Meiler Lab 2013 Meiler Lab 2013
picture The Bio Chemical Library (BCL)
The Bio Chemical Library (BCL) is a software package that provides unique tools for biological research, such as protein structure determination from sparse experimental data. The BCL contains the widely used secondary structure prediction program JUFO, a folding algorithm that assembles secondary structure elements, and loop construction tools that complete protein backbones. With this series of protocols the BCL allows construction of backbone models for large and membrane proteins from the more...
picture Protein Structure Prediction
Despite improvements on both experimental techniques and computational prediction methods for small and medium sized proteins, structure elucidation and prediction for larger proteins remains a major challenge. We are developing a structure prediction algorithm that incorporates data of various experimental techniques but also to be used as a standalone tool. The algorithm utilizes a novel sampling technique and employs the flexible combination of empirical and experimental scores.The pro more...
picture Fitting molecules in low resolution electron density maps

A growing technique in protein structure determination is cryo-electron microscopy. Cryo-EM provides low resolution electron density maps ( ~8 Ångström) . As this data become more accurate and you can use this data not only to determine the overall structure of protein complexes, but also to determine secondary structure elements and their assembly in the tertiary structure of a protein. The successful field of ab initio protein structure prediction ca more...
picture Antibody/Antigens Interactions
Antibody structural repertoires are determined through diversity of gene segment usage and the introduction of somatic mutations. This structural diversity is responsible for the recognition of an unlimited number of antigens. Traditional techniques for determining structure cannot characterize the breath of structural diversity that these antibody-antigen interactions can adopt because of limited throughput. Using the knowledge-based structural biology program Rosetta, we can use the results from c more...
picture Membrane Protein Structure Prediction using sparse NMR restraints
About 30% of the proteins in the human body are membrane proteins. They have a wide variety of functions within the cell and it is therefore not surprising that over half of all known drugs target them. However, less than 1% of the structures deposited in the ProteinDataBank belong to membrane proteins. The reason for this discrepancy is the difficulty to crystallize them. Also conventional liquid-state NMR techniques reach their limits for membrane proteins more...
picture BCL::Jufo: Simultaneous Prediction of Protein Secondary Structure and Trans-Membrane Spans
A first step towards protein tertiary structure prediction is the identification of secondary structure elements from the sequence. In addition, the identification of trans-membrane spans is required for membrane proteins.

The aim of this project is to simultaneously predict secondary structure and trans-membrane spans with a single tool. The rationale for this approach is the hypothesis that both phenomena are interrelated: more...
picture Rosetta Drug Design
Small molecule design consists of assembly, docking, and scoring. Since Rosetta already has a docking algorithm (RosettaLigand) and a scoring framework, all that is needed for small molecule design is an assembly algorithm. As an initial approach, we have chosen random assembly of fragments from an input library. The algorithm is represented in figure 1. Each cycle of design consists of extending the small molecule with random fragments chosen from a library, filtering small molecule designs based on energ more...
picture High resolution contact prediction
Learning systems have a long history in being applied to reduce the search space for protein structure prediction e.g. artificial neural networks (ANN) and hidden markov models (HMM) are used for protein secondary structure prediction and motif recognition. Recently, ANNs were successfully utilized to derive a consensus amino acid contact prediction for unknown folds from fold recognition techniques. These predictions drive de novo prediction of protein tertiary structure towards better r more...
picture EPR guided protein structure prediction using the BCL
Electron paramagnetic resonance (EPR) can provide structural information on proteins not easily studied by other biophysical techniques such as nuclear magnetic resonance and X-ray crystallography. Inter-residue distances of up to 60Å and residue specific solvent exposure can be measured. Such data can be critical to defining the topology of a protein. However, the amount of information obtained from an EPR dataset is limited by its sparseness and difficulty in r more...
picture Cryo-EM guided de novo Protein Fold Elucidation
Using cryo-electron microscopy (cryoEM) numerous sub-nanometer resolution density maps of large macromolecular assemblies have been recently reported. Although no atomic detail is generally resolved in these density maps, at 7 Å resolution α-helices are observed as density rods. The Primary goal of this project is the development of a computational protein structure prediction algorithm that incorporates the experimental cryoEM density map as restraints. The placemen more...
picture HIV-1 Protease Inhibitor Docking
HIV protease inhibitors (PIs) have been an important and successful model for structure-assisted drug design. At least ten PIs have been approved by the FDA since 1995. However because of HIV-1’s high mutation rate, PI therapies often succumb to drug resistance mutations. Computational methods that predict how a putative inhibitor will interact with various strains of HIV-1 protease will speed the development of new inhibitors that avoid resistance mutation. HIV-1 protease mutants more...
picture TIM Barrel Design
Six of the ten most frequent protein topologies have symmetry on the fold level. We postulate that the evolutionary origin of these symmetric superfolds lies in naturally occurring homo-oligomeric protein complexes that undergo gene duplication and fusion. To test this hypothesis the Rosetta protein design package was used to computationally design a two-fold symmetric variant of imidazole glycerol phosphate synthase (HisF). The new protein, termed FLR, adopts the symmetric βα TIM-barrel superfo more...

