Adam Godzik

Publication Activity (10 Years)

Years Active: 1993-2021
Publications (10 Years): 13

Top Topics

Structural Features

Nuclear Magnetic Resonance

Protein Structure

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

Lukasz Jaroszewski, Mallika Iyer, Arghavan Alisoltani, Mayya Sedova, Adam Godzik
The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins. PLoS Comput. Biol. 17 (7) (2021)
Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence. Bioinform. 36 (15) (2020)
Zhanwen Li, Lukasz Jaroszewski, Mallika Iyer, Mayya Sedova, Adam Godzik
FATCAT 2.0: towards a better understanding of the structural diversity of proteins. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Mayya Sedova, Mallika Iyer, Zhanwen Li, Lukasz Jaroszewski, Kai W. Post, Thomas Hrabe, Eduard Porta-Pardo, Adam Godzik
Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets. Nucleic Acids Res. 47 (Database-Issue) (2019)
Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski, Adam Godzik
PDBFlex: exploring flexibility in protein structures. Nucleic Acids Res. 44 (Database-Issue) (2016)
Thomas Hrabe, Lukasz Jaroszewski, Adam Godzik
Revealing aperiodic aspects of solenoid proteins from sequence information. Bioinform. 32 (18) (2016)
Mayya Sedova, Lukasz Jaroszewski, Adam Godzik
Protael: protein data visualization library for the web. Bioinform. 32 (4) (2016)
Eduard Porta-Pardo, Thomas Hrabe, Adam Godzik
Cancer3D: understanding cancer mutations through protein structures. Nucleic Acids Res. 43 (Database-Issue) (2015)
Eduard Porta-Pardo, Adam Godzik
Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics. PLoS Comput. Biol. 11 (1) (2015)
Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik
domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinform. 31 (13) (2015)
Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski, Adam Godzik
PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source Code Biol. Medicine 10 (2015)
Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew P. Yeh, Adam Godzik, L. Aravind
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. BMC Bioinform. 16 (2015)
Eduard Porta-Pardo, Luz Garcia-Alonso, Thomas Hrabe, Joaquín Dopazo, Adam Godzik
A Pan-Cancer Catalogue of Cancer Driver Protein Interaction Interfaces. PLoS Comput. Biol. 11 (10) (2015)
Anna Sheydina, Ruth Y. Eberhardt, Daniel J. Rigden, Yuanyuan Chang, Zhanwen Li, Christian M. Zmasek, Herbert L. Axelrod, Adam Godzik
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. BMC Bioinform. 15 (2014)
Daniel J. Rigden, Ruth Y. Eberhardt, Harry J. Gilbert, Qingping Xu, Yuanyuan Chang, Adam Godzik
Structure- and context-based analysis of the GxGYxYP family reveals a new putative class of Glycoside Hydrolase. BMC Bioinform. 15 (2014)
Eduard Porta-Pardo, Adam Godzik
e-Driver: a novel method to identify protein regions driving cancer. Bioinform. 30 (21) (2014)
Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai W. Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik
bNAber: database of broadly neutralizing HIV antibodies. Nucleic Acids Res. 42 (Database-Issue) (2014)
Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik
domain assembly server. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking. Bioinform. 30 (5) (2014)
Lukasz Jaroszewski, Laszlo Koska, Mayya Sedova, Adam Godzik
PubServer: literature searches by homology. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Debanu Das, Alexey G. Murzin, Neil D. Rawlings, Robert D. Finn, Penelope Coggill, Alex Bateman, Adam Godzik, L. Aravind
Structure and computational analysis of a novel protein with metallopeptidase-like and circularly permuted winged-helix-turn-helix domains reveals a possible role in modified polysaccharide biosynthesis. BMC Bioinform. 15 (2014)
Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
POSA: a user-driven, interactive multiple protein structure alignment server. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Thomas Hrabe, Adam Godzik
ConSole: using modularity of contact maps to locate Solenoid domains in protein structures. BMC Bioinform. 15 (2014)
Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina
MORPH-PRO: a novel algorithm and web server for protein morphing. Algorithms Mol. Biol. 8 (2013)
William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik
LUD, a new protein domain associated with lactate utilization. BMC Bioinform. 14 (2013)
Penelope Coggill, Ruth Y. Eberhardt, Robert D. Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L. Axelrod, L. Aravind, Alexey G. Murzin, Alex Bateman
Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila. BMC Bioinform. 14 (2013)
Christian M. Zmasek, Adam Godzik
Feeling - Analysis of Multidomain Protein Evolution in Eukaryotic Genomes. PLoS Comput. Biol. 8 (11) (2012)
Natalie Castellana, Andrey Lushnikov, Piotr Rotkiewicz, Natasha Sefcovic, Pavel A. Pevzner, Adam Godzik, Kira Vyatkina
MORPH-PRO: A Novel Algorithm and Web Server for Protein Morphing. WABI (2012)
Ying Zhang, Olga Zagnitko, Irina Rodionova, Andrei Osterman, Adam Godzik
The FGGY Carbohydrate Kinase Family: Insights into the Evolution of Functional Specificities. PLoS Comput. Biol. 7 (12) (2011)
Kyle Ellrott, Christian M. Zmasek, Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Adam Godzik, John C. Wooley
