Works by Madej, Thomas

Results: 20

Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.

Published in:

Nucleic Acids Research, 2010, v. 38, p. D518, doi. 10.1093/nar/gkp842

By:

Shoemaker, Benjamin A.;
Dachuan Zhang;
Thangudu, Ratna R.;
Tyagi, Manoj;
Fong, Jessica H.;
Marchler-Bauer, Aron;
Bryant, Stephen H.;
Madej, Thomas;
Panchenko, Anna R.

Publication type:

Article

MMDB: annotating protein sequences with Entrez's 3D-structure database.

Published in:

Nucleic Acids Research, 2007, v. 35, p. d298, doi. 10.1093/nar/gkl952

By:

Wang, Yanli;
Addess, Kenneth J.;
Chen, Jie;
Geer, Lewis Y.;
He, Jane;
He, Siqian;
Lu, Shennan;
Madej, Thomas;
Marchler-Bauer, Aron;
Thiessen, Paul A.;
Zhang, Naigong;
Bryant, Stephen H.

Publication type:

Article

CDD: a curated Entrez database of conserved domain alignments.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 383, doi. 10.1093/nar/gkg087

By:

Marchler-Bauer, Aron;
Anderson, John B.;
DeWeese-Scott, Carol;
Fedorova, Natalie D.;
Geer, Lewis Y.;
He, Siqian;
Hurwitz, David I.;
Jackson, John D.;
Jacobs, Aviva R.;
Lanczycki, Christopher J.;
Liebert, Cynthia A.;
Liu, Chunlei;
Madej, Thomas;
Marchler, Gabriele H.;
Mazumder, Raja;
Nikolskaya, Anastasia N.;
Panchenko, Anna R.;
Rao, Bachoti S.;
Shoemaker, Benjamin A.;
Simonyan, Vahan

Publication type:

Article

MMDB: Entrez's 3D-structure database.

Published in:

Nucleic Acids Research, 2003, v. 31, n. 1, p. 474, doi. 10.1093/nar/gkg086

By:

Chen, Jie;
Anderson, John B.;
DeWeese-Scott, Carol;
Fedorova, Natalie D.;
Geer, Lewis Y.;
He, Siqian;
Hurwitz, David I.;
Jackson, John D.;
Jacobs, Aviva R.;
Lanczycki, Christopher J.;
Liebert, Cynthia A.;
Liu, Chunlei;
Madej, Thomas;
Marchler-Bauer, Aron;
Marchler, Gabriele H.;
Mazumder, Raja;
Nikolskaya, Anastasia N.;
Rao, Bachoti S.;
Panchenko, Anna R.;
Shoemaker, Benjamin A.

Publication type:

Article

MMDB: Entrez’s 3D-structure database.

Published in:

Nucleic Acids Research, 2002, v. 30, n. 1, p. 249, doi. 10.1093/nar/30.1.249

By:

Wang, Yanli;
Anderson, John B.;
Chen, Jie;
Geer, Lewis Y.;
He, Siqian;
Hurwitz, David I.;
Liebert, Cynthia A.;
Madej, Thomas;
Marchler, Gabriele H.;
Marchler-Bauer, Aron;
Panchenko, Anna R.;
Shoemaker, Benjamin A.;
Song, James S.;
Thiessen, Paul A.;
Yamashita, Roxanne A.;
Bryant, Stephen H.

Publication type:

Article

MMDB: 3D structure data in Entrez.

Published in:

Nucleic Acids Research, 2000, v. 28, n. 1, p. 243, doi. 10.1093/nar/28.1.243

By:

Wang, Yanli;
Addess, Kenneth J.;
Geer, Lewis;
Madej, Thomas;
Marchler-Bauer, Aron;
Zimmerman, Diane;
Bryant, Stephen H.

Publication type:

Article

MMDB: Entrez's 3D structure database.

Published in:

Nucleic Acids Research, 1999, v. 27, n. 1, p. 240

By:

Marchler‐Bauer, Aron;
Addess, Kenneth J.;
Chappey, Colombe;
Geer, Lewis;
Madej, Thomas;
Matsuo, Yo;
Wang, Yanli;
Bryant, Stephen H.

Publication type:

Article

Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins.

Published in:

BMC Structural Biology, 2007, v. 7, p. 23, doi. 10.1186/1472-6807-7-23

By:

Madej, Thomas;
Panchenko, Anna R.;
Chen, Jie;
Bryant, Stephen H.

Publication type:

Article

Threading a database of protein cores.

Published in:

Proteins, 1995, v. 23, n. 3, p. 356, doi. 10.1002/prot.340230309

By:

Madej, Thomas;
Gibrat, Jean-François;
Bryant, Stephen H.

