The Protein Data Bank: unifying the archive

Westbrook, J.·2002·Nucleic Acids Research

Cited by (311)

Items 101–200 of 311

  1. Docking-based identification of small-molecule binding sites at protein-protein interfaces
    Mireia Rosell, Juan Fernández‐Recio · 2020 · Computational and Structural Biotechnology Journal
  2. Complementarity Between Public and Commercial Databases: New Opportunities in Medicinal Chemistry Informatics
    Christopher Southan, Peter Varkonyi, Sorel Mureşan · 2007 · Current Topics in Medicinal Chemistry
  3. Development of Extracellular Signal-Regulated Kinase Inhibitors
    Kimberly A. Burkhard, Sarice Smith, Rahul R Deshmukh, Alexander D. MacKerell, Paul Shapiro · 2009 · Current Topics in Medicinal Chemistry
  4. Construction of Complex Features for Computational Predicting ncRNA-Protein Interaction
    Qiguo Dai, Maozu Guo, Xiaodong Duan, Zhixia Teng, Yueyue Fu · 2019 · Frontiers in Genetics
  5. Gene prioritization in Type 2 Diabetes using domain interactions and network analysis
    Amitabh Sharma, Sreenivas Chavali, Rubina Tabassum, Nikhil Tandon, Dwaipayan Bharadwaj · 2010 · BMC Genomics
  6. Key Phytochemicals and Biological Functions of Chuanxiong Rhizoma Against Ischemic Stroke: A Network Pharmacology and Experimental Assessment
    Peng Hui Zeng, Yi Yao, Hong-Fei Su, Chao‐Yuan Ye, Yiwen Sun, Xinwen Zhou, Youming Lu, Anbing Shi, Qing Tian · 2021 · Frontiers in Pharmacology
  7. SEQATOMS: a web tool for identifying missing regions in PDB in sequence context
    Bernd Willem Brandt, Jaap Heringa, J.A.M. Leunissen · 2008 · Nucleic Acids Research
  8. Identifying Protein Domains with the Pfam Database
    Robert D. Finn, Sam Griffiths‐Jones, Alex G. Bateman · 2003 · Current Protocols in Bioinformatics
  9. De Novo Design and Characterization of a Helical Hairpin Eicosapeptide
    Rudresh, Suryanarayanarao Ramakumar, Udupi Anantharamachar Ramagopal, Yoshihito Inai, Suchi Goel, Dinkar Sahal, Virander S. Chauhan · 2004 · Structure
  10. Gene3D: structural assignments for the biologist and bioinformaticist alike
    Daniel W. A. Buchan · 2003 · Nucleic Acids Research
  11. Comparative analysis and unification of domain–domain interaction networks
    Patrik Björkholm, Erik L. L. Sonnhammer · 2009 · Bioinformatics
  12. The Protein Data Bank and lessons in data management
    Philip E. Bourne · 2004 · Briefings in Bioinformatics
  13. Biological data cleaning: a case study
    Katherine G. Herbert, Jason T.L. Wang · 2007 · International Journal of Information Quality
  14. Finding Homologs in Amino Acid Sequences Using Network BLAST Searches
    István Ladunga · 2009 · Current Protocols in Bioinformatics
  15. Thermostable xylanase fromThermoascus aurantiacusat ultrahigh resolution (0.89 Å) at 100 K and atomic resolution (1.11 Å) at 293 K refined anisotropically to small-molecule accuracy
    Ramanathan NATESH, K. Manikandan, P. Bhanumoorthy, M. A. Viswamitra, S. Ramakumar · 2002 · Acta Crystallographica Section D Biological Crystallography
  16. Tyr212: A Key Residue Involved in Strand Discrimination by the DNA Mismatch Repair Endonuclease MutH
    Peter Friedhoff, Evangelos Thomas, Alfred M. Pingoud · 2002 · Journal of Molecular Biology
  17. SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803
    Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak, Jong‐Soon Choi · 2008 · BMC Bioinformatics
