Adam Godzik's Research Focus
Our research is focused on biological systems and their evolution. We try to combine insights from mathematics and physics to answer basic questions about biological systems and to use them to develop new computational tools that could allow us to find new regularities and trends in biological data. In particular we are trying to understand how the topology, structure, and function of proteins and protein networks has evolved and how it reacts to perturbation, such as disease mutations or other genomics perturbations.
By combining structural information about proteins with data on cellular networks formed by these proteins in an approach we call structural systems biology we can explicitly model the networks in their perturbed state and try to predict their behavior. We study systems from bacterial metabolic and virulence networks, to human immunity, apoptosis and cancer networks.
Adam Godzik's Research Report
Cancer3D is a database that unites information on somatic missense mutations from TCGA and CCLE, allowing users to explore two different cancer-related problems at the same time: drug sensitivity/biomarker identification and prediction of cancer drivers. The database is an interface to two novel algorithms, e-Driver and e-Drug, that make use of information about the internal structure of a protein to predict novel cancer drivers or drug biomarkers respectively. Moreover, it maps somatic missense mutations from over 18,000 human proteins to more than 25,000 protein structures from PDB.
Adam Godzik's Bio
Dr. Adam Godzik earned his Ph.D. in physics from the Department of Physics, University of Warsaw, Poland in 1990. After postdoctoral work in the European Molecular Biology Laboratory in Heidelberg and The Scripps Research Institute in San Diego, he became an Assistant Professor at The Scripps Research Institute. In 1999 he joined Sanford-Burnham Medical Research Institute as an Associate Professor.
Zmasek CM, Godzik A
PLoS Comput Biol 2012 ;8(11):e1002701
Hrabe T, Li Z, Sedova M, Rotkiewicz P, Jaroszewski L, Godzik A
Nucleic Acids Res 2016 Jan 4 ;44(D1):D423-8
Porta-Pardo E, Kamburov A, Tamborero D, Pons T, Grases D, Valencia A, Lopez-Bigas N, Getz G, Godzik A
Nat Methods 2017 Aug ;14(8):782-788
Li Z, Jaroszewski L, Iyer M, Sedova M, Godzik A
Nucleic Acids Res 2020 Jul 2 ;48(W1):W60-W64
Difference contact maps: From what to why in the analysis of the conformational flexibility of proteins.
Iyer M, Li Z, Jaroszewski L, Sedova M, Godzik A
PLoS One 2020 ;15(3):e0226702
Xu Q, Biancalana M, Grant JC, Chiu HJ, Jaroszewski L, Knuth MW, Lesley SA, Godzik A, Elsliger MA, Deacon AM, Wilson IA
Protein Sci 2019 Sep ;28(9):1676-1689
Sedova M, Iyer M, Li Z, Jaroszewski L, Post KW, Hrabe T, Porta-Pardo E, Godzik A
Nucleic Acids Res 2019 Jan 8 ;47(D1):D895-D899
Retraction: Crystal structure of a Baeyer-Villiger flavin-containing monooxygenase from Staphylococcus aureus MRSA strain MU50, William C. Hwang, Qingping Xu, Bainan Wu, Adam Godzik.
Proteins 2018 Feb ;86(2):269