Search Results - "Oldfield, Thomas J."

Validation of Structures in the Protein Data Bank by Gore, Swanand, Sanz García, Eduardo, Hendrickx, Pieter M.S., Gutmanas, Aleksandras, Westbrook, John D., Yang, Huanwang, Feng, Zukang, Baskaran, Kumaran, Berrisford, John M., Hudson, Brian P., Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Mading, Steve, Mak, Lora, Mukhopadhyay, Abhik, Oldfield, Thomas J., Patwardhan, Ardan, Peisach, Ezra, Sahni, Gaurav, Sekharan, Monica R., Sen, Sanchayita, Shao, Chenghua, Smart, Oliver S., Ulrich, Eldon L., Yamashita, Reiko, Quesada, Martha, Young, Jasmine Y., Nakamura, Haruki, Markley, John L., Berman, Helen M., Burley, Stephen K., Velankar, Sameer, Kleywegt, Gerard J.

“…The Worldwide PDB recently launched a deposition, biocuration, and validation tool: OneDep. At various stages of OneDep data processing, validation reports for…”
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SIFTS: Structure Integration with Function, Taxonomy and Sequences resource by Velankar, Sameer, Dana, José M, Jacobsen, Julius, van Ginkel, Glen, Gane, Paul J, Luo, Jie, Oldfield, Thomas J, O'Donovan, Claire, Martin, Maria-Jesus, Kleywegt, Gerard J

“…The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank…”
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OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive by Young, Jasmine Y., Westbrook, John D., Feng, Zukang, Sala, Raul, Peisach, Ezra, Oldfield, Thomas J., Sen, Sanchayita, Gutmanas, Aleksandras, Armstrong, David R., Berrisford, John M., Chen, Li, Chen, Minyu, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M.S., Hudson, Brian P., Igarashi, Reiko, Ikegawa, Yasuyo, Kobayashi, Naohiro, Lawson, Catherine L., Liang, Yuhe, Mading, Steve, Mak, Lora, Mir, M. Saqib, Mukhopadhyay, Abhik, Patwardhan, Ardan, Persikova, Irina, Rinaldi, Luana, Sanz-Garcia, Eduardo, Sekharan, Monica R., Shao, Chenghua, Swaminathan, G. Jawahar, Tan, Lihua, Ulrich, Eldon L., van Ginkel, Glen, Yamashita, Reiko, Yang, Huanwang, Zhuravleva, Marina A., Quesada, Martha, Kleywegt, Gerard J., Berman, Helen M., Markley, John L., Nakamura, Haruki, Velankar, Sameer, Burley, Stephen K.

“…OneDep, a unified system for deposition, biocuration, and validation of experimentally determined structures of biological macromolecules to the PDB archive,…”
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PDBe: Protein Data Bank in Europe by Gutmanas, Aleksandras, Alhroub, Younes, Battle, Gary M, Berrisford, John M, Bochet, Estelle, Conroy, Matthew J, Dana, Jose M, Fernandez Montecelo, Manuel A, van Ginkel, Glen, Gore, Swanand P, Haslam, Pauline, Hatherley, Rowan, Hendrickx, Pieter M S, Hirshberg, Miriam, Lagerstedt, Ingvar, Mir, Saqib, Mukhopadhyay, Abhik, Oldfield, Thomas J, Patwardhan, Ardan, Rinaldi, Luana, Sahni, Gaurav, Sanz-García, Eduardo, Sen, Sanchayita, Slowley, Robert A, Velankar, Sameer, Wainwright, Michael E, Kleywegt, Gerard J

“…The Protein Data Bank in Europe (pdbe.org) is a founding member of the Worldwide PDB consortium (wwPDB; wwpdb.org) and as such is actively engaged in the…”
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The role of structural bioinformatics resources in the era of integrative structural biology by Gutmanas, Aleksandras, Oldfield, Thomas J., Patwardhan, Ardan, Sen, Sanchayita, Velankar, Sameer, Kleywegt, Gerard J.