About Meiler Lab



Research in our laboratory seeks to fuse computational and experimental efforts to investigate proteins, the fundamental molecules of biology, and their interactions with small molecule substrates, therapeutics, or probes. We develop computational methods with three major ambitions in mind.
 

A) To enable protein structure elucidation of membrane proteins the primary target of most therapeutics and large macromolecular complexes such as viruses;
B) Design proteins with novel structure and/or function to explore novel approaches to protein therapeutics and deepen our understanding of protein folding pathways.
C) Understand the relation between chemical structure and biological activity quantitatively in order to design more efficient and more specific drugs.

 

Crucial for our success is the experimental validation of our computational approaches which we pursue in our laboratory or in collaboration with other scientists.

 

Current research applications focus on new approaches to a) drug and probe development for neurodegenerative disorders and diseases including Schizophrenia, Alzheimer's, and Parkinson's, b) understanding the structural determinants of antidepressant binding to neurotransmitter transporters, c) cardiac arrhythmia as caused by the complex interplay of potassium channel regulation and drug interactions, d) multidrug resistance in cancer and bacterial cells related to multidrug transporter proteins, and e) structural basis of viral infections and antibody activity.

News


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Alex Geanes wins Division of Chemical Information (CINF) Scholarship for Scientific Excellence! 2014-08-26

Alex received this award for his poster presentation at the ACS meeting in San Francisco. Congratulations, Alex! 


Congratulations, Dr. DeLuca! 2014-08-19

Stephanie Hirst DeLuca successfully defended her dissertation entitled "Protein Structure Elucidation by Combining Computational and Experimental Methods" 


Alyssa Lokits passed Phase I of her qualifying exam! 2014-08-01

Congratulations!


"A conserved phenylalanine as relay between the alpha5 helix and the GDP binding region of heterotrimeric Gi protein alpha subunit" 2014-07-24

Published in JBC! Read all about it here: http://www.jbc.org/content/early/2014/07/18/jbc.M114.572875


Darwin Fu wins a Phrma Fellowship 2014-06-26

Darwin Fu won an informatics graduate student fellowship from the Phrma foundation. Congratulations, Darwin!


Meiler Lab awarded Vanderbilt University Central Discovery Grant! 2014-05-22

The Meiler Laboratory is one of several laboratories that have been awarded a University Central Discovery Grant for the proposal entitled "An Intel Xeon Phi Coprocessor (IXP-CPU) Computing Cluster for ACCRE". Congratulations! 


Alex Geanes receives CBI training grant! 2014-05-20

Congratulations, Alex! 


New ROSIE Ligand Docking App 2014-05-14

The Ligand Docking ROSIE app is now available! Please visit: http://rosie.rosettacommons.org/ligand_docking 


Snyder, B. "'Missing link' may spur new brain disorder drugs" VUMC Reporter March 14, 2014.

Windsor, M., "Vanderbilt, Leipzig research collaboration sees strong results." Research News @ Vanderbilt

Salisbury, D. "Leipzig collaboration yields valuable relationships." Vanderbilt Chemistry 2013.

Bartoo, C. "Controversial info release aids VUMC bird flu research" VUMC Reporter September 6, 2013.

Oak Ridge Associated Universities. "ORAU, ORNL announce winners of high-performance computing grant competition." Oak Ridge Today, 2013.

Snyder, B. "School for Science and Math students shine in Intel competition." VUMC Reporter, Jan 2013.

Meiler, J. "Die Bedeutung des FChO auf deinem akademischen Weg" Faszination Chemie 2013, 66.

Salisburg, D. "The Leipzig Connection," Research News@Vanderbilt, Vanderbilt University, Dec 2012.

Russel, J. "Bigger IS Better", Arts and Science, Vanderbilt University, Spring 2012.

Fortenberry, C. "International Chemistry: Shared reactions from Leipzig to Nashville." Vanderbilt International 2011.

Salisbury, David. "Creation of the largest human-design protein boosts protein engineering efforts." Vanderbilt Reporter, Nov 2011.

