006.02.003

Cited by (299)

Items 201–299 of 299

  1. The Structure-Based Virtual Screening for Natural Compounds that Bind with the Activating Receptors of Natural Killer Cells
    Adekunle Babajide Rowaiye, Solomon Oluwasunmibare Oni, Ikemefuna Chijioke Uzochukwu, Alex Akpa, Charles Okechukwu Esimone · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  2. Characterization of acyl-ACP thioesterases for the purpose of diversifying fatty acid synthesis pathway
    Fuyuan Jing · 2013
  3. Modeling aircraft emissions during the taxiing phase to assess air quality impacts: An Australian airport case study
    Manori Dissanayaka, Tim J. Ryley, Bojana Spasojević, Savindi Caldera · 2025 · Journal of Air Transport Management
  4. Three‐residue loop closure in proteins: A new kinematic method reveals a locus of connected loop conformations
    Ali Nekouzadeh, Yoram Rudy · 2011 · Journal of Computational Chemistry
  5. Cloning and characterization of lipoxygenase gene from germinating seedlings of green gram (Vigna radiata L.)
    Kasi Viswanath Kotapati, Bhagath Kumar Palaka, Raveendra Anangi, Thyagaraju Kedam, Dinakara Rao Ampasala · 2015 · Indian Journal of Plant Physiology
  6. Query-Adaptive Ranking with Support Vector Machines for Protein Homology Prediction
    Yan Fu, Rong Pan, Qiang Yang, Wen Gao · 2011 · Lecture notes in computer science
  7. CombAlign: a code for generating a one-to-many sequence alignment from a set of pairwise structure-based sequence alignments
    Carol L. Ecale Zhou · 2015 · Source Code for Biology and Medicine
  8. Molecular characterization of Capra hircus lysosomal α-mannosidase and potential mutant site for the therapy of locoweed poisoning.
    Xiangya Kong, Zhang Jiangye, Wu Ying, Jianfei Li, Qinfan Li · 2014 · Acta Biochimica Polonica
  9. Discovery of a potential lead compound for treating leprosy with dapsone resistance mutation in M. leprae folP1
    J. Nisha, K. Ramanathan, F. Nawaz Khan, Dhanasekaran Dharumadurai, Shanthi Veerappapillai · 2016 · Molecular BioSystems
  10. A Comprehensive Review on Homology Modelling in Drug Development: Methodologies, Tools, and Evaluation
    Priyanshu Nema, Arpana Purohit, Vandana Soni, Sushil K. Kashaw · 2026 · Mini-Reviews in Medicinal Chemistry
  11. Fluorescent Binding Protein Sensors for Detection and Quantification of Biochemicals, Metabolites, and Natural Products
    Salete Maria Cardozo Newton, Phillip E. Klebba · 2022 · BIO-PROTOCOL
  12. Novel computational biology methods and their applications to drug discovery
    Sharangdhar S. Phatak, Hoang T. Tran, Shuxing Zhang · 2011 · Frontiers in Biology
  13. Classification tree based protein structure distances for testing sequence–structure correlation
    Elias Zintzaras · 2008 · Computers in Biology and Medicine
  14. Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints
    Ryan Day, Xiaotao Qu, Rosemarie Swanson, Zach Bohannan, Robert Bliss, Jerry W. Tsai · 2011 · Journal of Computational Biology
  15. Improving the Prediction of Kinase Binding Affinity Using Homology Models
    Jeffrey Chyan, Mark Moll, Lydia E. Kavraki · 2013 · ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB)
  16. In Silico Analysis of the Dextransucrase Obtained From Leuconostoc mesenteroides Strain IBUN 91.2.98
    Luisa Alejandra García Galindo, Margarita González, Jairo Alonso Cerón Salamanca, Sonia Amparo Ospina · 2023 · Bioinformatics and Biology Insights
  17. Protein Tertiary Model Assessment Using Granular Machine Learning Techniques
    Anjum A. Chida · 2022 · Digital Archive @ GSU