“…The history and the current state of the PDB and EMDB archives is briefly described, as well as some of the challenges that they face. It seems natural that…”
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Automated tracing of electron-density maps of proteins by Oldfield, Thomas J.

“…The tracing of experimental electron maps in the field of protein crystallography is not a rate‐limiting step for structure elucidation, but does represent the…”
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A Java applet for multiple linked visualization of protein structure and sequence by Oldfield, Thomas J

“…The amount of biological data available from experimental techniques is huge, and rapidly expanding. The ability to make sense of this vast amount of data…”
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High-resolution crystallographic map interpretation by Oldfield, Thomas J.

“…This article describes a method for rapid interpretation of high‐resolution crystallographic electron‐density maps. The implemented algorithm searches for…”
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PDBe: improved accessibility of macromolecular structure data from PDB and EMDB by Velankar, Sameer, van Ginkel, Glen, Alhroub, Younes, Battle, Gary M, Berrisford, John M, Conroy, Matthew J, Dana, Jose M, Gore, Swanand P, Gutmanas, Aleksandras, Haslam, Pauline, Hendrickx, Pieter M S, Lagerstedt, Ingvar, Mir, Saqib, Fernandez Montecelo, Manuel A, Mukhopadhyay, Abhik, Oldfield, Thomas J, Patwardhan, Ardan, Sanz-García, Eduardo, Sen, Sanchayita, Slowley, Robert A, Wainwright, Michael E, Deshpande, Mandar S, Iudin, Andrii, Sahni, Gaurav, Salavert Torres, Jose, Hirshberg, Miriam, Mak, Lora, Nadzirin, Nurul, Armstrong, David R, Clark, Alice R, Smart, Oliver S, Korir, Paul K, Kleywegt, Gerard J

“…The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches,…”
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Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data by Young, Jasmine Y, Westbrook, John D, Feng, Zukang, Peisach, Ezra, Persikova, Irina, Sala, Raul, Sen, Sanchayita, Berrisford, John M, Swaminathan, G Jawahar, Oldfield, Thomas J, Gutmanas, Aleksandras, Igarashi, Reiko, Armstrong, David R, Baskaran, Kumaran, Chen, Li, Chen, Minyu, Clark, Alice R, Di Costanzo, Luigi, Dimitropoulos, Dimitris, Gao, Guanghua, Ghosh, Sutapa, Gore, Swanand, Guranovic, Vladimir, Hendrickx, Pieter M S, Hudson, Brian P, Ikegawa, Yasuyo, Kengaku, Yumiko, Lawson, Catherine L, Liang, Yuhe, Mak, Lora, Mukhopadhyay, Abhik, Narayanan, Buvaneswari, Nishiyama, Kayoko, Patwardhan, Ardan, Sahni, Gaurav, Sanz-García, Eduardo, Sato, Junko, Sekharan, Monica R, Shao, Chenghua, Smart, Oliver S, Tan, Lihua, van Ginkel, Glen, Yang, Huanwang, Zhuravleva, Marina A, Markley, John L, Nakamura, Haruki, Kurisu, Genji, Kleywegt, Gerard J, Velankar, Sameer, Berman, Helen M, Burley, Stephen K

“…Database URLhttps://www.wwpdb.org/…”
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A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent by Oldfield, Thomas J.

“…This paper describes the implementation of real‐space torsion‐angle refinement as a tool for model (re)building. The algorithmic details and parameterization…”
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SQUID: a program for the analysis and display of data from crystallography and molecular dynamics by Oldfield, T J

“…SQUID is a flexible computer program that allows the analysis and display of molecular coordinates from crystallography, NMR, and molecular dynamics. The…”
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Model structures and action of interleukin 1 and its antagonist by Oldfield, T J, Murray-Rust, P, Hubbard, R E

“…A comparison has been made between the homology and hydrophobicity profiles of six interleukin amino acid sequences and that of the human interleukin 1 beta…”
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