Synder, B. "School for Science and Math student sees paper published." VUMC Reporter, Vol XXI, 34. Sep 2011.

Snyder, B. "Study shows how G proteins get "turned on" by receptors" Vanderbilt Reporter 2011.

Baynham, D. Q.; Karakas, M.; Meiler, J. "Protein Structure Prediction Using Rosetta" Young Scientist, May 2011, p11-12

Smith, S. "As Beckman Scholars, undergraduates experience responsibility and research life" Arts & Science, Vanderbilt University, Spring 2011

Schreiber, A.; Meiler, J. "Modellierung G-Protein-gekoppelter Rezeptoren mit ROSETTA " Biospektrum

Joetten, F. "Formvollendet" Bild der Wissenschaft 2010, 4, 18-23.

Omlor, A.; Meiler, J. "Zu Gast im Meiler Lab an der Vanderbilt University in Nashville Tennessee!"

Jaehnigen, S.; Grjasnow, A.; Meiler, J. "Chemische und strukturelle Biologie waehrend eines Praktikum in den USA" Faszination Chemie 2009, 14., p12-16

Marino, M. "Undergraduate Open House" Vanderbilt Reporter 2008, 4.

Lerner, M. "Europe's Brain Drain" European Hospital 2008, 17, 4.

Marino, M. "Program promotes greater diversity in molecular sciences" Vanderbilt Reporter 2007, 3.

Salisbury, D. F. "Campus 'supercomputer' helps decipher mysteries of science" Vanderbilt Register 2

Joetten, F. "Ich, der Roboter" Die Zeit 2007, 41, 42-43.

Meiler, J. "Kuenstliche Intelligenz in Chemie und Biologie" Faszination Chemie 2001, 7, 35-43.

Huixian Wu;Chong Wang, Karen J. Gregory, Gye Won Han, Hyekyung P. Cho, Yan Xia, Colleen M. Niswender, Vsevolod Katritch, Jens Meiler, Vadim Cherezov, P. Jeffrey Conn, Raymond C. Stevens
Structure of a Class C GPCR Metabotropic Glutamate Receptor 1 Bound to an Allosteric Modulator (2014) Science

Holger Jaeschke;Joerg Schaarschmidt, Markus Eszlinger, Sandra Huth, Rudolf Puttinger, Olaf Rittinger, Jens Meiler, Ralf Paschke
A newly discovered TSHR variant (L665F) associated with non-autoimmune hyperthyroidism in an Austrian family induces constitutive TSHR activation by steric repulsion between TM1 and TM7 (2014) Journal of Clinical Endocrinology & Metabolism

Ali I Kaya;Alyssa D. Lokits, James A. Gilbert, Tina M. Iverson, Jens Meiler, Heidi E. Hamm
A conserved phenylalanine as a relay between the ?5 helix and the GDP binding region of heterotrimeric Gi protein alpha subunit (2014) Journal of Biological Chemistry

Xavier Pedragosa-Badia;Gregory R. Sliwoski, Elizabeth Dong Nguyen, Diana Lindner, Jan Stichel, Kristian W. Kaufmann, Jens Meiler
Pancreatic Polypeptide Is Recognized by Two Hydrophobic Domains of the Human Y4 Receptor Binding Pocket (2014) Journal of Biological Chemistry

Claudia Doberenz;Michael Zorn, Dörte Falke, David Nannemann, Doreen Hunger, Lydia Beyer, Christian H. Ihling, Jens Meiler, Andrea Sinz, R. Gary Sawers
Pyruvate Formate-Lyase Interacts Directly with the Formate Channel FocA to Regulate Formate Translocation (2014) Journal of Molecular Biology

Karen Joan Gregory;Elizabeth D Nguyen, Chrysa Malosh, Jeffrey L Mendenhall, Jessica Z Zic, Brittney S Bates, Meredith J Noetzel, Emma F Squire, Eric M Turner, Jerri M. Rook, Kyle A Emmitte, Shaun R. Stauffer, Craig W Lindsley, Jens Meiler, and P. Jeffrey Conn
Identification of specific ligand-receptor interactions that govern binding and cooperativity of diverse modulators to a common metabotropic glutamate receptor 5 allosteric site (2014) ACS Chemical Neuroscience

Thomas Austin;David P. Nannemann, Sam DeLuca, Jens Meiler, Eric Delpire
In silico Analysis and Experimental Verification of OSR1 Kinase - Peptide Interaction (2014) Journal of Structural Biology

Gregory Sliwoski;Sandeepkumar Kothiwale, Jens Meiler, and Edward W. Lowe, Jr.
Computational Methods in Drug Discovery (2013) Pharmacol Rev

Congratulations, Dr. Butkiewicz! 2014-04-08

Mariusz Butkiewicz successfully defended his dissertation entitled: Advancing Quantitative Structure Activity Relationship Strategies in ligand-based Computer-Aided Drug Design. 


