The Protein Data Bank: unifying the archive
Cited by (311)
Items 101–200 of 311
- Docking-based identification of small-molecule binding sites at protein-protein interfacesMireia Rosell, Juan Fernández‐Recio · 2020 · Computational and Structural Biotechnology Journal
- Complementarity Between Public and Commercial Databases: New Opportunities in Medicinal Chemistry InformaticsChristopher Southan, Peter Varkonyi, Sorel Mureşan · 2007 · Current Topics in Medicinal Chemistry
- Development of Extracellular Signal-Regulated Kinase InhibitorsKimberly A. Burkhard, Sarice Smith, Rahul R Deshmukh, Alexander D. MacKerell, Paul Shapiro · 2009 · Current Topics in Medicinal Chemistry
- Construction of Complex Features for Computational Predicting ncRNA-Protein InteractionQiguo Dai, Maozu Guo, Xiaodong Duan, Zhixia Teng, Yueyue Fu · 2019 · Frontiers in Genetics
- Gene prioritization in Type 2 Diabetes using domain interactions and network analysisAmitabh Sharma, Sreenivas Chavali, Rubina Tabassum, Nikhil Tandon, Dwaipayan Bharadwaj · 2010 · BMC Genomics
- Key Phytochemicals and Biological Functions of Chuanxiong Rhizoma Against Ischemic Stroke: A Network Pharmacology and Experimental AssessmentPeng Hui Zeng, Yi Yao, Hong-Fei Su, Chao‐Yuan Ye, Yiwen Sun, Xinwen Zhou, Youming Lu, Anbing Shi, Qing Tian · 2021 · Frontiers in Pharmacology
- SEQATOMS: a web tool for identifying missing regions in PDB in sequence contextBernd Willem Brandt, Jaap Heringa, J.A.M. Leunissen · 2008 · Nucleic Acids Research
- Identifying Protein Domains with the Pfam DatabaseRobert D. Finn, Sam Griffiths‐Jones, Alex G. Bateman · 2003 · Current Protocols in Bioinformatics
- De Novo Design and Characterization of a Helical Hairpin EicosapeptideRudresh, Suryanarayanarao Ramakumar, Udupi Anantharamachar Ramagopal, Yoshihito Inai, Suchi Goel, Dinkar Sahal, Virander S. Chauhan · 2004 · Structure
- Gene3D: structural assignments for the biologist and bioinformaticist alikeDaniel W. A. Buchan · 2003 · Nucleic Acids Research
- Comparative analysis and unification of domain–domain interaction networksPatrik Björkholm, Erik L. L. Sonnhammer · 2009 · Bioinformatics
- The Protein Data Bank and lessons in data managementPhilip E. Bourne · 2004 · Briefings in Bioinformatics
- Biological data cleaning: a case studyKatherine G. Herbert, Jason T.L. Wang · 2007 · International Journal of Information Quality
- Finding Homologs in Amino Acid Sequences Using Network BLAST SearchesIstván Ladunga · 2009 · Current Protocols in Bioinformatics
- 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 accuracyRamanathan NATESH, K. Manikandan, P. Bhanumoorthy, M. A. Viswamitra, S. Ramakumar · 2002 · Acta Crystallographica Section D Biological Crystallography
- Tyr212: A Key Residue Involved in Strand Discrimination by the DNA Mismatch Repair Endonuclease MutHPeter Friedhoff, Evangelos Thomas, Alfred M. Pingoud · 2002 · Journal of Molecular Biology
- SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seongwoong Cho, Jong Bhak, Jong‐Soon Choi · 2008 · BMC Bioinformatics
- Sensory Ion Channel Candidates Inform on the Clinical Course of Pancreatic Cancer and Present Potential Targets for Repurposing of FDA-Approved AgentsWenjie 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
- Anti-inflammatory, antioxidant and in silico studies of Buddleja salviifolia (L). Lam leaf constituentsSrinivasa C. Pendota, Ashwell Rungano Ndhlala, Adeyemi Oladapo Aremu, M.A. Aderogba, J. Van Staden · 2014 · South African Journal of Botany
