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ORCIDAdam Godzik
Person information
- affiliation: University of California, Riverside, CA, USA
- affiliation: Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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2020 – today
- 2021
[j59]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)- 2020
- [j58]Mayya Sedova, Lukasz Jaroszewski, Arghavan Alisoltani, Adam Godzik:
Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence. Bioinform. 36(15): 4360-4362 (2020) - [j57]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): W60-W64 (2020)
2010 – 2019
- 2019
- [j56]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): D895-D899 (2019) - 2016
- [j55]Mayya Sedova, Lukasz Jaroszewski, Adam Godzik:
Protael: protein data visualization library for the web. Bioinform. 32(4): 602-604 (2016) - [j54]Thomas Hrabe, Lukasz Jaroszewski, Adam Godzik:
Revealing aperiodic aspects of solenoid proteins from sequence information. Bioinform. 32(18): 2776-2782 (2016) - [j53]Thomas Hrabe, Zhanwen Li, Mayya Sedova, Piotr Rotkiewicz, Lukasz Jaroszewski, Adam Godzik:
PDBFlex: exploring flexibility in protein structures. Nucleic Acids Res. 44(Database-Issue): 423-428 (2016) - 2015
- [j52]Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. Bioinform. 31(13): 2098-2105 (2015) - [j51]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: 7:1-7:9 (2015) - [j50]Eduard Porta-Pardo, Thomas Hrabe, Adam Godzik:
Cancer3D: understanding cancer mutations through protein structures. Nucleic Acids Res. 43(Database-Issue): 968-973 (2015) - [j49]Eduard Porta-Pardo, Adam Godzik:
Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics. PLoS Comput. Biol. 11(1) (2015) - [j48]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) - [j47]Samad Jahandideh, Fatemeh Sharifi, Lukasz Jaroszewski, Adam Godzik:
PROPER: Performance visualization for optimizing and comparing ranking classifiers in MATLAB. Source Code Biol. Medicine 10: 15 (2015) - 2014
- [j46]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): 660-667 (2014) - [j45]Eduard Porta-Pardo, Adam Godzik:
e-Driver: a novel method to identify protein regions driving cancer. Bioinform. 30(21): 3109-3114 (2014) - [j44]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: 75 (2014) - [j43]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: 112 (2014) - [j42]Thomas Hrabe, Adam Godzik:
ConSole: using modularity of contact maps to locate Solenoid domains in protein structures. BMC Bioinform. 15: 119 (2014) - [j41]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: 196 (2014) - [j40]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): 1133-1139 (2014) - [j39]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): 240-245 (2014) - [j38]Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik:
AIDA: ab initio domain assembly server. Nucleic Acids Res. 42(Webserver-Issue): 308-313 (2014) - [j37]Lukasz Jaroszewski, Laszlo Koska, Mayya Sedova, Adam Godzik:
PubServer: literature searches by homology. Nucleic Acids Res. 42(Webserver-Issue): 430-435 (2014) - 2013
- [j36]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: 19 (2013) - [j35]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: 265 (2013) - [j34]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: 341 (2013) - 2012
- [j33]Christian M. Zmasek, Adam Godzik:
This Déjà Vu Feeling - Analysis of Multidomain Protein Evolution in Eukaryotic Genomes. PLoS Comput. Biol. 8(11) (2012) - [c8]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: 262-273 - 2011
- [j32]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): 494-496 (2011) - [j31]Lukasz Jaroszewski, Zhanwen Li, Xiao-hui Cai, Christoph Weber, Adam Godzik:
FFAS server: novel features and applications. Nucleic Acids Res. 39(Web-Server-Issue): 38-44 (2011) - [j30]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) - 2010
- [j29]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): 2983-2985 (2010) - [j28]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: 426 (2010) - [j27]John C. Wooley, Adam Godzik, Iddo Friedberg:
A Primer on Metagenomics. PLoS Comput. Biol. 6(2) (2010) - [j26]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)
2000 – 2009
- 2009
- [j25]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): 611-618 (2009) - 2008