Congratulations, Dr. Willis! 2014-03-27

Jordan Willis successfully defended his dissertation entitled: Rational Antibody Design: From Mechanisms of Binding to Novel Vaccine Strategies.


Amanda Duran passed her qualifying exam! 2014-03-25

Congratulations! 


"Energetic analysis of the rhodopsin-G-protein complex links the alpha-5 helix to GDP release." gets a F1000 recommendation! 2014-03-20

http://f1000.com/prime/718194532#recommendations-content


"Scientists Create Most Detailed Picture Ever of Membrane Protein Linked to Learning, Memory, Anxiety, Pain and Brain Disorders" 2014-03-07

http://www.scripps.edu/news/press/2014/20140306stevens.html


Yan constructed a full length model of Metabotropic Glutamate Receptor 1 and docked a focused library of ligands according to their Structure-Activity Relation.


http://www.sciencemag.org/content/early/2014/03/05/science.1249489


Sign up now for the 2014 Rosetta Workshop 2014-02-18

Whether you are a Rosetta newcomer or an advanced user, you are invited to take part in our 2014 Rosetta workshop, April 28 - May 1, to learn how Rosetta can be used for protein modeling, with an emphasis of membrane proteins.  Details and Registration Information Tutorials from the 2011 workshop


After learning about using Rosetta to model membrane proteins, stick around to learn more about them at the Vanderbilt Center for Structural Biology conference entitled Biomolecular Structure, Dynamics, and Function: Membrane Proteins!


Register for the BSDF: Membrane Proteins Symposium! 2014-02-18

The Vanderbilt Center for Structural Biology is hosting the Biomolecular Structure, Dynamics, and Function: Membrane Proteins Symposium from May 2-4, 2014. The Early Registration deadline is March 1, 2014Details and Registration Information


BCL 3.1 released 2014-02-06

The BioChemical Library (BCL) version 3.1 is now released for Linux, Windows, and Apple and is available for download on meilerlab.org.  This release features a new single user academic license, which is now distributed via a webserver on the meilerlab.org website.  The new licensing systems enables users at academic and other non-profit institutions to receive a license file within seconds, along with an email detailing how to use it and install the BCL.  

This release also includes a number of bug fixes and enhancements, as well as a new application (protein:FusionProtein) for working with chimeric proteins.  Brief summaries of all released BCL applications are available on the bclcommons webpage.

Friends and collaborators outside the lab can download the newest release from meilerlab.org and use it with a license file obtained from http://www.meilerlab.org/servers/bcl-academic-license 


Daniel Putnam passes his qualifying exam 2014-01-10

Congratulations to Daniel!


“Interaction of a G protein with an activated receptor opens the interdomain interface in the alpha subunit” is a winner of the 2014 Vanderbilt Institute for Chemiical Biology's Highly-Cited Article Award 2014-01-06

The VICB award recognizes high-impact research by Vanderbilt researchers.  This publication is one of only 6 in the department with a sufficiently high impact (45 citations in total) for the 2014 awards.  


Yan Xia and Jessica Finn passed their qualification exams 2013-12-05

Congrats Yan and Jessica!


VU researchers report G protein advancement that could lead to more effective drugs 2013-12-03

http://news.vanderbilt.edu/2013/12/vu-researchers-report-g/


Dr. Edward W. Lowe, Jr. awarded state-of-the-art GPUs from NVIDIA 2013-11-07

Dr. Edward W. Lowe, Jr. received a second high performance GPU hardware award from NVIDIA for his work in accelerating algorithms important in biology and chemistry using multiple GPUs. Congrats Will!


Steven McIntyre receives Littlejohn fellowship 2013-08-30

Steven McIntyre, an undergraduate student advised by Axel Fischer in the Meiler laboratory, was selected as one of the first recipients of the Littlejohn fellowship. The fellowship encourages undergraduates to participate in research and scholarship across the humanities, natural sciences, and social sciences.  Congats Steven!


MeilerLab receives NSF grant to study GPCRs with structure activity relations 2013-08-30

Drs. Annette Beck-Sickinger and Torsten Schoeneberg from Leipzig University and Jens Meiler from Vanderbilt University receive a grant "Ensemble Docking Interrogates Structural Determinants of Ligand-Protein Interactions" that is jointly funded by the National Science Foundation (NSF) and the Deutsche Forschungsgemeinschaft (DFG). The grant will develop a novel docking algorithm that leverages Structure-Activity-Relations (SAR) and apply this algorithm to understand regulation of G-Protein Coupled Receptors (GPCRs).


