Thomas Madej

13 papers Journal 12
YearRankTypeTitle / Venue / Authors
2025 J jnl
IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.
PLoS Comput. Biol.
Caesar Tawfeeq, Jiyao Wang, Umesh Khaniya, Thomas Madej, James Song, Ravinder Abrol, Philippe Youkharibache
2020 J jnl
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures.
Bioinform.
Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J. Lanczycki, Renata C. Geer, Thomas Madej, Lon Phan, Minghong Ward, Shennan Lu, Gabriele H. Marchler, Yanli Wang, Stephen H. Bryant, Lewis Y. Geer, Aron Marchler-Bauer
2014 J jnl
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Nucleic Acids Res.
Thomas Madej, Christopher J. Lanczycki, Dachuan Zhang, Paul A. Thiessen, Renata C. Geer, Aron Marchler-Bauer, Stephen H. Bryant
2012 J jnl
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.
Nucleic Acids Res.
Benjamin A. Shoemaker, Dachuan Zhang, Manoj Tyagi, Ratna R. Thangudu, Jessica H. Fong, Aron Marchler-Bauer, Stephen H. Bryant, Thomas Madej, Anna R. Panchenko
2012 J jnl
MMDB: 3D structures and macromolecular interactions.
Nucleic Acids Res.
Thomas Madej, Kenneth J. Addess, Jessica H. Fong, Lewis Y. Geer, Renata C. Geer, Christopher J. Lanczycki, Chunlei Liu, Shennan Lu, Aron Marchler-Bauer, Anna R. Panchenko, Jie Chen, Paul A. Thiessen, Yanli Wang, Dachuan Zhang, Stephen H. Bryant
2010 J jnl
Knowledge-based annotation of small molecule binding sites in proteins.
BMC Bioinform.
Ratna R. Thangudu, Manoj Tyagi, Benjamin A. Shoemaker, Stephen H. Bryant, Anna R. Panchenko, Thomas Madej
2007 J jnl
MMDB: annotating protein sequences with Entrez's 3D-structure database.
Nucleic Acids Res.
Yanli Wang, Kenneth J. Addess, Jie Chen, Lewis Y. Geer, Jane He, Siqian He, Shennan Lu, Thomas Madej, Aron Marchler-Bauer, Paul A. Thiessen, Naigong Zhang, Stephen H. Bryant
2003 J jnl
CDD: a curated Entrez database of conserved domain alignments.
Nucleic Acids Res.
Aron Marchler-Bauer, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Anna R. Panchenko, Bachoti S. Rao, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2003 J jnl
MMDB: Entrez's 3D-structure database.
Nucleic Acids Res.
Jie Chen, John B. Anderson, Carol DeWeese-Scott, Natalie D. Fedorova, Lewis Y. Geer, Siqian He, David I. Hurwitz, John D. Jackson, Aviva R. Jacobs, Christopher J. Lanczycki, Cynthia A. Liebert, Chunlei Liu, Thomas Madej, Aron Marchler-Bauer, Gabriele H. Marchler, Raja Mazumder, Anastasia N. Nikolskaya, Bachoti S. Rao, Anna R. Panchenko, Benjamin A. Shoemaker, Vahan Simonyan, James S. Song, Paul A. Thiessen, Sona Vasudevan, Yanli Wang, Roxanne A. Yamashita, Jodie J. Yin, Stephen H. Bryant
2002 J jnl
MMDB: Entrez's 3D-structure database.
Nucleic Acids Res.
Yanli Wang, John B. Anderson, Jie Chen, Lewis Y. Geer, Siqian He, David I. Hurwitz, Cynthia A. Liebert, Thomas Madej, Gabriele H. Marchler, Aron Marchler-Bauer, Anna R. Panchenko, Benjamin A. Shoemaker, James S. Song, Paul A. Thiessen, Roxanne A. Yamashita, Stephen H. Bryant
2000 J jnl
MMDB: 3D structure data in Entrez.
Nucleic Acids Res.
Yanli Wang, Kenneth J. Addess, Lewis Y. Geer, Thomas Madej, Aron Marchler-Bauer, Diane Zimmerman, Stephen H. Bryant
1999 J jnl
MMDB: Entrez's 3D structure database.
Nucleic Acids Res.
Aron Marchler-Bauer, Kenneth J. Addess, Colombe Chappey, Lewis Y. Geer, Thomas Madej, Yo Matsuo, Yanli Wang, Stephen H. Bryant
1989 — —
Topics in combinatorics and combinatorial algorithms
Thomas Madej