- [j24]Mallika Veeramalai, Yuzhen Ye, Adam Godzik:
TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinform. 9 (2008) - 2007
- [j23]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): 219-224 (2007) - [j22]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): 3403-3405 (2007) - [j21]Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg:
The 2006 Automated Function Prediction Meeting. BMC Bioinform. 8(S-4) (2007) - [j20]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): 546-549 (2007) - [c7]Lukasz Slabinski, Adam Godzik, Leszek Rychlewski:
TOM - Task and Object Management for Grid Clusters. GCA 2007: 199-205 - 2006
- [j19]Weizhong Li, Adam Godzik:
VISSA: a program to visualize structural features from structure sequence alignment. Bioinform. 22(7): 887-888 (2006) - [j18]Weizhong Li, Adam Godzik:
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinform. 22(13): 1658-1659 (2006) - [j17]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: 460 (2006) - [j16]Zhanwen Li, Yuzhen Ye, Adam Godzik:
Flexible Structural Neighborhood - a database of protein structural similarities and alignments. Nucleic Acids Res. 34(Database-Issue): 277-280 (2006) - [j15]Iddo Friedberg, Tim Harder, Adam Godzik:
JAFA: a protein function annotation meta-server. Nucleic Acids Res. 34(Web-Server-Issue): 379-381 (2006) - [c6]Yuzhen Ye, Zhanwen Li, Adam Godzik:
Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins. Pacific Symposium on Biocomputing 2006: 439-450 - 2005
- [j14]Yuzhen Ye, Adam Godzik:
Multiple flexible structure alignment using partial order graphs. Bioinform. 21(10): 2362-2369 (2005) - [j13]Iddo Friedberg, Adam Godzik:
Fragnostic: walking through protein structure space. Nucleic Acids Res. 33(Web-Server-Issue): 249-251 (2005) - [j12]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): 284-288 (2005) - [c5]Yuzhen Ye, Andrei Osterman, Ross A. Overbeek, Adam Godzik:
Automatic detection of subsystem/pathway variants in genome analysis. ISMB (Supplement of Bioinformatics) 2005: 478-486 - 2004
- [j11]Dariusz Plewczynski, Leszek Rychlewski, Yuzhen Ye, Lukasz Jaroszewski, Adam Godzik:
Integrated web service for improving alignment quality based on segments comparison. BMC Bioinform. 5: 98 (2004) - [j10]Yuzhen Ye, Adam Godzik:
FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res. 32(Web-Server-Issue): 582-585 (2004) - [c4]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: 375-386 - 2003
- [j9]Yuzhen Ye, Lukasz Jaroszewski, Weizhong Li, Adam Godzik:
A segment alignment approach to protein comparison. Bioinform. 19(6): 742-749 (2003) - [j8]Marcin Grynberg, Lukasz Jaroszewski, Adam Godzik:
Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization. BMC Bioinform. 4: 46 (2003) - [c3]Yuzhen Ye, Adam Godzik:
Flexible structure alignment by chaining aligned fragment pairs allowing twists. ECCB 2003: 246-255 - 2002
- [j7]Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinform. 18(1): 77-82 (2002) - [c2]Baohong Zhang, Adam Godzik:
The Meaning and Limitations of Protein Structure Alignments. 3DPVT 2002: 729-736 - 2001
- [j6]Weizhong Li, Lukasz Jaroszewski, Adam Godzik:
Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinform. 17(3): 282-283 (2001) - 2000
- [j5]Weizhong Li, Frederic Pio, Krzysztof Pawlowski, Adam Godzik:
Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology. Bioinform. 16(12): 1105-1110 (2000) - [j4]Krzysztof Pawlowski, Leszek Rychlewski, John C. Reed, Adam Godzik:
From Fold to Function Predictions: An Apoptosis Regulator Protein BID. Comput. Chem. 24(3-4): 511-517 (2000) - [c1]Lukasz Jaroszewski, Adam Godzik:
Search for a New Description of Protein Topology and Local Structure. ISMB 2000: 211-217
1990 – 1999
- 1994
- [j3]Adam Godzik, Jeffrey Skolnick:
Flexible algorithm for direct multiple alignment of protein structures and sequences. Comput. Appl. Biosci. 10(6): 587-596 (1994) - 1993
- [j2]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
De novo and inverse folding predictions of protein structure and dynamics. J. Comput. Aided Mol. Des. 7(4): 397-438 (1993) - [j1]Adam Godzik, Andrzej Kolinski, Jeffrey Skolnick:
Lattice representations of globular proteins: How good are they? J. Comput. Chem. 14(10): 1194-1202 (1993)
Coauthor Index
Jim Zhanwen Li
aka: Zhanwen Li
aka: Zhanwen Li
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