Publications by authors named "Thomas Madej"

Claim this Profile
I
IgStrand: A universal residue numbering scheme for the immunoglobulin-fold (Ig-fold) to study Ig-proteomes and Ig-interactomes.
Caesar Tawfeeq, Jiyao Wang, Umesh Khaniya, Thomas Madej, James Song

PLoS Comput Biol· April 2025

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
U
Unusual traits shape the architecture of the Ig ancestor molecule.
Alejandro Urdiciain, Thomas Madej, Jiyao Wang, James Song, Elena Erausquin

Commun Biol· March 2025

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
T
Towards a structural and functional analysis of the immunoglobulin-fold proteome.
Caesar Tawfeeq, James Song, Umesh Khaniya, Thomas Madej, Jiyao Wang

Adv Protein Chem Struct Biol· January 2024

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
I
iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode.
Jiyao Wang, Philippe Youkharibache, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Thomas Madej

Front Mol Biosci· February 2022

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
B
Biological Assembly Comparison with VAST.
Thomas Madej, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Stephen H Bryant

Methods Mol Biol· January 2021

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
I
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures.
Jiyao Wang, Philippe Youkharibache, Dachuan Zhang, Christopher J Lanczycki, Renata C Geer, Thomas Madej

Bioinformatics· January 2020

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
MMDB and VAST+: tracking structural similarities between macromolecular complexes.
Thomas Madej, Christopher J Lanczycki, Dachuan Zhang, Paul A Thiessen, Renata C Geer

Nucleic Acids Res· January 2014

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
E
Evolutionary, physicochemical, and functional mechanisms of protein homooligomerization.
Hafumi Nishi, Kosuke Hashimoto, Thomas Madej, Anna R Panchenko

Prog Mol Biol Transl Sci· December 2013

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
H
Homology inference of protein-protein interactions via conserved binding sites.
Manoj Tyagi, Ratna R Thangudu, Dachuan Zhang, Stephen H Bryant, Thomas Madej

PLoS One· June 2012

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
I
IBIS (Inferred Biomolecular Interaction Server) reports, predicts and integrates multiple types of conserved interactions for proteins.
Benjamin A Shoemaker, Dachuan Zhang, Manoj Tyagi, Ratna R Thangudu, Jessica H Fong, Thomas Madej

Nucleic Acids Res· January 2012

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
MMDB: 3D structures and macromolecular interactions.
Thomas Madej, Kenneth J Addess, Jessica H Fong, Lewis Y Geer, Renata C Geer

Nucleic Acids Res· January 2012

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
Modulating protein-protein interactions with small molecules: the importance of binding hotspots.
Ratna Rajesh Thangudu, Stephen H Bryant, Anna R Panchenko, Thomas Madej

J Mol Biol· January 2012

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
K
Knowledge-based annotation of small molecule binding sites in proteins.
Ratna R Thangudu, Manoj Tyagi, Benjamin A Shoemaker, Stephen H Bryant, Anna R Panchenko, Thomas Madej

BMC Bioinformatics· July 2010

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
F
Functional states of homooligomers: insights from the evolution of glycosyltransferases.
Kosuke Hashimoto, Thomas Madej, Stephen H Bryant, Anna R Panchenko

J Mol Biol· May 2010

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
I
Inferred Biomolecular Interaction Server--a web server to analyze and predict protein interacting partners and binding sites.
Benjamin A Shoemaker, Dachuan Zhang, Ratna R Thangudu, Manoj Tyagi, Jessica H Fong, Thomas Madej

Nucleic Acids Res· January 2010

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.
Shaolei Teng, Thomas Madej, Anna Panchenko, Emil Alexov

Biophys J· March 2009

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
P
Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins.
Thomas Madej, Anna R Panchenko, Jie Chen, Stephen H Bryant

BMC Struct Biol· April 2007

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
L
Long-term trends in evolution of indels in protein sequences.
Yuri Wolf, Thomas Madej, Vladimir Babenko, Benjamin Shoemaker, Anna R Panchenko

BMC Evol Biol· February 2007

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
MMDB: annotating protein sequences with Entrez's 3D-structure database.
Yanli Wang, Kenneth J Addess, Jie Chen, Lewis Y Geer, Jane He, Thomas Madej

Nucleic Acids Res· January 2007

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
E
Evolutionary plasticity of protein families: coupling between sequence and structure variation.
Anna R Panchenko, Yuri I Wolf, Larisa A Panchenko, Thomas Madej

Proteins· November 2005

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
S
Structural similarity of loops in protein families: toward the understanding of protein evolution.
Anna R Panchenko, Thomas Madej

BMC Evol Biol· February 2005

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
A
Analysis of protein homology by assessing the (dis)similarity in protein loop regions.
Anna R Panchenko, Thomas Madej

Proteins· November 2004

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
C
CDD: a curated Entrez database of conserved domain alignments.
Aron Marchler-Bauer, John B Anderson, Carol DeWeese-Scott, Natalie D Fedorova, Lewis Y Geer, Thomas Madej

Nucleic Acids Res· January 2003

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
MMDB: Entrez's 3D-structure database.
Jie Chen, John B Anderson, Carol DeWeese-Scott, Natalie D Fedorova, Lewis Y Geer, Thomas Madej

Nucleic Acids Res· January 2003

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis
M
MMDB: Entrez's 3D-structure database.
Yanli Wang, John B Anderson, Jie Chen, Lewis Y Geer, Siqian He, Thomas Madej

Nucleic Acids Res· January 2002

Social Media Activity not collected for this article yet.

Sign Up to Request Social Media Analysis