  18. Sensory Ion Channel Candidates Inform on the Clinical Course of Pancreatic Cancer and Present Potential Targets for Repurposing of FDA-Approved Agents
    Wenjie Shi, Chen Li, Thomas Wartmann, Christoph Kahlert, Renfei Du, Aristotelis Perrakis, Thomas Baptist Brunner, Roland S. Croner, Ulf D. Kahlert · 2022 · Journal of Personalized Medicine
  19. Anti-inflammatory, antioxidant and in silico studies of Buddleja salviifolia (L). Lam leaf constituents
    Srinivasa C. Pendota, Ashwell Rungano Ndhlala, Adeyemi Oladapo Aremu, M.A. Aderogba, J. Van Staden · 2014 · South African Journal of Botany
  20. Clustering HLA Class I Superfamilies Using Structural Interaction Patterns
    Sumitro Harjanto, Lisa F. P. Ng, Joo Chuan Tong · 2014 · PLoS ONE
  21. Using the Tools and Resources of the RCSB Protein Data Bank
    Shuchismita Dutta, Helen Miriam Berman, Wolfgang F. Bluhm · 2007 · Current Protocols in Bioinformatics
  22. The rapid emergence of multiple sublineages of Omicron (B.1.1.529) variant: Dynamic profiling via molecular phylogenetics and mutational landscape studies
    Chiranjib Chakraborty, Manojit Bhattacharya, Ashish Ranjan Sharma, Kuldeep Dhama, Sang‐Soo Lee · 2022 · Journal of Infection and Public Health
  23. Structural Heterogeneity in Single Particle Imaging Using X-ray Lasers
    Thomas Mandl, Christofer Östlin, Ibrahim Eliah Dawod, Maxim N. Brodmerkel, Erik G. Marklund, Andrew V. Martin, Nicuşor Tı̂mneanu, Carl Caleman · 2020 · The Journal of Physical Chemistry Letters
  24. Introduction to Cheminformatics
    David Scott Wishart · 2016 · Current Protocols in Bioinformatics
  25. Using a residue clash map to functionally characterize protein recombination hybrids
    Manish C. Saraf, Costas D. Maranas · 2003 · Protein Engineering Design and Selection
  26. Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular Simulation
    Leandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel · 2019 · Journal of Chemical Information and Modeling
  27. Modeling the Semantics of 3D Protein Structures
    Sudha Ram, Wei Wei · 2004 · Lecture notes in computer science
  28. Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruit
    Felipe Valenzuela-Riffo, Carlos Gaete-Eastman, Yazmina Stappung, Rodrigo Lizana, Raúl Herrera, María Alejandra Moya‐León, Luis Morales‐Quintana · 2018 · Journal of Biomolecular Structure and Dynamics
  29. Estimation of the Number of Authentic Orphan Genes in Bacterial Genomes
    F. Satoshi · 2004 · DNA Research
  30. MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences
    Julie Thompson · 2005 · Nucleic Acids Research
  31. Application of InChI to curate, index, and query 3‐D structures
    M.D. Prasanna, Jiřı́ Vondrášek, Alexander Wlodawer, Talapady N. Bhat · 2005 · Proteins Structure Function and Bioinformatics
  32. D ATABASES AND T OOLS FOR B ROWSING G ENOMES
    Ewan Birney, Michele E. Clamp, Tim Hubbard · 2002 · Annual Review of Genomics and Human Genetics
  33. Protein Data Bank (PDB)
    Eric Martz · 2004 · Dictionary of Bioinformatics and Computational Biology
  34. SAHA-based novel HDAC inhibitor design by core hopping method
    Lanlan Zang, Xuejiao Wang, Xiaobo Li, Shuqing Wang, Weiren Xu, Xie Xian-bin, Xian‐Chao Cheng, Huan Ma, Run‐Ling Wang · 2014 · Journal of Molecular Graphics and Modelling