  18. Homology modeling: Developing 3D structures of target proteins missing in databases
    Om Silakari, Pankaj Kumar Singh · 2021 · Elsevier eBooks
  19. Modelagem computacional de proteínas
    Letícia Xavier Silva, Luana Luiza Bastos, Lucianna Helene Santos · 2021 · Alfahelix eBooks
  20. Approaches to Kinase Homology Modeling: Successes and Considerations for the Structural Kinome
    Victoria A. Feher, J. David Lawson · 2009
  21. Ab initio Protein Structure Prediction
    Rahul Kaushik, Ankita Singh, Bhyravabhotla Jayaram · 2018 · Elsevier eBooks
  22. SeqStruct: A New Amino Acid Similarity Matrix Based on Sequence Correlations and Structural Contacts Yields Sequence-Structure Congruence
    Kejue Jia, Robert L. Jernigan · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  23. Comparative Protein Modeling, Prediction of Conserved Residue and Active Sites in Cold Resistant Protein Isolated from CRPF1, A Cold Tolerant Mutant of Pseudomonas fluorescens
    Mahejibin Khan, Amit Kumar, Reeta Goel · 2009 · Current Microbiology
  24. A novel protocol of energy optimisation for predicted protein structures built by homology modelling
    Tao Xu, Lujia Zhang, Xuedong Wang, Dongzhi Wei · 2010 · Molecular Simulation
  25. Computational studies of the binding modes of CCR1 antagonists
    Yuan Liu, Binhui Chen, Jing Wei · 2012 · Molecular Simulation
  26. A scoring function based on solvation thermodynamics for protein structure prediction
    Shiqiao Du, Yuichi Harano, Masahiro Kinoshita, Minoru Sakurai · 2012 · BIOPHYSICS
  27. New Method for Sequence Alignment Based on Probabilities of Nucleotide Correspondences
    R. Dimitrov, Dilnora E. Gouliamova · 2012 · Biotechnology & Biotechnological Equipment
  28. Coarse-Grained Contact Potential Helps Improve Fold Recognition Sensitivity in Template-Based Protein Structure Modeling
    Maha Abdelrasoul, Yaohang Li · 2016
  29. A Systematic Mapping on High-Performance Computing for Protein Structure Prediction
    Gesiel Rios Lopes, Paulo Sérgio Lopes de Souza, Alexandre C. B. Delbem · 2019 · Lecture notes in computer science
  30. Structure elucidation of Staphylococcus capitis lipase. Molecular dynamics simulations to investigate the effects of calcium and zinc ions on the structural stability
    Fatma Rmili, Fakher Frikha, Mohamed Chamkha, Adel Sayari, Ahmed Fendri · 2022 · Journal of Biomolecular Structure and Dynamics
  31. Biochemist Investigates Protein Folding
    Richard F. Dods · 2023 · Biomedical Materials & Devices
  32. The asymmetric expression of plasma membrane H+‐ ATPase family genes in response to pulvinus‐driven leaf phototropism movement in Vitis vinifera
    Fanwei Zeng, Yongqing Feng, Tian Wang, Xiyuan Ma, Shuzhen Jiao, Shangwen Yang, Miao Shao, Zonghuan Ma, Juan Mao, Baihong Chen · 2024 · Physiologia Plantarum
  33. Prediction of Protein Function from Theoretical Models
    Iwona A. Cymerman, Daniel John Rigden, Janusz Marek Bujnicki · 2008 · Springer eBooks
  34. Pspace: a program that assesses protein space
    Mihaly Mezei, Ming‐Ming Zhou · 2007 · Source Code for Biology and Medicine
  35. Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175
    Kiran Kumar Singarapu, Jeffrey Mills, Rong Xiao, Thomas Acton, Marco Punta, Markus J. Fischer, Barry H. Honig, Burkhard Rost, Gaetano Thomas Montelione, Thomas Szyperski · 2009 · Proteins Structure Function and Bioinformatics
  36. Homology Modelling, Structure-Based Pharmacophore Modelling, High-Throughput Virtual Screening and Docking Studies of L-Type Calcium Channel for Cadmium Toxicity