Publication type:

Article

Unusual traits shape the architecture of the Ig ancestor molecule.

Published in:

Communications Biology, 2025, v. 8, n. 1, p. 1, doi. 10.1038/s42003-025-07830-5

By:

Urdiciain, Alejandro;
Madej, Thomas;
Wang, Jiyao;
Song, James;
Erausquin, Elena;
Youkharibache, Philippe;
López-Sagaseta, Jacinto

Publication type:

Article

Knowledge-based annotation of small moleculebinding sites in proteins.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 365, doi. 10.1186/1471-2105-11-365

By:

Thangudu, Ratna R.;
Tyagi, Manoj;
Shoemaker, Benjamin A.;
Bryant, Stephen H.;
Panchenko, Anna R.;
Madej, Thomas

Publication type:

Article

iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures.

Published in:

Bioinformatics, 2020, v. 36, n. 1, p. 131, doi. 10.1093/bioinformatics/btz502

By:

Wang, Jiyao;
Youkharibache, Philippe;
Zhang, Dachuan;
Lanczycki, Christopher J;
Geer, Renata C;
Madej, Thomas;
Phan, Lon;
Ward, Minghong;
Lu, Shennan;
Marchler, Gabriele H;
Wang, Yanli;
Bryant, Stephen H;
Geer, Lewis Y;
Marchler-Bauer, Aron

Publication type:

Article

MMDB and VAST+: tracking structural similarities between macromolecular complexes.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D297, doi. 10.1093/nar/gkt1208

By:

Madej, Thomas;
Lanczycki, Christopher J.;
Zhang, Dachuan;
Thiessen, Paul A.;
Geer, Renata C.;
Marchler-Bauer, Aron;
Bryant, Stephen H.

Publication type:

Article

IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.

Published in:

Nucleic Acids Research, 2012, p. D834, doi. 10.1093/nar/gkr997

By:

Shoemaker, Benjamin A.;
Zhang, Dachuan;
Tyagi, Manoj;
Thangudu, Ratna R.;
Fong, Jessica H.;
Marchler-Bauer, Aron;
Bryant, Stephen H.;
Madej, Thomas;
Panchenko, Anna R.

Publication type:

Article

MMDB: 3D structures and macromolecular interactions.

Published in:

Nucleic Acids Research, 2012, p. D461, doi. 10.1093/nar/gkr1162

By:

Madej, Thomas;
Addess, Kenneth J.;
Fong, Jessica H.;
Geer, Lewis Y.;
Geer, Renata C.;
Lanczycki, Christopher J.;
Liu, Chunlei;
Lu, Shennan;
Marchler-Bauer, Aron;
Panchenko, Anna R.;
Chen, Jie;
Thiessen, Paul A.;
Wang, Yanli;
Zhang, Dachuan;
Bryant, Stephen H.

Publication type:

Article

Homology Inference of Protein-Protein Interactions via Conserved Binding Sites.

Published in:

PLoS ONE, 2012, v. 7, n. 1, p. 1, doi. 10.1371/journal.pone.0028896

By:

Tyagi, Manoj;
Thangudu, Ratna R.;
Dachuan Zhang;
Bryant, Stephen H.;
Madej, Thomas;
Panchenko, Anna R.

Publication type:

Article

Evolutionary plasticity of protein families: Coupling between sequence and structure variation.

Published in:

Proteins, 2005, v. 61, n. 3, p. 535, doi. 10.1002/prot.20644

By:

Panchenko, Anna R.;
Wolf, Yuri I.;
Panchenko, Larisa A.;
Madej, Thomas

Publication type:

Article

Analysis of protein homology by assessing the (dis)similarity in protein loop regions.

Published in:

Proteins, 2004, v. 57, n. 3, p. 539, doi. 10.1002/prot.20237

By:

Panchenko, Anna R.;
Madej, Thomas

Publication type:

Article

Structural similarity of loops in protein families: toward the understanding of protein evolution.

Published in:

BMC Evolutionary Biology, 2005, v. 5, p. 10, doi. 10.1186/1471-2148-5-10

By:

Panchenko, Anna R;
Madej, Thomas

Publication type:

Article

IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.

Published in:

PLoS Computational Biology, 2025, v. 21, n. 4, p. 1, doi. 10.1371/journal.pcbi.1012813

By:

Tawfeeq, Caesar;
Wang, Jiyao;
Khaniya, Umesh;
Madej, Thomas;
Song, James;
Abrol, Ravinder;
Youkharibache, Philippe

Publication type:

Article