Our INCITE Award was competitively renewed for 2022 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
Congratulations to Chunli Yan, Tom Dodd and Jina Yu who are co-authors on a just accepted paper in the journal Nature Communications. The paper is entitled “Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair.” Our integrative modeling study elucidates the mechanism by which Cockayne Syndrome B protein (CSB) binds to lesion-arrested RNA Polymerase […]
Ivaylo Ivanov receives a Maximizing Investigators’ Research Award (MIRA) from the National Institute of General Medical Sciences.
Oak Ridge National Lab highlights our recent work on pathways for conformational switching in high fidelity DNA polymerases: “Simulations reveal Nature’s design for error correction during DNA replication“.
Our group received a new INCITE Award from the U.S. Department of Energy Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and […]
Congratulations to Tom Dodd who is the first author on a just accepted paper in the journal Nature Communications. The paper is entitled “Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path” and addresses a grand challenge for the DNA replication field by demonstrating through combined computational and biochemical analyses […]
Ivaylo Ivanov was promoted to the rank of Full Professor at Georgia State starting in August 2020.
Ivaylo Ivanov receives a new four-year award from the National Science Foundation.
Congratulations to Tom Dodd on receiving a Hopkins Endowed Award from GSU. The Harry P. Hopkins, Jr. Scholarship in Physical Chemistry was endowed in 2017 to honor the memory of GSU Physical Chemistry Professor Harry P. Hopkins.
Our group was among the 47 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among the projects in the areas of Biological Sciences/Biophysics. Here are the 2020 INCITE Announcement and the list of 2020 […]
Our INCITE Award was competitively renewed for 2020 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and engineering. Our […]
Oak Ridge National Lab highlights our recent work on the transcription preinitiation complex (PIC): “Summit Charts a Course to Uncover the Origins of Genetic Diseases”.
Congratulation to Chunli Yan and Tom Dodd who published a new paper in the journal Nature Structural & Molecular Biology on the molecular architecture and functional dynamics of the transcription preinitiation complex (PIC). Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural […]
Congratulation to group alumnus Dr. Max Xu and Dr. Chunli Yan and who published a new paper in the Journal of Molecular Biology that unravels the common origins of DNA clamp proteins’ subunit interface stability with implications for the function of these proteins in DNA replication. Perumal, S.K.; Xu, X.; Yan, C.; Ivanov, I. & Benkovic, S.J. Recognition of a […]
Congratulation to Dr. Kathleen Carter who published a new paper in the jounal Physical Chemistry Chemical Physics detailing the mechanism of sequence-specific DNA binding of a designed small molecule binder DB2277. Carter, E.K.; Laughlin, S.; Dodd, T.; Wilson, W.D. & Ivanov, I* Small molecule binders recognize DNA microstructural variations via an induced fit mechanism Physical Chemistry […]
Congratulations to Kathleen Carter who defended her Ph.D. dissertation today. Best wishes to Kathleen for success in her future career!
Our group was among the 62 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among 8 projects in the areas of Biological Sciences/Biophysics awarded nationwide. Here are the 2019INCITEAnnouncement and the […]
Ivaylo received a new INCITE Award from the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science […]
Group members recently traveled to Augusta, GA to present at the 2018 Southeastern Regional Meeting of the American Chemical Society. Many thanks to all who presented! (Chunli Yan, Ashutosh Shandilya, Tom Dodd, Kurt Martin and Zhenyu Wang) At the meeting Ivaylo gave two invited talks: Emerging unified description of transcription initiation from cryo-EM and integrative computational […]
Group members recently traveled to Boston, MA to present at the 2018 National Meeting of the American Chemical Society. Ivaylo gave a talk entitled “Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling ” in the COMP division (New Frontiers in Flexible Fitting, Image Processing & Refinement of Cryo-EM Data session). Many […]
Congratulation to Dr. Chunli Yan who published a new paper combining computational modeling and cryo-electron microscopy to unveil structures of pre-initiation complexes of RNA Polymerase III. Han, Y.; Yan, C.; Fishbain, S.; Ivanov, I. & He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018) (in press)
Our project on the base extrusion mechanism of thymine DNA glycosylase (TDG) was highlighted by the San Diego Supercomputer Center. How an Enzyme Repairs DNA via a “Pinch-Push-Pull” Mechanism
Congratulation to Tom Dodd, Chunli Yan, Kurt Martin and Brad Kossmann who published a new paper in the journal Proceedings of the National Academy of Sciences USA. Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I. Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018) doi:10.1073/pnas.1803323115 […]
Ivaylo visited Lawrence Berkeley National Lab in Feb. 2018 and gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the Advanced Light Source synchrotron facility.