Meet Dr. Combs 2013-08-16

Steven Combs successfully defended his dissertation entitled "Identification and Scoring of Partial Covalent Interactions in Proteins and Protein Ligand Complexes."  Congrats Steven!


MeilerLab to study Y-Receptor Ligands 2013-07-03
The Meiler and Weaver laboratories at Vanderbilt University received a grant
from the National Institute of Diabetes and Digestive and Kidney Diseases
(NIDDK, NIH) for the development of "Small Molecule Probes to Investigate
Structure and Function of Y Receptors". This project is a collaboration Annette
Beck-Sickinger at Leipzig University, Germany who is an expert on Y-receptor
biochemistry. The project is the first federally funded research grant that developed
under a collaboration of Vanderbilt and Leipzig Universities in chemical biology.
Vanderbilt-Leipzig collaborations strengthened with grant from Max Kade Foundation 2013-07-03
Vanderbilt University receives a grant from the Max Kade Foundation in support
of undergraduate and graduate student exchange in a collaboration with Leipzig
University spear-headed by Drs. Jens Meiler (Vanderbilt University) and Annette
Beck-Sickinger (Leipzig University).
Vanderbilt - Leipzig University Symposium and Workshop 2013-07-03
From July 6th to July 12th 2013 researchers from Vanderbilt and Leipzig University
meet in Leipzig for the 4th partnership symposium and scientific workshop.
Drs. Gurevich, Lybrand, Mchaourab, and Meiler from Vanderbilt University
participate in scientific presentations and meet faculty from Leipzig University.
The Memorandum of Understanding between the two institutions will be renewed
and faculty discuss the strategic objectives of the collaboration. Further, Dr. Lybrand
presents a workshop in "Molecular Modeling" and Dr. Mchaourab presents a workshop
in "Biomolecular EPR Spectroscopy" for graduate students
BCL 3.0 Released 2013-05-14

The BioChemical Library version 3.0 is available for download on meilerlab.org.  This release features our suite of cheminformatics and QSAR applications, along with new and improved extensions to bioinformatics applications, including JUFO9D, membrane-folding protocols, and SAXS simulation.

User-interface improvements include a friendlier command line interface that offers suggestions whenever options are mistyped, and earier to read help dialogues (and many more of them!),

Download the newest release from the bcl downloads page.


Darwin Fu selected for appointment to the Molecular Biophysics Training Grant 2013-05-10

Congratulations Darwin!


Stephanie Deluca receives NFB scholarship 2013-04-30

Stephanie is one of only 30 recipients of this year's National Federation of the Blind Fellowship, for which there were over 700 applicants.  Congratulations Stephanie!


Congratulations Tyler Gilcrest! 2013-04-25

Tyler Gilcrest, a VU undergraduate researcher in the Meiler Lab, graduated with honors from the Vanderbilt chemistry program. Tyler's performance earned him the Thomas W. Martin award for excelling in physical chemistry.  Excellent job Tyler!


Elizabeth Nguyen (co-) wins Vanderbilt's 3-minute thesis competition 2013-04-01

The 3 Minute Thesis competition sponsored by the Vanderbilt Graduate Student Council challenged graduate students in all fields across campus to present their thesis in only 3 minutes to a diverse audience. Students were challenged to present their research topic, explain how the research is conducted, and identify what impact it will have on the general or academic community. Elizabeth Nguyen, a graduate student in the Meiler Lab, received a co-first place prize for her presentation on "Progress Towards Unlocking the Treatment for Cognitive Impairment". Her research involves the computational modeling of G-protein coupled receptors, specifically metabatropic glutamate receptor 5 and its binding site for drugs used to treat schizophrenia and Fragile X Syndrome.


Amanda Duran receives 3-year stipend from the NSF 2013-03-29

Amanda's stipend will allow her to explore computational design of membrane protein ligand interactions.  Congratulations to Amanda!


Stephanie Deluca to give talk in 2013 Biophysics conference 2013-03-01

Stephanie will be giving a talk on RosettaEPR at the 2013 Biophysics conference in South Korea, May 22, at 10:15-10:30 AM


Meiler Lab receives grant to collaborate with researchers at Oak Ridge National Labs (ORNL) 2013-02-19

The Meiler lab receives an ORAU/ORNL High Performance Computing (HPC) Grant: "Investigation of the Mechanism of Cellulose Synthesis in Plants Using Neutron Scattering and High Performance Computing"


Gordon Lemmon receives Biosecurity Fellowship 2013-01-08

Dr. Lemmon received a fellowship from Emerging Leaders in Biosecurity Initiative to facilitate meeting with leaders in Biosecurity.