    Madhu Sudhana Saddala, A. Usha Rani · 2017 · Translational medicine research
  37. Prediction of Protein Function from Theoretical Models
    Daniel John Rigden, Iwona A. Cymerman, Janusz Marek Bujnicki · 2017 · Springer eBooks
  38. Exploration of interaction property between nonylphenol and G protein-coupled receptor 30 based on molecular simulation and biological experiments
    Lijuan Yang, Si‐Chong Chen, Zihao Chen, Xuefei Sun, Qinghua Gao, Ming Lei, Liying Hao · 2022 · Steroids
  39. Integrative Protein Fold Recognition by Alignments and Machine Learning
    Allison N. Tegge, Zheng Wang, Jianlin Jack Cheng · 2010
  40. Computational Methods Related to Reaction Chemistry
    Andrew Shih, Shannon Telesco, Yue Liu, Ravindra Venkatramani, Ravi Radhakrishnan · 2011 · Comprehensive Biomaterials
  41. 3D Structure Development of Chikungunya Virus and its Structural Characterization – an In silico approach
    Anuraj Nayarisseri, Mukesh Yadav, Dowlathabad Muralidhara Rao, Sonam Kukreja, Sheaza Ahmed, Pooja Singh · 2010 · Nature Precedings
  42. Investigations of signaling pathways and their potential benefits in combating trypanosomatid diseases
    Sharon King Keller · 2013
  43. Structural Information and Hidden Markov Models for Biological Sequence Analysis
    Jeanette Tångrot · 2008 · KTH Publication Database DiVA (KTH Royal Institute of Technology)
  44. The Structural Biology and Critical Evaluation of Bacterial Proteases as Targets in New Drug Design
    Maria Antony Dhivyan JE · 2014 · arXiv (Cornell University)
  45. Streptococcus pneumoniae Genome‐wide Identification and Characterization of BOX Element‐binding Domains
    Qiao Zhang, Changzheng Wang, Min Wan, Yin Wu, Qianli Ma · 2015 · Molecular Informatics
  46. Unveiling the Molecular Mechanisms Regulating the Activation of the ErbB Family Receptors at Atomic Resolution through Molecular Modeling and Simulations
    Andrew Shih · 2011 · ScholarlyCommons (University of Pennsylvania)
  47. Bayesian structure reconstruction from single molecule X-ray scattering data
    Michał Walczak · 2015
  48. Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns
    Alexander E. Kister · 2009 · Lecture notes in computer science
  49. New statistical potentials for improved protein structure prediction
    Yaping Feng · 2008
  50. Databases and computational interaction models of Toll-like receptors
    Jing Gong · 2010 · Elektronische Hochschulschriften der LMU München (Ludwig-Maximilians-Universität München)
  51. Molecular Modelling of Multi-Drug Resistance Transporters
    Thomas Evangelidis · 2011 · Research Explorer (The University of Manchester)
  52. Prediction of the spatial structure of proteins: Emphasis on membrane targets
    Anton O. Chugunov, Roman G. Efremov · 2009 · Russian Journal of Bioorganic Chemistry
  53. Uso de modelagem comparativa na determinação estrutural de fitase de Yersinia
    Mariane Oliveira Lemuchi, Mariana Sousa Vieira, Paulo Afonso Granjeiro, José Antônio da Silva, William James Nogueira Lima, Daniel Bonoto Gonçalves, Alexsandro Sobreira Galdino, Moacyr Comar, Alex Gutterres Taranto · 2013 · BBR - Biochemistry and Biotechnology Reports
  54. Homology Modeling of the Calcium Sensing Receptor Extracellular Domain
    Jamal Shamsara · 2011
  55. The putative synaptotagmin protein encoded by the SYT1 gene of the picoplanktonic alga Micromonas is a novel member of C2-domain containing proteins: evidence from in silico characterization and homology modeling
    Ashutosh Mukherjee · 2012
  56. Follicle-stimulating hormone glycoform interactions with the FSH receptor