  35. A computational pipeline for protein structure prediction and analysis at genome scale
    Manesh B. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong He Xu, Ying Xu · 2003 · Bioinformatics
  36. RPI-GGCN: Prediction of RNA-Protein Interaction Based on Interpretability Gated Graph Convolution Neural Network and Co-Regularized Variational Autoencoders
    Yifei Wang, Pengju Ding, Congjing Wang, Shiyue He, Xin Gao, Bin Yu · 2024 · IEEE Transactions on Neural Networks and Learning Systems
  37. Expression, characterization and molecular docking of the assimilatory NaDH-nitrite reductase from Acidovorax wautersii QZ-4
    Qiaozhi Song, Binbin Wang, Fangkun Zhao, Ye Han, Zhijiang Zhou · 2020 · Biochemical Engineering Journal
  38. Functional analysis and structure determination of alkaline protease from Aspergillus flavus
    Rabbani Syed, Roja Rani, Sabeena, Tariq Masoodi, Gowher Shafi, Khalid Saad Alharbi · 2012 · Bioinformation
  39. Biological Units and their Effect upon the Properties and Prediction of Protein–Protein Interactions
    Emily Jefferson, Thomas P. Walsh, Geoffrey J. Barton · 2006 · Journal of Molecular Biology
  40. Synthesis and molecular docking of new roflumilast analogues as preferential-selective potent PDE-4B inhibitors with improved pharmacokinetic profile
    Bahia Abbas Moussa, Asmaa A. El‐Zaher, Mohamed Kandeel El-Ashrey, Marwa A. Fouad · 2018 · European Journal of Medicinal Chemistry
  41. NMR refinement and peptide folding using the GROMACS software
    Anna Sinelnikova, David van der Spoel · 2021 · Journal of Biomolecular NMR
  42. Reproducibility of single protein explosions induced by X-ray lasers
    Christofer Östlin, Nicuşor Tı̂mneanu, H. Olof Jönsson, Tomas Ekeberg, Andrew V. Martin, Carl Caleman · 2018 · Physical Chemistry Chemical Physics
  43. Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments
    Manikandan Karuppasamy, Debnath Pal, Suryanarayanarao Ramakumar, Nathan E. Brener, Sitharama S. Iyengar, Guna S. Seetharaman · 2008 · Genome biology
  44. Functional Analysis of Peptidyl-prolyl cis-trans Isomerase from Aspergillus flavus
    Saleem Ahmad, Sen Wang, Weizhong Wu, Kunlong Yang, Yanfeng Zhang, Elisabeth Tumukunde, Shihua Wang, Yu Wang · 2019 · International Journal of Molecular Sciences
  45. Instituto Oswaldo Cruz
    Annes Dias, Ulysses de Nonohay, Guerra Blessmann · 2012 · Arquivos rio-grandenses de medicina
  46. Evolution of different oligomeric glycyl‐tRNA synthetases
    Su‐Ni Tang, Jing‐Fei Huang · 2005 · FEBS Letters
  47. eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments
    G. L. Moore · 2002 · Nucleic Acids Research
  48. The Protein Data Bank: A Case Study in Management of Community Data
    Helen Miriam Berman, Philip E. Bourne, John Westbrook · 2004 · Current Proteomics
  49. Ontological Foundation for Protein Data Models
    Amandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2005 · Lecture notes in computer science
  50. Active site analysis of cis-epoxysuccinate hydrolase from Nocardia tartaricans using homology modeling and site-directed mutagenesis
    Vinayagam Vasu, Kumaresan Jayaraman, Ganesh babu Manoharan, Sankaranarayanan Meenakshisundaram · 2011 · Applied Microbiology and Biotechnology
  51. Analysis and prediction of human acetylation using a cascade classifier based on support vector machine