Sign up now for the 2012 Rosetta Workshop 2012-11-13

Whether you are a Rosetta newcomer or an advanced user, you are invited to take part in our 2012 Rosetta workshop, Nov 13-16, to learn how Rosetta can be used for protein structure prediction.  Details and Registration Information Tutorials from the 2011 workshop


Meiler Lab publication recommended by Faculty of 1000 2012-10-02

Faculty of 1000, a large group of researchers in the fields of biology and medicine that identify the most relevant research in the field, has recommend EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps., Structure, 2012


Brian Weiner was promoted to Research Assistant Professor in Chemistry 2012-09-08

Congrats Brian!


BCL CASP team awarded CASP10 attendance fellowship 2012-09-04

The BCL CASP team (Sten Heinze, Daniel Putnam, and Pedro Teixeira) have been awarded an attendance fellowship to defray the costs of attending the CASP conference.  Congrats to the BCL CASP team!


Dr. Edward W. Lowe awarded state-of-the-art GPU from NVIDIA 2012-08-23

Dr. Edward W. Lowe, Jr. received a high performance GPU hardware donation from NVIDIA for his work in accelerating algorithms important in biology and chemistry.  Congrats Will!


VICB research symposium successes 2012-08-09

The annual Vanderbilt Institute for Chemical Biology proved especially rewarding this year, with two winners from Meiler Lab. Daniel Putnam won an Ipad through a raffle.  Mariusz Butkiewicz co-authored a poster together with Rebecca Sandlin from the David Wright laboratory "Finding the Pathway: New Machine Learning Paradigms for the Identification of Lead Compound Targets from Phenotypic Antimalarial Assays" that won a poster prize.  Congratulations!


Daniel Putnam accepted into the HHMI/VUMC Certificate Program in Molecular Medicine 2012-08-06

Congrats Daniel!


Meiler Lab awarded R01 to investigate theraputic strategies using computational design of protein-ligand interfaces 2012-08-03

The Meiler lab was awarded a grant "Computational Design of Protein-Ligand Interfaces - a Therapeutic Strategy" from the NIH National Institute of General Medical Sciences (NIGMS). The grant will create advanced methodology to computationally design and experimentally verify protein-ligand interfaces. It will further explore use of these methods to create protein therapeutics for treatment of prostate cancer, bacterial infection, and cocaine overdosing.


RosettaCon 2012 2012-08-01

Gordon Lemmon, Steven Combs, Jordan Willis, and Sam DeLuca presented research talks at the Rosetta conference. The topics include: "Refactoring Rosetta for Chemistry", " Knowledge-Based Potentials for Partial Covalent Interactions", "Anti-HIV antibody design using Rosetta", and "RosettaQSAR - protein-ligand docking guided by pharmacophore maps"


Vanderbilt Leipzig collaboration to study Ligand -Macromolecule Recognition 2012-08-01

The Meiler laboratory was awarded a grant "Ligand-Macromolecule Recognition: A Collaboration in Research and Education Between Vanderbilt and Leipzig University" from the NSF Office of International Science and Engineering (OISE). It is the objective of this proposal to develop a sustainable collaboration in education and research between Vanderbilt and Leipzig Universities in the area of chemical biology.


Meiler Lab alumnus Dr. Steffen Lindert is awarded postdoc fellowship 2012-05-25

Congrats to Steffen, who received a postdoctoral fellowship from the American Heart Association


Dr. Edward W. Lowe Jr., and Dr. Nils Woetzel give talks at the 2012 GPU Technology Conference in San Jose, CA. 2012-05-15

The topics were Bcl::ChemInfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs, and  GPGPU Accelerated Protein Similarity Measures Identifying Biologically Relevant Structure


Congratulations Dr. Alexander! 2012-04-25

Dr. Nathan Alexander successfully defended his dissertation: Protein structure elucidation from computational techniques and sparse EPR data


Daniel Putnam defends research proposal! 2012-04-19

Daniel's research will be on the topic of Small Angle X-ray Scattering (SAXS) Restraints to Promote de Novo Protein Structure Prediction


Congratulations Dr. Koehler! 2012-04-11

Dr. Julia Koehler successfully defended her dissertation: Method development for membrane protein structure determination using NMR spectroscopy and computational techniques


Stephanie Hirst and Sam DeLuca receive travel awards! 2012-04-07

The awards provide financial support for presenting their research at the Computational Biophysics to Systems Biology (CBSB12) symposium.