Ivaylo gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the 3rd DNA Replication/Repair Structures and Cancer Conference in Cancun Mexico.
Ivaylo attended the 2018 Annual Meeting of the Biophysical Society and presented our new findings on the transcription initiation by RNA polymerase I.
Ivaylo attended the 2018 Keystone Symposium “Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems” and presented our new findings on the transcription initiation by RNA polymerase I.
Group members recently traveled to Charlotte, NC to present at the 2017 Southeastern Regional Meeting of the American Chemical Society. Many thanks to all who presented! (Kathleen Carter, Chunli Yan and Tom Dodd)
Congratulations to Bernard Scott who successfully defended his Masters thesis in June 2017! He has accepted an offer of admission to the Ph.D. program at the University of Utah and will continue doing research albeit in an experimental lab. We wish him all the best in his future endeavors.
Congratulation to Dr. Chunli Yan who published a new paper on combining computational modeling and Cryo-electron microscopy to uncover the mechanisms of transcription initiation. Han, Y.; Yan, C.; Nguyen, K.; Jackobel, A.; Ivanov, I.; Knutson, B.A.; He, Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife (2017) 6, e27414, doi:10.7554/eLife.27414
Group members recently attended and presented at two conferences: Nucleic Acids Research Gordon Conference in Biddeford, ME and CBSB2017: From Compuational Biophysics to Systems Biology 2017. Many thanks to all who presented! (Kathleen Carter, Chunli Yan and Tom Dodd)
Congratulations to Tom Dodd who received a competitive doctoral fellowship from the Molecular Basis of Disease program at Georgia State.
Congratulations to Brad Kossmann who received two competitive awards from Georgia State: 1) the Award for Outstanding Research at the Ph.D. level (only two such awards are given yearly in our department) 2) the Molecular Basis of Disease Outstanding Fellow Award
Congratulations to Tom Dodd on passing his writtten qualifying exam.
Congratulations to Brad Kossmann who successfully defended his doctoral dissertation on March 21th 2017! He has accepted a new position in data science based right here in Atlanta. We wish him all the best in his future endeavors.
Congratulations to Kathleen Carter who published a new paper in the journal Nucleic Acids Research: Laughlin S.; Carter E.K.; Ivanov, I* & Wilson, W.D. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences Nucleic Acids Research (2016) doi:10.1093/nar/gkw1232
Ivaylo Ivanov gives a presentation at the EMBO Conference “Molecular Machines: Integrative Structural and Molecular Biology” in Heidelberg, Germany.
Our project on transcription pre-initiation complexes was highlighted by the Texas Advanced Computing Center. https://www.tacc.utexas.edu/-/how-to-see-living-machines
Congratulations to Chunli Yan who published as a co-author on a new paper in the journal Nature Communications entitled “Rational design of a protein that binds integrin αvβ3 outside the ligand binding site”. The paper reports a new desinged protein which targets integrn at a novel site outside the canonocal Arg-Gly-Asp (RGD) binding site.