    Ning Qiao, Miao Yu, Jinchao Ji, Zhiqiang Ma, Xiaowei Zhao · 2019 · BMC Bioinformatics
  52. Demonstration of Ubiquitin Thiolester Formation of UBE2Q2 (UBCi), a Novel Ubiquitin-Conjugating Enzyme with Implantation Site-Specific Expression1
    Michael H. Melner, Arthur L. Haas, Jennifer M. Klein, ALAN R. BRASH, William E. Boeglin, Subir Kumar Nagdas, Virginia P. Winfrey, Gary E. Olson · 2006 · Biology of Reproduction
  53. CADB: Conformation Angles DataBase of proteins
    S. S. Sheik · 2003 · Nucleic Acids Research
  54. Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residue
    Ansuman Biswas, Arpit Shukla, Ramachandran Vijayan, Jeyaraman Jeyakanthan, K. Sekar · 2016 · Journal of Structural Biology
  55. New putative therapeutic targets against Serratia marcescens using reverse vaccinology and subtractive genomics
    Lígia Carolina da Silva Prado, Andrei Giacchetto Felice, Thaís Cristina Vilela Rodrigues, Sandeep Tiwari, Bruno Silva Andrade, Rodrigo Bentes Kato, Carlo José Freire Oliveira, Marcos Vinicius da Silva, Debmalya Barh, Vasco Azevedo et al. · 2021 · Journal of Biomolecular Structure and Dynamics
  56. Identification of a Novel Nucleocytoplasmic Shuttling RNA Helicase of Trypanosomes
    Alexandre Haruo Inoue, Mariana Serpeloni, Priscila Mazzochi Hiraiwa, Sueli Fumie Yamada‐Ogatta, J.R.C. Muniz, María Cristina M. Motta, Newton Medeiros Vidal, Samuel Goldenberg, Andréa Rodrigues Ávila · 2014 · PLoS ONE
  57. Chemical compound navigator: A web‐based chem‐BLAST, chemical taxonomy‐based search engine for browsing compounds
    M.D. Prasanna, Jiřı́ Vondrášek, Alexander Wlodawer, Henry Rodriguez, Talapady N. Bhat · 2006 · Proteins Structure Function and Bioinformatics
  58. Searching and Mapping of B-Cell Epitopes in Bcipep Database
    Sudipto Saha, Gajendra P. S. Raghava · 2007 · Methods in molecular biology
  59. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities
    Paul Shafer, Timothy Isganitis, Golan Yona · 2006 · BMC Bioinformatics
  60. The evolution of structural databases
    Oliviero Carugo, Sándor Pongor · 2002 · Trends in biotechnology
  61. Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thaliana
    Karim Kherraz, Khaled Kherraz, Abdelkrim Kameli · 2011 · Bioinformation
  62. Mechanistic insights into the anti-depressant effect of emodin: an integrated systems pharmacology study and experimental validation
    Peng Hui Zeng, Xiaoming Wang, Chao‐Yuan Ye, Hong-Fei Su, Ying‐Yan Fang, Teng Zhang, Qing Tian · 2021 · Aging
  63. Scaling the walls of discovery: using semantic metadata for integrative problem solving
    Maurice Manning, A. Aggarwal, Kevin Gao, Greg Tucker‐Kellogg · 2009 · Briefings in Bioinformatics
  64. Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulation
    Jiaxing Chen, Leslie A. Kuhn · 2019 · Journal of Molecular Graphics and Modelling
  65. PRECISE: a Database of Predicted and Consensus Interaction Sites in Enzymes
    Shu‐Hsien Sheu · 2004 · Nucleic Acids Research
  66. Hibiscus sabdariffa L. polyphenolic‐rich extract promotes muscle glucose uptake and inhibits intestinal glucose absorption with concomitant amelioration of Fe 2+ ‐induced hepatic oxidative injury
    Almahi I. Mohamed, Veronica F. Salau, Ochuko Lucky Erukainure, Md. Shahidul Islam · 2022 · Journal of Food Biochemistry