    Ramy Elsaid · 2015 · Holmes Museum Of Anthropology (Wichita State University)
  57. A novel framework for protein structure prediction
    Rajkumar Bondugula · 2007
  58. Applications of Molecular Modeling in Endocrinology- Review Article
    Azadeh Ebrahim‐Habibi, Bagher A. Larijani · 2014
  59. Strawberry Dioxygenase: Vorapaxar A model for Antiplatelet Therapy
    Alok Jha · 2013 · IOSR Journal of Pharmacy and Biological Sciences
  60. Prediction of Structural and Functional Aspects of Protein
    Arun G. Ingale · 2014 · Advances in information security, privacy, and ethics book series
  61. Hunting Drugs for Potent Antigens in the Silicon Valley
    Ashish Runthala · 2010 · Advances in bioinformatics and biomedical engineering book series
  62. Bioinformatics applications through visualization of variations on protein structures, comparative functional genomics, and comparative modeling for protein structure studies
    Alper Uzun · 2009
  63. A Prediction Method of Protein Disulfide Bond Based on Hybrid Strategy
    Pengfei Sun, Yunhong Ding, Yuyan Huang, Lei Zhang · 2016 · Journal of Biomedical Science and Engineering
  64. An Improved Prediction Method of Protein Disulfide Bond
    Pengfei Sun, Yunhong Ding · 2016 · International Conference on Information Science and Control Engineering
  65. Estudos estruturais das enzimas envolvidas com o mecanismo de produção de ácidos orgânicos da bactéria Gluconacetobacter diazotrophicus utilizando métodos computacionais
    Isabel Pereira Caminha · 2011
  66. Biophysical characterization of squid’s sucker ring teeth proteins
    Kumar Dhawan Akshita · 2017
  67. Discovery of new selective antagonists of G-protein coupled receptors of therapeutic interest
    Cecylia S. Lupala · 2016
  68. Modelagem estrutural e análise In silico da proteína E6 do genêro Deltapapillomavirus.
    Jacqueline Mazzuchelli de Souza · 2018
  69. Aplicações de química teórica no estudo de materiais: métodos in silico para nanomateriais
    Luiz Carlos Gomide Freitas, Guedmiller S. Oliveira · 2018
  70. Desenvolvimento de nanodispositivos baseados em biomoléculas: abordagens computacionais
    Eduardo de Faria Franca, Guedmiller S. Oliveira, Jéssica Cristiane Magalhães Ierich, Ana Carolina Araujo Vig, Caroline P. Brandini, Ariana de Souza Moraes, Fábio L. Leite · 2018
  71. MECHANISTIC CHARACTERIZATION AND DESIGNING POSSIBLE MOLECULAR LIGAND INTERACTIONS WITH RDRP FROM CHIKV
    D. P. Jobidhas, Joseph Baby · 2018 · International Journal of Pharmaceutical Sciences and Drug Research
  72. Análise genética dos pigmentos visuais da Tartaruga-de-Orelha-Vermelha,Trachemys scriptaelegans (Testudine, Emydidae)
    Vitor Henrique Corredor · 2020 · Digital Library of Theses and Dissertations (Universidade de São Paulo)
  73. Investigating the structural impact of hiv-1 integrase natural occurring polymorphisms and novel mutations identified among group m subtypes circulating in sub-Saharan Africa
    Sello Given Mikasi · 2020 · SUNScholar (Stellenbosch University)
  74. Computational Chemistry Tools
    Rainer S. Metcalf, Kenyon G. Daniel, Wesley H. Brooks, Wayne C. Guida · 2021 · Burger's Medicinal Chemistry and Drug Discovery
  75. Computational protein structure prediction using deep learning
    Zhaoyu Li · 2020
  76. Sequence homology based protein-protein interacting residue predictions and the applications in ranking docked conformations
    Li C. Xue · 2012
  77. Introduction
    Jinbo Xu, Sheng Wang, Jianzhu Ma · 2015 · SpringerBriefs in computer science