Please join us in welcoming the Meiler Lab's newest graduate students: Amanda Duran and Yan Xia 2012-04-03

 


 


Stephanie Hirst receives prestigious NRSA fellowship! 2012-03-24

Stephanie Hirst receives the prestigious Ruth L. Kirschstein National Research Service Award (NRSA) from NIH for her project "Investigating the Role of Substrate Binding in LeuT Transport With RosettaEPR." Congrats Stephanie!


Meiler Lab receives an REU grant from the NSF 2012-03-24

The Meiler laboratory receives a Research Experiences for Undergraduates (REU) grant from NSF for research related to the CAREER award: "Cryo-EM guided de novo Protein Fold Elucidation"


Meiler Lab receives grant to investigate Y4 Receptor! 2012-03-24

The Meiler laboratory receives a pilot project grant from the Vanderbilt Diabetes Research and Training Center (DRTC) "Exploring Allosteric Modulators of Neuropeptide Y4 Receptor"


Congrats to Brittany Allsion for passing qualifying exams! 2012-03-09

Brittany presented her research plan entitled "Computational Design of Protein-Ligand Interfaces in (beta/alpha)8 Barrels for Applications in Protein Therapeutics"


Jordan Willis invited to give a talk 2012-01-12

Jordan Willis was invited to give an oral presentation at the Keystone Symposia on HIV Vaccines


Sam Deluca wins fellowship from Phrma foundation! 2011-12-09
Sam DeLuca, graduate student in the Meiler laboratory, wins an "Informatics" graduate student fellowship from the Phrma foundation. Sam's research focuses on computational modeling of protein-small molecule interactions for drug discovery.

Brittany Allison receives NSF fellowship! 2011-11-23

Brittany Allison, a chemistry student in the Meiler laboratory, received a prestigious National Science Foundation (NSF) Graduate Research Fellowship. Brittany works on computationally engineering proteins that bind small molecules. Her research has implications for understanding the fundamentals of protein-ligand interaction, engineering enzymes, and protein therapeutics. Brittany will start her fellowship after completing her training on the Chemical Biology Training Program, an NIH-funded initiative of Vanderbilt's Institute for Chemical Biology and the Chemistry Department.


Congrats to Sandeep Kothiwale for passing prequalifying exams 2011-11-11

Sandeep presented his research plan entitled "Enhancement of drug discovery tools through knowledge based conformational sampling and chemical shift predictions"


Congrats to Daniel Putnam: 2nd place Finalist in AMIA Student Paper Competition! 2011-10-28

Daniel Putnam's AMIA paper - "Exploring Schizophrenia Drug-Gene Interactions Through Molecular Network and Pathway Modeling", has been accepted as one of the eight finalists in the Student Paper Competition at the American Medical Informatics Association conference in October. Update 10/28/2011: Daniel was awarded 2nd place at the conference, congratulations, Daniel!


Congratulations Dr. Woetzel! 2011-09-28

Nils Woetzel successfully defended his thesis, “A novel approach to de novo protein structure prediction using knowledge based energy functions and experimental restraints."  


Zollie White receives Top Prize at the 2011 Herty Medalist Undergraduate Research Symposium 2011-09-19

Zollie White, an undergrad from Morehouse College, spent the summer of 2011 researching with Will Lowe in the Meiler Lab through the Vanderbilt REU program. He presented this research at the 2011 Herty Medalist Undergraduate Research Symposium held at Morehouse College was awarded the top prize. For this, he received a one-year membership to the American Chemical Society (ACS) and a $500 travel award to a national ACS conference. Congrats, Zollie!


Congratulations Dr. Karakas! 2011-09-01

Congrations to Mert Karakas for having successfully defended his thesis "BCL::Fold-De novo Protein Structure Prediction by Assembly of Secondary Structure Elements"


Will Lowe Receives NSF Fellowship 2011-08-12

Will Lowe received an NSF fellowship for his project "PROPMAP: A Novel GPU-accelerated Structure-Property Relationship Mapping Algorithm Utilizing Volunteer Computing." The prestigious award supports Dr. Lowe's research for three years in the Meiler Lab. Congrats, Will!


Liz Dong Receives DAAD Award 2011-08-08

Liz Dong of the Jens Meiler lab at Vanderbilt recently received a short term research grant to study at the Univeristy of Leipzig in Leipzig, Germany. She will spend one month this fall developing a computational method that will allow for the binding pose of a drug within a receptor to be determined. Her method will be guided by experimental data collected on drugs that bind G-protein coupled receptors, working with the lab of Torsten Schöneberg. Congrats, Liz!


