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IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih
2013 Nucleic Acids Research  

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We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures.  ...  in the search query.  ...  ACKNOWLEDGEMENTS The authors gratefully acknowledge the Genome Computing Centre of the Malaysia Genome Institute for providing the computational infrastructure.  ... 
doi:10.1093/nar/gkt431 pmid:23716645 pmcid:PMC3692123 fatcat:b62lorcwm5fbpffpl2v6prjth4
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Nurul Nadzirin, Peter Willett, Peter J. Artymiuk, Mohd Firdaus-Raih. "IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank." Nucleic Acids Research 41.W1 (2013) W432-W440

GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA

Nur Syatila Ab Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih
2022 Nucleic Acids Research  

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https://web.archive.org/web/20220608205035/https://watermark.silverchair.com/gkac402.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAtMwggLPBgkqhkiG9w0BBwagggLAMIICvAIBADCCArUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMcGhY78dG0CxcecaLAgEQgIIChjLiCcTLKbFJ4bXaHLgSi2LGeRL-IaBvNrE_khfWapDE8XdwOtcpS5HPoz7ZOfHYloPTcNIugNQRoPM03CPnERyXSOYcOF0HBFelFMw0JM1WDkWgiwWWudCe0sWST8WMMa4_teaHsa8-pqBL9ET5J8sQcYUmsMOR83OKv53HrIJZohkJUHlraM9xuSqnuvVqCYrPmYhnWHMSp9OkyIzUdNbxBJ1_p_MusAcYnbRyzjywKftx-TRNsIEdX-wXBKdxb41q6Wv7d41nJYnM_YpGdfIQRLAVEH5CsH9esnGxj9CF3ihA3f2tF5u4GnYtZ4r0I5aD0s3qVCJqDjLKaM3Lc__1BbzbnQ1n2ZV8qR4E8qx8snVro0bZtIAi5dOJXt3JI0V7cVd0NBgStfikVXN0U1Z9FjHzAK2TtXx1Jcc_7hb1T7r9r17-SChM2SIwYy_PqF5JOk-v3nCZNgNhre6tJOqDUkvv_0FDhJF4Jjf_pIl1l8_oMF9kFsAMHKvtBmZeFzWep6StToDK-8T47SJdpWwNwUhRMkC6NMHW9sbZaRMxFYfTIrCJFH6IWfqugwh-DpT3tzXIMWTi12NS4XQLyDY7Y4Z75L4dAFf5mn-x1y8JIwGBz54YC4-6yiOG7ItotG7CTfZ3XHkAN_WaMGSODsN-MQTZ1Qx6TK1Va_WCOZIoqKjo8UoNgXkIImEB2tiYDtufXOtkEjRvQSQ619O-wEboMLW2R6ot53IAtJhEKa82WDafE6K_YB2n-794pd8XWSkNINZBhTTTg3ieU5_DGs1EgGA0vOu-mGgQ5HJ6HLiOr_FzaIawRR5Wt0sKsumiMYKoXkeb3POiMEwoEc8WlRcivNrpZzw

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The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii  ...  available in the Protein Data Bank (PDB).  ...  Joel Sussman (Weizmann Institute of Science) for his feedback and recommendations on the webserver during its development.  ... 
doi:10.1093/nar/gkac402 pmid:35639505 pmcid:PMC9252811 fatcat:x7ex6w75ajavlpt4xnxig5v2kq
DOAJ
Citation

Nur Syatila Ab Ghani, Reeki Emrizal, Sabrina Mohamed Moffit, Hazrina Yusof Hamdani, Effirul Ikhwan Ramlan, Mohd Firdaus-Raih. "GrAfSS: a webserver for substructure similarity searching and comparisons in the structures of proteins and RNA." Nucleic Acids Research 50.W1 (2022)