  78. 3D Structure Development of Chikungunya Virus and its Structural Characterization – an In silico approach
    Anuraj Nayarisseri, Mukesh Yadav, Dowlathabad Muralidhara Rao, Sonam Kukreja, Sheaza Ahmed, Pooja Singh · 2010 · Nature Precedings
  79. Prediction of Structural and Functional Aspects of Protein
    Arun G. Ingale · 2016 · IGI Global eBooks
  80. Descubrimiento de nuevos anticonvulsivos que actúan mediante interacciones con canales iónicos
    Manuel A. Llanos · 2022
  81. A Hybrid Predictor for Protein Tertiary Structures
    Alexandre Almeida, Telma Woerle de Lima · 2022 · Lecture notes in networks and systems
  82. Improved KCNQ2 gene missense variant interpretation with artificial intelligence
    Alba Sáez-Matía, Arantza Muguruza‐Montero, Sara M‐Alicante, Eider Núñez, Rafael Ramis, Óscar R. Ballesteros, Markel G. Ibarluzea, Carmen Fons, Aritz Leonardo, Aitor Bergara et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  83. New methods for protein structure prediction using machine learning and deep learning
    Junlin Wang · 2022
  84. Ab initio Protein Structure Prediction
    Rahul Kaushik, Ankita Singh, Bhyravabhotla Jayaram · 2019 · Elsevier eBooks
  85. In silico Screening of Protein–Protein Interaction Modulators Using the p53 and 14-3-3γ Proteins as an Example
    A. A. Sargsyan, Nelli Muradyan, Vahram Arakelov, Adrine Paronyan, Grigor Arakelov, Karen Nazaryan · 2025 · Molecular Biology
  86. Advanced Protein Modeling Method: Benchmarking and Applications in Computer-Aided Drug Discovery
    Sharangdhar S. Phatak · 2012 · Digital Commons-TMC (Texas Medical Center)
  87. 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
  88. Scoring matrix based on similarity of protein backbone dihedral angles
    W. Pokuta · 2011 · Metody Informatyki Stosowanej
  89. Modélisation de l'assemblage de protéines multi-domaines avec des contraintes expérimentales de microscopie à force atomique.
    Minh Hieu Trinh · 2010
  90. Evolution of the retinoic acid receptor
    Juliana Gutierrez-Mazariegos · 2014
  91. Conception d'un logiciel pour la recherche de nouvelles molécules bioactives
    Colin Bournez · 2019 · theses.fr (ABES)
  92. In silico investigation of xenobiotic interactions with lipid bilayers and ABC membrane transporters, the case of ABCC4/MRP4
    Benjamin Chantemargue · 2018
  93. Exploiting selected Mur enzyme characteristics for antibacterial drug design
    Gizachew Muluneh Amera, Giulia Canarutto, Monika Jain, Rashmi Prabha Singh, Gedefaw Wubie, Mussa Adal, Jayaraman Muthukumaran, Amit Kumar Singh, Silvano Piazza · 2026 · Journal of Microbiological Methods
  94. Four IgG Antibodies and Protein G Are Shapeshifters
    Michael O. Glocker, Manuela Ruß, Cornelia Koy, Michael Kreutzer, F. Teresa I. Melder, Yelena Diebler, Harald Illges, Kwabena F.M. Opuni · 2026 · International Journal of Molecular Sciences
  95. BindingDB Entry 50022194: Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening.
    BindingDB · 2009 · UC San Diego
  96. BindingDB Entry 50026214: Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2.
    BindingDB · 2010 · UC San Diego
  97. BindingDB Entry 50032921: Chemical validation of phosphodiesterase C as a chemotherapeutic target in Trypanosoma cruzi, the etiological agent of Chagas' disease.
    BindingDB · 2011 · UC San Diego
  98. Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics
    Edda Kloppmann · 2009 · EPub Bayreuth (University of Bayreuth)
  99. Clonagem e expressão do gene E6 do Papilomavírus Bovino do tipo 1.
    Jacqueline Mazzuchelli de Souza · 2013