- Clustering HLA Class I Superfamilies Using Structural Interaction PatternsSumitro Harjanto, Lisa F. P. Ng, Joo Chuan Tong · 2014 · PLoS ONE
- Using the Tools and Resources of the RCSB Protein Data BankShuchismita Dutta, Helen Miriam Berman, Wolfgang F. Bluhm · 2007 · Current Protocols in Bioinformatics
- The rapid emergence of multiple sublineages of Omicron (B.1.1.529) variant: Dynamic profiling via molecular phylogenetics and mutational landscape studiesChiranjib Chakraborty, Manojit Bhattacharya, Ashish Ranjan Sharma, Kuldeep Dhama, Sang‐Soo Lee · 2022 · Journal of Infection and Public Health
- Structural Heterogeneity in Single Particle Imaging Using X-ray LasersThomas 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
- Introduction to CheminformaticsDavid Scott Wishart · 2016 · Current Protocols in Bioinformatics
- Using a residue clash map to functionally characterize protein recombination hybridsManish C. Saraf, Costas D. Maranas · 2003 · Protein Engineering Design and Selection
- Making Soup: Preparing and Validating Models of the Bacterial Cytoplasm for Molecular SimulationLeandro Oliveira Bortot, Zahedeh Bashardanesh, David van der Spoel · 2019 · Journal of Chemical Information and Modeling
- Modeling the Semantics of 3D Protein StructuresSudha Ram, Wei Wei · 2004 · Lecture notes in computer science
- Comparative in silico study of the differences in the structure and ligand interaction properties of three alpha-expansin proteins from Fragaria chiloensis fruitFelipe 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
- Estimation of the Number of Authentic Orphan Genes in Bacterial GenomesF. Satoshi · 2004 · DNA Research
- MAO: a Multiple Alignment Ontology for nucleic acid and protein sequencesJulie Thompson · 2005 · Nucleic Acids Research
- Application of InChI to curate, index, and query 3‐D structuresM.D. Prasanna, Jiřı́ Vondrášek, Alexander Wlodawer, Talapady N. Bhat · 2005 · Proteins Structure Function and Bioinformatics
- D ATABASES AND T OOLS FOR B ROWSING G ENOMESEwan Birney, Michele E. Clamp, Tim Hubbard · 2002 · Annual Review of Genomics and Human Genetics
- Protein Data Bank (PDB)Eric Martz · 2004 · Dictionary of Bioinformatics and Computational Biology
- SAHA-based novel HDAC inhibitor design by core hopping methodLanlan 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
- A computational pipeline for protein structure prediction and analysis at genome scaleManesh B. Shah, Sergei Passovets, Dongsup Kim, Kyle Ellrott, Li Wang, Inna Vokler, Philip F. LoCascio, Dong He Xu, Ying Xu · 2003 · Bioinformatics
- RPI-GGCN: Prediction of RNA-Protein Interaction Based on Interpretability Gated Graph Convolution Neural Network and Co-Regularized Variational AutoencodersYifei Wang, Pengju Ding, Congjing Wang, Shiyue He, Xin Gao, Bin Yu · 2024 · IEEE Transactions on Neural Networks and Learning Systems
- Expression, characterization and molecular docking of the assimilatory NaDH-nitrite reductase from Acidovorax wautersii QZ-4Qiaozhi Song, Binbin Wang, Fangkun Zhao, Ye Han, Zhijiang Zhou · 2020 · Biochemical Engineering Journal
- Functional analysis and structure determination of alkaline protease from Aspergillus flavusRabbani Syed, Roja Rani, Sabeena, Tariq Masoodi, Gowher Shafi, Khalid Saad Alharbi · 2012 · Bioinformation
- Biological Units and their Effect upon the Properties and Prediction of Protein–Protein InteractionsEmily Jefferson, Thomas P. Walsh, Geoffrey J. Barton · 2006 · Journal of Molecular Biology
