News

April 2021

· Welcome Keya Joshi to join us as a graduate student in the lab!

· Congratulations to Hung and Sana for publishing a paper on "Pathways and Mechanism of Caffeine Binding to Human Adenosine A2A Receptor" in Frontiers in Molecular Biosciences: https://doi.org/10.3389/fmolb.2021.673170.

· Our recent GaMD review in WIREs Computational Molecular Science has been highlighted in Advanced Science News: A “time-accelerated computational microscope” provides biologists with powerful insights.

· Apurba has given an oral virtual talk on "Pathway and mechanisms of drug binding to ACE2, the functional receptor for SARS-COV1/2" in the Symposium "A Call to Action: The Many Roles of Computational Chemistry in Addressing COVID-19" in the ACS Spring 2021 meeting.

March 2021

· Congratulations to Jinan and Pablo from the Palermo lab at UC Riverside for publishing a co-first authored review on "Gaussian accelerated molecular dynamics: Principles and applications" in WIREs Computational Molecular Science: https://doi.org/10.1002/wcms.1521. This is in collaboratin with the Palermo lab at UC Riverside and Huang Lab at Wayne State University. Apurba and Shristi also contributed to the review! 

· Yinglong has given an invited virtual talk on "Accelerated Molecular Simulations and Computer-Aided Drug Design" at the Center for Molecular Biophysics, Oak Ridge National Laboratory (Host: Prof. Jeremy Smith).

· Welcome Rahi Dasgupta (Olathe North High School) to join our lab for research internship! 

January 2021

· Welcome Keya Joshi to start graduate rotation in the lab.

November 2020

· Welcome Samuel Lim to start graduate rotation in the lab.

October 2020

· Congratulations to Jinan for publishing a first authored paper on "Peptide Gaussian accelerated molecular dynamics (Pep-GaMD): Enhanced sampling and free energy and kinetics calculations of peptide binding" in Journal of Chemical Physics: https://doi.org/10.1063/5.0021399.

· Yinglong has given an invited talk on "Accelerated Molecular Simulations and Computer-Aided Drug Design" in the Chemistry Colloquium at Illinois Institute of Technology (Host: Prof. David Minh), Virtual, October 13, 2020.

· Welcome Utsab Shrestha to join us as a Postdoctoral Researcher in the lab! 

August 2020

· Welcome Jordon Statton (Emerging Scholar Student, Chemical Engineering) to join us as an Undergraduate Researcher in the lab! 

July 2020

· Congratulations to Shristi Pawnikar and Karen John for publishing a co-authored paper on "Structure of the Human Respiratory Syncytial Virus M2-1 Protein in Complex with a Short Positive-Sense Gene-End RNA" in Structure: https://doi.org/10.1016/j.str.2020.07.001. This work is in collaboration with Prof. Bo Liang and his group at Emory University.

· Our ligand GaMD (LiGaMD) method paper has been published online in JCTC: https://doi.org/10.1021/acs.jctc.0c00395 

May 2020

· Congratulations to Apurba Bhattarai for passing the third year PhD candidacy oral exam with flying colors! 

· Congratulations to Hailey Young for being a winner of Outstanding Presentation Award at the 2020 Online Undergraduate Research Symposium at KU! Hailey has presented her research about "Retrospective docking of gamma-secretase modulators" and worked with Waseem Ahmad on the project, as mentored by our graduate student Apurba Bhattarai.  

· Congratulations to Apurba Bhattarai for a first-authored paper on "Mechanisms of γ-Secretase Activation and Substrate Processing", which has been accpted by the ACS Central Science. This work is in collaboration with Prof. Michael Wolfe and his group members Dr. Sujan Devkota and Dr. Sanjay Bhattarai in the KU Department of Medicinal Chemistry.

· Yinglong Miao was a co-Investigator with Prof. Michael Wolfe (PI, Medicinal Chemistry) for an awarded NIH-NIA R01 research grant entitled “Structure and Function of Gamma-Secretase in Familial Alzheimer's Disease”.

April 2020

· Welcome Sana Akhter and Hung Do to join us as graduate students in the lab!

· Congratulations to Apurba Bhattarai and Jinan Wang for publishing a co-first-authored paper on "Retrospective ensemble docking of allosteric modulators in an adenosine G-protein-coupled receptor", which is dedicated to a Special Issue “Advances in Computational Molecular Biophysics in honor of Dr. Jeremy C. Smith's 60th birthday” for BBA - General Subjects! You can click this link for free access until June 10, 2020: https://authors.elsevier.com/a/1axV%7E15Dr%7EZchS

· Congratulations to Shristi Pawnikar for publishing a first-authored paper on "Pathway and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations", which is currently in press in the Future Medicinal Chemsitry journal!