  67. Systems Biology Resources Arising from the Human Metabolome Project
    David Scott Wishart · 2012 · Springer eBooks
  68. Topological analysis of DPY 19L3, a human C‐mannosyltransferase
    Yuki Niwa, Yoshihiko Nakano, Takehiro Suzuki, Mizuo Yamagishi, Kei Otani, Naoshi Dohmae, Siro Simizu · 2018 · FEBS Journal
  69. Databases for Protein–Protein Interactions
    Natsu Nakajima, Tatsuya Akutsu, Ryuichiro Nakato · 2021 · Methods in molecular biology
  70. eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity
    Gaoqi He, Yiping Amy Song, Wenhao Wei, Xia Wang, Xingjian Lu, Honglin Li · 2019 · Journal of Computational Chemistry
  71. Integrative approach for computationally inferring protein domain interactions
    See-Kiong Ng, Zhuo Zhang, Soon-Heng Tan · 2003 · ACM Symposium on Applied Computing
  72. Advances in Protein Ontology Project
    Amandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2006 · Proceedings - IEEE Symposium on Computer-Based Medical Systems
  73. Mechanisms of main components in Curcuma longa L. on hepatic fibrosis based on network pharmacology and molecular docking: A review
    Qiang Han, Jiahui Zhu, Peng Zhang · 2023 · Medicine
  74. A Comparative Analysis of Cockroach and Mosquito, Octopamine Receptor Homologues Produced Using Chimera, Swiss-Model, and AlphaFold Molecular Modeling Tools
    Steve D. Kamguia, Eric N. Njabon, Issofa Patouossa, Alphonse Emadak, Neville Y. Forlemu · 2025 · ACS Omega
  75. Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XEC
    Chiranjib Chakraborty, Manojit Bhattacharya, Ali S. Abdelhameed · 2025 · Virology
  76. Data Mining of Macromolecular Structures
    Bart van Beusekom, Anastassis Perrakis A, Robbie P. Joosten · 2016 · Methods in molecular biology
  77. A simple and effective method based on enzyme-ligand complex for affinity analysis of lipase inhibitor from Schisandra chinensis (Turcz.) Baill
    Shanshan Tang, Shuo Liu, Yunxiao Wang, Dongyu Gu, Jing Tian, Yi Yang · 2022 · Journal of Chromatography B
  78. Comparative Protein Structure Prediction
    Marc A. Martı́-Renom, Bozidar Jerkovic, Andrej Šali · 2002 · Current Protocols in Protein Science
  79. A comparison of SCOP and CATH with respect to domain–domain interactions
    Emily Jefferson, Thomas P. Walsh, Geoffrey J. Barton · 2007 · Proteins Structure Function and Bioinformatics
  80. Ontology-based knowledge representation for protein data
    Amandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang, Baldev S. Sidhu · 2005 · IEEE International Conference on Industrial Informatics (INDIN)
  81. Repurposing of renin inhibitors as SARS-COV-2 main protease inhibitors: A computational study
    Rana H. Refaey, Mohamed Kandeel El-Ashrey, Yassin Mohammed Nissan · 2020 · Virology
  82. Binding of Pollutants to Biomolecules: A Simulation Study
    Ahmet Yıldırım, Jin Zhang, Sergio Manzetti, David van der Spoel · 2016 · Chemical Research in Toxicology
  83. Modeling Protein Structure from its Sequence
    Marc A. Martı́-Renom, Mallur Srivatsan Madhusudhan, Narayanan Eswar, Ursula Pieper, Min‐Yi Shen, Andrej Šali, András Fiser, Nebojša Mirković, Bino John, Ashley C. Stuart · 2003 · Current Protocols in Bioinformatics
  84. Deconvolution of Targeted Protein–Protein Interaction Maps
    Alexey Stukalov, Giulio Superti‐Furga, Jacques Colinge · 2012 · Journal of Proteome Research