- Synthesis and molecular docking of new roflumilast analogues as preferential-selective potent PDE-4B inhibitors with improved pharmacokinetic profileBahia Abbas Moussa, Asmaa A. El‐Zaher, Mohamed Kandeel El-Ashrey, Marwa A. Fouad · 2018 · European Journal of Medicinal Chemistry
- NMR refinement and peptide folding using the GROMACS softwareAnna Sinelnikova, David van der Spoel · 2021 · Journal of Biomolecular NMR
- Reproducibility of single protein explosions induced by X-ray lasersChristofer Östlin, Nicuşor Tı̂mneanu, H. Olof Jönsson, Tomas Ekeberg, Andrew V. Martin, Carl Caleman · 2018 · Physical Chemistry Chemical Physics
- Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragmentsManikandan Karuppasamy, Debnath Pal, Suryanarayanarao Ramakumar, Nathan E. Brener, Sitharama S. Iyengar, Guna S. Seetharaman · 2008 · Genome biology
- Functional Analysis of Peptidyl-prolyl cis-trans Isomerase from Aspergillus flavusSaleem Ahmad, Sen Wang, Weizhong Wu, Kunlong Yang, Yanfeng Zhang, Elisabeth Tumukunde, Shihua Wang, Yu Wang · 2019 · International Journal of Molecular Sciences
- Instituto Oswaldo CruzAnnes Dias, Ulysses de Nonohay, Guerra Blessmann · 2012 · Arquivos rio-grandenses de medicina
- Evolution of different oligomeric glycyl‐tRNA synthetasesSu‐Ni Tang, Jing‐Fei Huang · 2005 · FEBS Letters
- eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experimentsG. L. Moore · 2002 · Nucleic Acids Research
- The Protein Data Bank: A Case Study in Management of Community DataHelen Miriam Berman, Philip E. Bourne, John Westbrook · 2004 · Current Proteomics
- Ontological Foundation for Protein Data ModelsAmandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2005 · Lecture notes in computer science
- Active site analysis of cis-epoxysuccinate hydrolase from Nocardia tartaricans using homology modeling and site-directed mutagenesisVinayagam Vasu, Kumaresan Jayaraman, Ganesh babu Manoharan, Sankaranarayanan Meenakshisundaram · 2011 · Applied Microbiology and Biotechnology
- Analysis and prediction of human acetylation using a cascade classifier based on support vector machineNing Qiao, Miao Yu, Jinchao Ji, Zhiqiang Ma, Xiaowei Zhao · 2019 · BMC Bioinformatics
- Demonstration of Ubiquitin Thiolester Formation of UBE2Q2 (UBCi), a Novel Ubiquitin-Conjugating Enzyme with Implantation Site-Specific Expression1Michael 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
- CADB: Conformation Angles DataBase of proteinsS. S. Sheik · 2003 · Nucleic Acids Research
- Crystal structures of an archaeal thymidylate kinase from Sulfolobus tokodaii provide insights into the role of a conserved active site Arginine residueAnsuman Biswas, Arpit Shukla, Ramachandran Vijayan, Jeyaraman Jeyakanthan, K. Sekar · 2016 · Journal of Structural Biology
- New putative therapeutic targets against Serratia marcescens using reverse vaccinology and subtractive genomicsLígia 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
- Identification of a Novel Nucleocytoplasmic Shuttling RNA Helicase of TrypanosomesAlexandre 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
- Chemical compound navigator: A web‐based chem‐BLAST, chemical taxonomy‐based search engine for browsing compoundsM.D. Prasanna, Jiřı́ Vondrášek, Alexander Wlodawer, Henry Rodriguez, Talapady N. Bhat · 2006 · Proteins Structure Function and Bioinformatics
- Searching and Mapping of B-Cell Epitopes in Bcipep DatabaseSudipto Saha, Gajendra P. S. Raghava · 2007 · Methods in molecular biology
- Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entitiesPaul Shafer, Timothy Isganitis, Golan Yona · 2006 · BMC Bioinformatics