· Congratulations to Khushi Kohli for winning the 1st place in the Computational Biology category and the 2nd place overall in the Greater Kansas City Science Fair! Khushi has been mentored by our postdoc Dr. Jinan Wang in the lab. She presented her research project about "An Optimized Molecular Docking Protocol Targeting Musashi 2 RNA Binding Proteins for Cancer Drug Design".

March 2020

· Welcome Carina Hoering as a visiting gradaute student from Prof. Andrea Strasser's group at the Institute of Pharmacy at University of Regensburg (Germany). During her 3-month visit, Carina will work on enhanced sampling simulations and combine them with wet-lab experiments on studies of mini-G protein interactions with Histamine receptors.

· Congratulations to Khushi Kohli for being accepted to a summer research internship program at the MIT Research Science Institute (RSI) in the summer 2020! Khushi has been mentored by our postdoc Dr. Jinan Wang in the lab.

January 2020

· Sana Akhter and Hung Do have started graduate rotation in the lab.

November 2019

• Amar Kumar has started graduate rotation in the lab.

October 2019

· The Miao Lab has given invited talk and poster presentations in the "Southwest Theoretical and Computational Chemistry 2019 meeting" (University of Oklahoma, October 25-27), including "Gaussian Accelerated Molecular Dynamics (GaMD): Method Developments and Applications" by Yinglong, "Improved Modeling of Peptide-Protein Binding through Global Docking and Accelerated Molecular Dynamics Simulations" by Jinan Wang, "G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation State" by Apurba Bhattarai and "Pathways and Mechanism of Drug Binding to Chemokine Receptors Revealed by Accelerated Molecular Simulations" by Shristi Pawnikar.

Congratuations to Shristi for wining the Outstanding Poster Award!

· Yinglong has given an invited talk on "Gaussian accelerated molecular dynamics (GaMD): Bridging gap for multiscale simulations" in the First International Conference on Mathematical Multiscale Modeling in Biology” (Organizers: Andrzej Kloczkowski, Marek Cieplak and Grzegorz Rempala), Guanacaste, Costa Rica, October 21-25, 2019.

· Congratulations to Jinan for publishing a paper in Frontiers in Molecular Biosciences in collaboration with Andrey Alekseenko and Dima Kozakov on "Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations"!

• Congratulations to Apurba and Jinan for publishing a paper in Journal of Computaitonal Chemistry on "G-Protein-Coupled Receptor-Membrane Interactions Depend on the Receptor Activation state"!

September 2019

• Keeley Collins has started graduate rotation in the lab.

August 2019

• Jinan has published a first-authored article on "Mechanistic Insights into Specific G Protein Interactions with Adenosine Receptors" in the Journal of Physical Chemistry B: https://doi.org/10.1021/acs.jpcb.9b04867. The paper is hilighted on the journal cover: "Specific G protein coupling to adenosine G-protein-coupled receptors revealed from all-atom enhanced sampling simulations: the adenosine A1 receptor (A1AR) prefers to bind the Gi protein to the Gs. The Gs could not stabilize adenosine binding in the active A1AR and vice versa. In contrast, the adenosine A2A receptor (A2AAR) could bind both the Gs and Gi proteins."

Congratulations, Jinan!

June 2019

· Yinglong has given an invited talk: Miao, Y; Wang, JA; Bhattarai, A (2019). Gaussian Accelerated Molecular Dynamics: Free Energy Calculations of Biomolecular Interactions. Santa Fe Workshop “Free energy calculations: Entering the fourth decade of adventure in chemistry and biophysics (2019)” (Organizers: Gregory Voth, Pengyu Ren and Wei Yang), Santa Fe, NM. June 16 – 21, 2019.

April 2019

• Shristi Pawnikar has joined us as a graduate student in the lab.

• Christian Soeldner from Prof. Dr. Heinrich Sticht Group in Bioinformatics at Erlangen University (Germany) starts his 3-month visit in our lab. He will work on enhanced sampling of Histamine receptors.

· Yinglong has given invited talks in the 2019 Spring American Chemical Society meeting in Orlando, Florida: (1) "Activation dependent G-protein-coupled receptor-membrane interactions", (2) "Enhanced molecular dynamics simulations of G-protein-coupled receptor-G protein interactions", and (3) "Gaussian accelerated molecular dynamics (GaMD): Enhanced sampling of ligand binding and protein-protein interactions".

· Yinglong has given an invited talk entitled "Accelerated Simulations and Drug Design of G-Protein-Coupled Receptors" in the Department of Anatomy & Physiology at Kansas State University.

