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[wwPDB] Announcement of mandatory mmCIF submission published in Acta Cryst D

A new publication in Acta Cryst D announces the mandatory submission of PDBx/mmCIF to the PDB for crystallographic depositions. (wwPDB news)

Theoretical models

... SYNTHASE L.M.MCDOWELL,B.POLIKS,D.R.STUDELSKA,R.D.O'CONNOR,D.D.BEUSEN, J.SCHAEFER DisplayDownload 1q0jROTATIONAL-ECHO ... PHOSPHATE SYNTHASE L.M.MCDOWELL,B.POLIKS,D.R.STUDELSKA,R.D.O'CONNOR,D.D.BEUSEN DisplayDownload 1q1xCORONAVIRUS MAIN PROTEINASE (3CLPRO) ...

Staff

... Osaka Univ.) - PRF branch office Kurisu, Genji, Ph.D. (Guest Researcher, Protein Research Foundation (PRF)) Isoyama, Masaharu ... (Protein Research Foundation (PRF)) - Kurisu, Genji, Ph.D. (Guest Researcher, Protein Research Foundation (PRF)) - Isoyama, ...

List of Publications

... sequence and structural information in protein functional mapping. Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H ... alignment package: sensitivity and selectivity in domain classification Standley, D.M., Toh, H., Nakamura, H. BMC Bioinformatics 8 ...

PDBj Mine 2: SQL Search

... Search for all entries containing polypeptide chains with both type D-form and L-form: - Search for all entries containing ... - Search for all entries with chain type [all no except polysaccharide(D)]: - Search for exptl/method, unit axes, unit angles, exptl ...

Cite Us / Terms and Conditions

... the Protein Data Bank. Chenghua Shao, Zukang Feng, John D Westbrook, Ezra Peisach, John Berrisford, Yasuyo Ikegawa, Genji ... : balancing sequence and structural information in protein functional mapping. Standley, D.M., Yamashita, R., Kinjo, A.R., Toh, H., ...

About PDBMLplus, PDBMLadd, and mmjson-plus

... _iso_Wilson_estimate, Rmerge_F_obs, auth_validate, d_resolution_high, d_resolution_low, number_all, number_obs, observed_criterion_sigma ... id reflns_shell_pdbmlplus Rmerge_I_obs, auth_validate, d_res_high, d_res_low, meanI_over_sigI_obs, number_measured_ ...

[wwPDB] CASP16 Call for Targets

... H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, ... Barradas-Bautista D, Cao Z, Chawla M, ...

Celebrating 10 Years of the wwPDB

... HF DeLuca (2004) Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 ... convened. J Trewhella, WA Hendrickson, M Sato, T Schwede, D Svergun, JA Tainer, J Westbrook, GJ Kleywegt, HM Berman. ...

[wwPDB] Paper Published on CryoEM Archiving and Validation Recommendations

... on cryoEM data archiving and validation Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, ... , Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey ...

[wwPDB] Preprint Published on CryoEM Archiving and Validation Recommendations

... on cryoEM data archiving and validation Gerard J. Kleywegt, Paul D. Adams, Sarah J. Butcher, Cathy Lawson, Alexis Rohou, ... , Scott M. Stagg, Zhe Wang, Rangana Warshamanage, John D. Westbrook, Martyn D. Winn, Jasmine Y. Young, Stephen K. Burley, Jeffrey ...

EDM viewer

... or (Fo-Fc) maps (amplitude = m*Fobs-D*Fcalc, phase = phicalc). m and D are weighting factors, varying with reflections and containing information ... Fobs that were deposited and Fcalc, phicalc, m and D obtained from the refined model. The extent of the map ...

Advanced search

... composed of L-amino acids - Polypeptide(D):polypeptide composed of D-amino acids - polydeoxyribonucleotide:DNA chain composed ... composed of ribonucleotid - polysaccharide(D):polysaccharide composed of D-monosaccharides - polysaccharide(L):polysaccharide ...

[wwPDB] Small Angle Scattering News

... T. E., Cowieson, N., Crossett, B., Duff, A. P., Franke, D., Gabel, F., Gillilan, R. E., Graewert, M., Grishaev, A., Guss, ... ., Rajkovic, I., Rocco, M., Rosenberg, D. J., Ryan, T. M., Seifert, S., Sekiguchi, H., Svergun, D., Teixeira, S., Thureau, A., Weiss, ...

[wwPDB] New Publication: PDBx/mmCIF Ecosystem

... mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology John D. Westbrook, Jasmine Y. Young, Chenghua Shao, Zukang ... , Vladimir Guranovic, Catherine L. Lawson, Brinda Vallat, Paul D. Adams, John M. Berrisford, Gerard Bricogne, Kay Diederichs, ...

[wwPDB] Obituary for John Westbrook

... of the International Union of Crystallography in Hyderabad, India John D. Westbrook Jr. (1957-2021), Research Professor at Rutgers University ... survived by his wife, Bonnie J. Wagner-Westbrook, Ed.D. and his devoted Mother-in-Law, Joan N. Wagner ...

[wwPDB] Celebrating 20 Years of the wwPDB

... process of PDBc joining the wwPDB has been submitted to Acta Cryst D (PDF, 3). PDBc has received training and support from the wwPDB ... Associate Member of the Worldwide Protein Data Bank (wwPDB) Partnership Acta Cryst. D, submitted (PDF) [ wwPDB News ]

ASH

... a structural perspective. Annu Rev Biochem 74, 867-900. [3]Standley,D.M., Toh, H. and Nakamura, H. (2004) Detecting local ... maximizing number of equivalent residues. Proteins 57, 381-91. [4]Standley,D.M., Toh, H. and Nakamura, H. (2005) GASH: an ...

[wwPDB] Future Planning: Entries with extended PDB and CCD ID codes will be distributed in PDBx/mmCIF format only

... 2.pdbx_DOI PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb WWPDB D_1xxxxxxxxx ? ?

FAQ

... PDBML: The representation of archival macromolecular structure data in XML Westbrook, J.D., Ito, N., Nakamura, H., Henrick, K., Berman, H.M. ... of Japan is written in uppercase? A) PDBj ( P rotein D ata B ank J apan) maintains a centralized PDB archive of ...

ASH

... a structural perspective. Annu Rev Biochem 74, 867-900. 3. Standley, D.M., Toh, H. and Nakamura, H. (2004) Detecting local structural ... maximizing number of equivalent residues. Proteins 57, 381-91. 4. Standley, D.M., Toh, H. and Nakamura, H. (2005) GASH: an ...

[wwPDB] Paper Published on NMR Restraint Validation

... , Ezra Peisach, Irina Persikova, Theresa A Ramelot, Monica Sekharan, James Tolchard, John D Westbrook, Benjamin Bardiaux, Charles Schwieters, Ardan Patwardhan, Sameer Velankar, Stephen K Burley ...

[wwPDB] Enhanced Validation of Small-Molecule Ligands and Carbohydrates

... -Molecule Ligands and Carbohydrates in the Protein Data Bank Zukang Feng, John D. Westbrook, Raul Sala, Oliver S. Smart, Gérard Bricogne, Masaaki Matsubara, Issaku Yamada ...

[wwPDB] Paper Published on NextGen Archive

... , Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Y. Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch ...

[wwPDB] Extended PDB IDs and PDB DOIs now available in PDBx/mmCIF files

... _2.pdbx_DOI PDB 1abc pdb_00001abc 10.2210/pdb1abc/pdb WWPDB D_1xxxxxxxxx ? ? wwPDB asks journals, users, and software developers to review code and ...

 

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