- The evolution of structural databasesOliviero Carugo, Sándor Pongor · 2002 · Trends in biotechnology
- Homology modeling of Ferredoxin-nitrite reductase from Arabidopsis thalianaKarim Kherraz, Khaled Kherraz, Abdelkrim Kameli · 2011 · Bioinformation
- Mechanistic insights into the anti-depressant effect of emodin: an integrated systems pharmacology study and experimental validationPeng Hui Zeng, Xiaoming Wang, Chao‐Yuan Ye, Hong-Fei Su, Ying‐Yan Fang, Teng Zhang, Qing Tian · 2021 · Aging
- Scaling the walls of discovery: using semantic metadata for integrative problem solvingMaurice Manning, A. Aggarwal, Kevin Gao, Greg Tucker‐Kellogg · 2009 · Briefings in Bioinformatics
- Deciphering the three-domain architecture in schlafens and the structures and roles of human schlafen12 and serpinB12 in transcriptional regulationJiaxing Chen, Leslie A. Kuhn · 2019 · Journal of Molecular Graphics and Modelling
- PRECISE: a Database of Predicted and Consensus Interaction Sites in EnzymesShu‐Hsien Sheu · 2004 · Nucleic Acids Research
- Hibiscus sabdariffa L. polyphenolic‐rich extract promotes muscle glucose uptake and inhibits intestinal glucose absorption with concomitant amelioration of Fe 2+ ‐induced hepatic oxidative injuryAlmahi I. Mohamed, Veronica F. Salau, Ochuko Lucky Erukainure, Md. Shahidul Islam · 2022 · Journal of Food Biochemistry
- Systems Biology Resources Arising from the Human Metabolome ProjectDavid Scott Wishart · 2012 · Springer eBooks
- Topological analysis of DPY 19L3, a human C‐mannosyltransferaseYuki Niwa, Yoshihiko Nakano, Takehiro Suzuki, Mizuo Yamagishi, Kei Otani, Naoshi Dohmae, Siro Simizu · 2018 · FEBS Journal
- Databases for Protein–Protein InteractionsNatsu Nakajima, Tatsuya Akutsu, Ryuichiro Nakato · 2021 · Methods in molecular biology
- eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarityGaoqi He, Yiping Amy Song, Wenhao Wei, Xia Wang, Xingjian Lu, Honglin Li · 2019 · Journal of Computational Chemistry
- Integrative approach for computationally inferring protein domain interactionsSee-Kiong Ng, Zhuo Zhang, Soon-Heng Tan · 2003 · ACM Symposium on Applied Computing
- Advances in Protein Ontology ProjectAmandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2006 · Proceedings - IEEE Symposium on Computer-Based Medical Systems
- Mechanisms of main components in Curcuma longa L. on hepatic fibrosis based on network pharmacology and molecular docking: A reviewQiang Han, Jiahui Zhu, Peng Zhang · 2023 · Medicine
- A Comparative Analysis of Cockroach and Mosquito, Octopamine Receptor Homologues Produced Using Chimera, Swiss-Model, and AlphaFold Molecular Modeling ToolsSteve D. Kamguia, Eric N. Njabon, Issofa Patouossa, Alphonse Emadak, Neville Y. Forlemu · 2025 · ACS Omega
- Recent SARS-CoV-2 evolution trajectories indicate the emergence of Omicron's several subvariants and the current rise of KP.3.1.1 and XECChiranjib Chakraborty, Manojit Bhattacharya, Ali S. Abdelhameed · 2025 · Virology
- Data Mining of Macromolecular StructuresBart van Beusekom, Anastassis Perrakis A, Robbie P. Joosten · 2016 · Methods in molecular biology
- A simple and effective method based on enzyme-ligand complex for affinity analysis of lipase inhibitor from Schisandra chinensis (Turcz.) BaillShanshan Tang, Shuo Liu, Yunxiao Wang, Dongyu Gu, Jing Tian, Yi Yang · 2022 · Journal of Chromatography B
- Comparative Protein Structure PredictionMarc A. Martı́-Renom, Bozidar Jerkovic, Andrej Šali · 2002 · Current Protocols in Protein Science