  85. Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emission
    H. Olof Jönsson, Carl Caleman, Jakob Andreasson, Nicuşor Tı̂mneanu · 2017 · IUCrJ
  86. IN SILICO BINDING INTERACTION STUDY OF MEFENAMIC ACID AND PIROXICAM ON HUMAN ALBUMIN
    Joshita Djajadisastra, Hamka Decky Purnama, Arry Yanuar · 2017 · International Journal of Applied Pharmaceutics
  87. Structural and biological evaluation of halogen derivatives of 1,9-pyrazoloanthrones towards the design of a specific potent inhibitor of c-Jun-N-terminal kinase (JNK)
    Ramesh Ganduri, Vikas Singh, Ansuman Biswas, Durga Prasad Karothu, K. Sekar, Kithiganahalli Narayanaswamy Balaji, T.N.G. Row · 2018 · New Journal of Chemistry
  88. Detection of Underrepresented Biological Sequences Using Class-Conditional Distribution Models
    Slobodan Vučetić, Dragoljub Pokrajac, Hongbo Michael Xie, Zoran Obradovic A · 2003 · SIAM International Conference on Data Mining
  89. The Structure Superposition Database
    Ranyee A. Chiang · 2003 · Nucleic Acids Research
  90. NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0
    W. L. A. K. Chiu · 2003 · Nucleic Acids Research
  91. An Ontology for Protein Data Models
    Amandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2005 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
  92. Identifying functionally important cis ‐peptide containing segments in proteins and their utility in molecular function annotation
    Sreetama Das, Suryanarayanarao Ramakumar, Debnath Pal · 2014 · FEBS Journal
  93. Quality assurance for the query and distribution systems of the RCSB Protein Data Bank
    Wolfgang F. Bluhm, Bojan Beran, C. Bi, Dimitris Dimitropoulos, Andreas Prlić, Gregory B. Quinn, Peter W. Rose, Chirag Suresh Shah, Jasmine Y. Young, Benjamin T. Yukich et al. · 2011 · Database
  94. Databases and QSAR for Cancer Research
    Adeel Malik, Hemajit Singh, Munazah Andrabi, Syed Akhtar Husain, Shandar Ahmad · 2006 · Cancer Informatics
  95. Genomic and Proteomic Databases and Applications: A Challenge for Database Technology
    Shamkant B. Navathe, Upen Patil · 2004 · Lecture notes in computer science
  96. Methods and protocols for the assessment of protein allergenicity and cross-reactivity
    Joo Chuan Tong · 2008 · Frontiers in bioscience
  97. ANTXR1 blockade enhances cardiac function in preclinical models of heart failure
    Nicola Boccella, Guojun Yu, Steven Seaman, Yang Feng, Jaewon Lee, Francesco Tomassoni‐Ardori, Liping Yang, Kuo-Sheng Hsu, James M. Dunleavey, Jodi Becker et al. · 2025 · Nature Cardiovascular Research
  98. The active components of Erzhi wan and their anti-Alzheimer's disease mechanisms determined by an integrative approach of network pharmacology, bioinformatics, molecular docking, and molecular dynamics simulation
    Meng Yu, Zhongqi Shen, Shaozhi Zhang, Yang Zhang, Hongwei Zhao, Longfei Zhang · 2024 · Heliyon
  99. Rationale design and synthesis of new roflumilast analogues as preferential selective and potent PDE-4B inhibitors
    Ahmed M. Moussa, Heba Abdelrasheed Allam, Mohamed Kandeel El-Ashrey, Marwa A. Fouad, Ahmed Ali Al-Karmalawy · 2024 · Bioorganic Chemistry
  100. Role of Bioinformatics in Drug Design and Discovery
    Pinkal H. Patel, A. N. JHA, G. S. Chakraborthy · 2023 · Interdisciplinary biotechnological advances