March 2019

• Jinan has won a Travel Award to attend the 2019 Biophysical Society Meeting in Baltimore, Maryland. He has also served as a Co-Chair for session "Platform: Membrane Receptors and Signal Transduction" and presented an oral talk entitled "Mechanism of specific G protein coupling to adenosine receptors". Congratulations, Jinan!

• Miao Lab has received NIH R01 grant for a project, entitled "Enhanced Sampling of G-Protein-Coupled Receptor-G protein interactions". Thanks to everyone for the great work!

Feburary 2019

· Yinglong has given an invited talk, entitled "Enhanced sampling of G-protein-coupled receptor-G protein interactions", at the CECAM workshop "Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations" in Lausanne, Switzerland.

• Hailey Young has joined the lab as an undergraduate researcher.

January 2019

• Jinan has published a first-authored review article on "Recent advances in computational studies of GPCR-G protein interactions" in the Advances in Protein Chemistry and Structural Biology: https://doi.org/10.1016/bs.apcsb.2018.11.011. Congratulations, Jinan!

• Ryan Feehan and Adam Podgorny have started graduate rotation in the lab.

November 2018

• We have published a research article in collaboration with Anh Nguyen, Arthur Christopoulos and Lauren May at Monash University on "Structural Basis for Binding of Allosteric Drug Leads in the Adenosine A1 Receptor" in the Scientific Reports: https://doi.org/10.1038/s41598-018-35266-x.

• Shristi Pawnikar has started graduate rotation in the lab.

October 2018

• Apurba has published a first-authored review article on "Gaussian Accelerated Molecular Dynamics for Elucidation of Drug Pathways" in the Expert Opinion On Drug Discovery: http://dx.doi.org/10.1080/17460441.2018.1538207. Congratulations, Apurba!

August 2018

· Yinglong has given talks in the 2018 American Chemical Society National Meeting in Boston, MA during Aug 19-23: (1) “Binding Modes and Effects of Allosteric Drug Leads in the Adenosine A1 Receptor”; (2) “Ligand Binding Pathways and Conformational Transitions of the HIV Protease”; (3) “Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor”; and (4) “Acceleration of Biomolecular Kinetics in Gaussian Accelerated Molecular Dynamics".

• Khushi Kohli (Olathe North High School) has joined the Miao lab for research internship.

July 2018

• Shulammite Lim (Olathe North High School) has finished research internship in the Miao Lab and is admitted to MIT School of Engineering. Congratulations and all the best, Shulammite!

April 2018

• PNAS study "Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor" is highlighted in the Extreme Science and Engineering Discovery Environment (XSEDE) Science Stories: “XSEDE Helps Reveal How a Heart Drug Molecular Switch Is Turned On and Off

March 2018

• New PNAS paper "Mechanism of the G-Protein Mimetic Nanobody Binding to a Muscarinic G-Protein-Coupled Receptor" is highlighted in the San Diego Supercomputer News: “SDSC Simulations Reveal How a Heart Drug Molecular Switch Is Turned On and Off

• Apurba Bhattarai has joined us as the first graduate student in the lab!

• Yinglong has given an invited talk entitled “Accelerated Computer Simulations and Drug Discovery of G-Protein-Coupled Receptors” and a hands-on tutorial entitled "Gaussian Accelerated Molecular Dynamics" at the Frontiers in Computational Drug Discovery (FCDD) Symposium, in Academia Sinica, Taipei.

• Yinglong has given an invited talk entitled “Accelerated Computer Simulations and Drug Discovery of G-Protein-Coupled Receptors” in the Department of Biochemistry and Molecular Biophysics, Kansas State University in Manhattan, Kansas.

Feburary 2018

• Jinan Wang (Ph.D., Shanghai Institute of Materia Medica, Chinese Academy of Sciences) has joined the lab as a postdoctoral researcher

• Shulammite Lim (Olathe North High School) has joined the Miao lab for research internship.

• We have published a new article in Biochemistry: Ligand Binding Pathways and Conformational Transitions of the HIV Protease

January 2018

• Karen John has joined the lab as an undergraduate researcher.

December 2017

• Yinglong has received an Allocation Year 2018 award with 4,000,000 supercomputing SUs from the National Energy Research Scientific Computing Center (NERSC): "Accelerated Computer Simulations of G-Protein-Coupled Receptors"

November 2017

• Waseem Ahmad (freshman in Microbiology) and Treyton Farnan (freshman in Human Biology) have joined the lab as undergraduate researchers

• Apurba Bhattarai has started graduate rotation in the lab

August 2017

• Yinglong has given an invited talk entitled “Accelerated Computer Simulations and Drug Discovery of G-Protein-Coupled Receptors” at the 4th Biennial Symposium – Optical Micro-spectroscopy & Molecular Imaging held at the University of Wisconsin, Milwaukee

• Yinglong has started as Assistant Professor at the University of Kansas

 


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