- A comparison of SCOP and CATH with respect to domain–domain interactionsEmily Jefferson, Thomas P. Walsh, Geoffrey J. Barton · 2007 · Proteins Structure Function and Bioinformatics
- Ontology-based knowledge representation for protein dataAmandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang, Baldev S. Sidhu · 2005 · IEEE International Conference on Industrial Informatics (INDIN)
- Repurposing of renin inhibitors as SARS-COV-2 main protease inhibitors: A computational studyRana H. Refaey, Mohamed Kandeel El-Ashrey, Yassin Mohammed Nissan · 2020 · Virology
- Binding of Pollutants to Biomolecules: A Simulation StudyAhmet Yıldırım, Jin Zhang, Sergio Manzetti, David van der Spoel · 2016 · Chemical Research in Toxicology
- Modeling Protein Structure from its SequenceMarc 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
- Deconvolution of Targeted Protein–Protein Interaction MapsAlexey Stukalov, Giulio Superti‐Furga, Jacques Colinge · 2012 · Journal of Proteome Research
- Hit detection in serial femtosecond crystallography using X-ray spectroscopy of plasma emissionH. Olof Jönsson, Carl Caleman, Jakob Andreasson, Nicuşor Tı̂mneanu · 2017 · IUCrJ
- IN SILICO BINDING INTERACTION STUDY OF MEFENAMIC ACID AND PIROXICAM ON HUMAN ALBUMINJoshita Djajadisastra, Hamka Decky Purnama, Arry Yanuar · 2017 · International Journal of Applied Pharmaceutics
- 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
- Detection of Underrepresented Biological Sequences Using Class-Conditional Distribution ModelsSlobodan Vučetić, Dragoljub Pokrajac, Hongbo Michael Xie, Zoran Obradovic A · 2003 · SIAM International Conference on Data Mining
- The Structure Superposition DatabaseRanyee A. Chiang · 2003 · Nucleic Acids Research
- NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0W. L. A. K. Chiu · 2003 · Nucleic Acids Research
- An Ontology for Protein Data ModelsAmandeep Singh Sidhu, Tharam Singh Dillon, Elizabeth J. Chang · 2005 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
- Identifying functionally important cis ‐peptide containing segments in proteins and their utility in molecular function annotationSreetama Das, Suryanarayanarao Ramakumar, Debnath Pal · 2014 · FEBS Journal
- Quality assurance for the query and distribution systems of the RCSB Protein Data BankWolfgang 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
- Databases and QSAR for Cancer ResearchAdeel Malik, Hemajit Singh, Munazah Andrabi, Syed Akhtar Husain, Shandar Ahmad · 2006 · Cancer Informatics
- Genomic and Proteomic Databases and Applications: A Challenge for Database TechnologyShamkant B. Navathe, Upen Patil · 2004 · Lecture notes in computer science
- Methods and protocols for the assessment of protein allergenicity and cross-reactivityJoo Chuan Tong · 2008 · Frontiers in bioscience
- ANTXR1 blockade enhances cardiac function in preclinical models of heart failureNicola 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
- 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 simulationMeng Yu, Zhongqi Shen, Shaozhi Zhang, Yang Zhang, Hongwei Zhao, Longfei Zhang · 2024 · Heliyon
- Rationale design and synthesis of new roflumilast analogues as preferential selective and potent PDE-4B inhibitorsAhmed M. Moussa, Heba Abdelrasheed Allam, Mohamed Kandeel El-Ashrey, Marwa A. Fouad, Ahmed Ali Al-Karmalawy · 2024 · Bioorganic Chemistry
- Role of Bioinformatics in Drug Design and DiscoveryPinkal H. Patel, A. N. JHA, G. S. Chakraborthy · 2023 · Interdisciplinary biotechnological advances