Ivaylo Ivanov was selected to join the Editorial Board of Frontiers in Molecular Biosciences (Biophysics specialty section). Frontiers publishes several of the most cited Open-access journals in the world, is today one the largest and fastest-growing open-access publishers, receives millions of monthly page views, received the ALPSP Gold Award for Innovation in Publishing in 2014, has publishing agreements […]
Congratulations to Bernard Scott who has won a fellowship from the XSEDE Scholars Program. The XSEDE Scholars Program (XSP) is a selective year-long program for U.S. students from underrepresented groups in the computing sciences who receive opportunities to learn more about high performance computing and XSEDE resources. XSEDE, the Extreme Science and Engineering Discovery Environment, is the most […]
Congratulations to Brad Kossmann who published a new paper in the journal Bioorganic & Medicinal Chemistry Letters entitled “Discovery of selective inhibitors of tyrosyl-DNA phosphodiesterase 2 by targeting the enzyme DNA-binding cleft”. The paper details the characterization of three new selective inhibitors of the enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2). TDP2processes protein/DNA adducts resulting from abortive DNA topoisomerase II […]
Our project on transcription pre-initiation complexes was picked up by the Science360 site of the National Science Foundation. https://news.science360.gov/archives/20160513/
An unprecedented molecular view of the critical early events in gene expression, a process essential for all life, has been provided by researchers at Georgia State University, the University of California at Berkeley and Northwestern University. Source: Researchers unveil new, detailed images of DNA transcription
Scientists reveal how evolutionary fine-tuning has obscured the origin of the glucocorticoid receptor’s ability to adopt different shapes. It highlights how proteins that evolve ‘new’ functions may have had those capacities — in some cases, for millions of years — because of their flexibility. Source: Ancient protein flexibility can drive ‘new’ functions
An unprecedented molecular view of the critical early events in gene expression, a process essential for all life, has been provided by researchers in a new study. Cryo-electron microscopy (cryo-EM), a technique that studies samples at cryogenic temperatures, combined with state-of-the-art computational modeling, allowed researchers to visualize large transcription pre-initiation complexes (PIC) at near-atomic resolution. […]
Computation and experiment reveal how protein switching provides right tool for the job Source: Researchers Show How Proteins Help DNA Replicate Past a Damaged Site
Scientists use Jaguar to model replisome components to understand their role in health and disease. Source: Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
Ivaylo Ivanov, associate professor of chemistry at Georgia State University, has received a five-year, $1.675 million federal grant to study how problems with DNA replication and repair may lead to cancer susceptibility and inheritable genetic diseases. Source: Georgia State scientist gets $1.675 million to study link between cancer and DNA replication, repair
“New study provides a framework for understanding how protein works and how it stimulates the DNA processing machines” Source: Oak Ridge National Laboratory
The National Institute of General Medical Sciences (NIGMS) has funded our project “Integrative Modeling of PCNA Assemblies Engaged in Genome Duplication and Repair” as a 5-year R01 grant.
The Journal of Computational and Structural Biotechnology has just published our invited review paper ‘Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution’.
Another paper, ‘Functional Dynamics in Replication Protein A DNA Binding and Protein Recruitment Domains’ has also appeared in Structure.
Our paper ‘Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response’ has been published by the journal Structure.
Congratulations to Shih-Wei Chuo who successfully defended his M.S. thesis and received a masters degree in May 2015! Shih-Wei will continue his studies toward a Ph.D. degree at the University of California and we wish him all the best in his future endeavors.
Our paper ‘Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases’ was published in PLOS Computational Biology. We employed chain-of-replicas path optimization strategy to determine a minimum energy path (MEP) for flipping out a 3-methyl adenine lesion by the DNA glycosylase AlkD. The path showed that AlkD acts by […]
Congratulations to Max Xu who successfully defended his doctoral dissertation on March 26th 2014! Max is the first Ph.D. recipient from our group and we wish him all the best in his future endeavors.
Our paper ‘Diamidine Compounds for Selective Inhibition of Protein Arginine Methyltransferase 1’ has just been accepted by the Journal of Medicinal Chemistry. Misregulation of protein arginine methyltransferase enzymes (PRMTs) have been linked to many pathological conditions. In collaboration with Dr. Zheng’s group at UGA we report diamidine compounds as specific inhibitors of PRMT1, the primary […]
Our paper ‘Opening Pathways of the DNA Clamps Proliferating Cell Nuclear Antigen and Rad9-Rad1-Hus1’ has just been accepted by the journal Nucleic Acids Research. The recently solved structures of the DNA clamp protein 9-1-1 led to competing proposals regarding how 9-1-1 is loaded onto DNA. Through detailed subunit interface analysis, we identified the subunit interface […]
Our paper ‘Probing DNA clamps with single-molecule force spectroscopy’ has just been published in Nucleic Acids Research and sheds light on the mechanisms of DNA clamp opening under external forces by combining molecular simulation with single-molecule micromanipulation experiments.
Integrative Biomolecular Modeling 