TOPSAN: a dynamic web database for structural genomics. Nucleic Acids Res. 39 (Database-Issue) (2011)
Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, Adam Godzik
FFAS server: novel features and applications. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Dana Weekes, S. Sri Krishna, Constantina Bakolitsa, Ian A. Wilson, Adam Godzik, John C. Wooley
TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinform. 11 (2010)
John C. Wooley, Adam Godzik, Iddo Friedberg
A Primer on Metagenomics. PLoS Comput. Biol. 6 (2) (2010)
Kyle Ellrott, Lukasz Jaroszewski, Weizhong Li, John C. Wooley, Adam Godzik
Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families. PLoS Comput. Biol. 6 (6) (2010)
Andreas Prlic, Spencer Bliven, Peter W. Rose, Wolfgang Bluhm, Chris Bizon, Adam Godzik, Philip E. Bourne
Pre-calculated protein structure alignments at the RCSB PDB website. Bioinform. 26 (23) (2010)
Yoshinobu Igarashi, Emily Heureux, Kutbuddin S. Doctor, Priti Talwar, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Michael L. Blinov, Salmaz S. Ibragimova, Sarah E. Boyd, Boris I. Ratnikov, Piotr Cieplak, Adam Godzik, Jeffrey W. Smith, Andrei Osterman, Alexey M. Eroshkin
PMAP: databases for analyzing proteolytic events and pathways. Nucleic Acids Res. 37 (Database-Issue) (2009)
Mallika Veeramalai, Yuzhen Ye, Adam Godzik
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinform. 9 (2008)
Lukasz Slabinski, Lukasz Jaroszewski, Leszek Rychlewski, Ian A. Wilson, Scott A. Lesley, Adam Godzik
XtalPred: a web server for prediction of protein crystallizability. Bioinform. 23 (24) (2007)
Lukasz Slabinski, Adam Godzik, Leszek Rychlewski
TOM - Task and Object Management for Grid Clusters. GCA (2007)
Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik
Using an alignment of fragment strings for comparing protein structures. Bioinform. 23 (2) (2007)
Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg
The 2006 Automated Function Prediction Meeting. BMC Bioinform. 8 (S-4) (2007)
Yoshinobu Igarashi, Alexey M. Eroshkin, Svetlana Gramatikova, Kosi Gramatikoff, Ying Zhang, Jeffrey W. Smith, Andrei Osterman, Adam Godzik
CutDB: a proteolytic event database. Nucleic Acids Res. 35 (Database-Issue) (2007)
Weizhong Li, Adam Godzik
VISSA: a program to visualize structural features from structure sequence alignment. Bioinform. 22 (7) (2006)
Weizhong Li, Adam Godzik
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinform. 22 (13) (2006)
Degui Zhi, S. Sri Krishna, Haibo Cao, Pavel A. Pevzner, Adam Godzik
Representing and comparing protein structures as paths in three-dimensional space. BMC Bioinform. 7 (2006)
Yuzhen Ye, Zhanwen Li, Adam Godzik
Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing (2006)
Zhanwen Li, Yuzhen Ye, Adam Godzik
Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res. 34 (Database-Issue) (2006)
Iddo Friedberg, Tim Harder, Adam Godzik
JAFA: a protein function annotation meta-server. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, Adam Godzik
FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Yuzhen Ye, Adam Godzik
Multiple flexible structure alignment using partial order graphs. Bioinform. 21 (10) (2005)
Iddo Friedberg, Adam Godzik
Fragnostic: walking through protein structure space. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik
Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) (2005)
Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5 (2004)
Philip E. Bourne, C. K. J. Allerston, Werner G. Krebs, Wilfred W. Li, Ilya N. Shindyalov, Adam Godzik, Iddo Friedberg, Tong Liu, David L. Wild, Seungwoo Hwang, Zoubin Ghahramani, Li Chen, John D. Westbrook
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing (2004)
Yuzhen Ye, Adam Godzik
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 32 (Web-Server-Issue) (2004)
Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik
A segment alignment approach to protein comparison. Bioinform. 19 (6) (2003)
Yuzhen Ye, Adam Godzik
Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB (2003)
Marcin Grynberg, Lukasz Jaroszewski, Adam Godzik
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinform. 4 (2003)
Baohong Zhang, Adam Godzik
The Meaning and Limitations of Protein Structure Alignments. 3DPVT (2002)
Weizhong Li, Lukasz Jaroszewski, Adam Godzik
Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinform. 18 (1) (2002)
Weizhong Li, Lukasz Jaroszewski, Adam Godzik
Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinform. 17 (3) (2001)
Lukasz Jaroszewski, Adam Godzik
Search for a New Description of Protein Topology and Local Structure. ISMB (2000)
Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik
Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinform. 16 (12) (2000)
Krzysztof Pawlowski, Leszek Rychlewski, John C. Reed, Adam Godzik
From Fold to Function Predictions: An Apoptosis Regulator Protein BID. Comput. Chem. 24 (3-4) (2000)
Adam Godzik, Jeffrey Skolnick
Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput. Appl. Biosci. 10 (6) (1994)
Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
Lattice representations of globular proteins: How good are they? J. Comput. Chem. 14 (10) (1993)
Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick
De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. 7 (4) (1993)