Mariusz passes his qualifying exam! 2011-06-29

Mariusz passed his qualifying exam with his proposal: Comprehensive protein-ligand interaction mapping through quantitative structure activity relationships. Congratulations Mariusz!


Joe Crivelli's cancer research project in the Meiler lab covered in Vanderbilt's Arts and Sciences magazine! 2011-06-09

http://www.vanderbilt.edu/magazines/arts-and-science/2011-05/in-the-lab-early


Meiler lab undergraduate Zachary Glaser received early acceptance into VU Medical School 2011-06-09

Congratulations Zach!


Kelli Kazmier awarded a doctoral fellowship 2011-06-01

Kelli's was awarded an NIH NRSA doctoral fellowship to investigate "Conformational Changes Underlying Intracellular Gating of the Leucine
Transporter."  Congratulations Kelli!


Sten passes his qualifying exam! 2011-05-05

Sten passed his qualifying exam with his proposal: A novel approach
to de novo protein structure prediction using multiple partial templates. Congratulations Sten!


Ralf Mueller earns his PhD! 2011-05-04

Ralf successfully defended his thesis, Machine Learning Algorithms for Prediction of Biological Activity and Chemical Properties, earning his PhD,  Congratulations Ralf!


Congratulations to Dr. Jens Meiler 2011-04-29

Dr. Jens Meiler was promoted to Associate Professor with tenure.


Andrew Morin's Successful Ph.D. Defense 2011-04-26

Congratulations to Andrew Morin on successfully defending his PhD thesis on April 26, 2011. The thesis was presented on "The Computaional Design of Protein Ligand Interfaces".


Congratulations to Steven Combs !!! 2011-04-22

Steven Combs has successfully passed his qualifying exam on April 23, 2011 and proposed his research on "Thermostabilization of industrially relevant proteins through computational design of partial covalent interactions".


Grant awarded from Vanderbilt University Discovery Grant. 2011-04-22

Meiler Laboratory has been awarded Vanderbilt University Discovery Grant for research on "De novo Design of Large protein".


Best Oral Presentation at CPB retreat from Meiler Lab 2011-04-22

Liz Dong has won best oral presentation prize at Chemical & Physical Biology retreat at Nashville Zoo on April 18, 2011. She gave her oral presentation on "Structural studies of the interaction between mDlu5 and allosteric modulator". Congratulations to Liz !!!


Julia Koehler Won Travel Grant!! 2011-04-18

Julia Koehler won a travel grant to attend the Gordon Research Conference "Computational Aspects - Biomolecular NMR" in May 2011 and will present her work on " De novo membrane protein folding from sparse NMR data ". Congratulations!!!


Brittany's Preliminary Qualification Exam 2011-04-06

Brittany Allison, a graduate student at Meiler Lab has successfully passed her Priliminary Qualification Exam on April 6, 2011.


Summer Student from Meiler Lab Won Goldwater Fellowship 2011-04-01

Louesa Akin is a undergraduate student attending Centre College in Kentucky who pursues research in the Meiler laboratory focused on Membrane Protein Structure Prediction using sparse NMR restraints. She was selected to receive the Goldwater Scholarship for undergraduate students. Louesa participated in the Summer Science Academy program in summer 2010 and will participate in the Research Experience for Undergraduates in chemical biology in summer 2011. 


Congratulations to Elizabeth Dong!!! 2011-04-01

Liz Dong is a MD/PhD student in the second year of her graduate studies. She won the prestigious PhRMA-Paul Calabresi Medical Student Research Fellowship. The fellowship is offered to medical students who have substantial interests in research and teaching careers in pharmacology - clinical pharmacology. Liz works on new technologies in the Meiler laboratory to develop allosteric modulators of metabotropic glutamate receptors, important targets for many neurological diseases.


David Nannemann - Dissertation Defense on March 25th 2011 2011-03-24

David Nannemann will be defending his Doctoral research on "Directed Biosynthesis of the Nucleoside Analog Drug Didanosine", at the Stevenson Center, Room 5502, 2:00 pm.


Stephanie Hirst successfully passed her Qualifying Exam 2011-02-11

Stephanie Hirst unconditionally  passed her Qualifying Exam on February 3, 2011 and the proposal was called "Structural Elucidation of the Role of Na+ and Leucine Binding in the LeuT Transport Mechanism using ROSETTAEPR". Congratulations to Stephanie!!!


Steffen Lindert successfully defends his research dissertation 2010-12-13

Steffen presented his doctoral research dissertation “CryoEM guided de-novo protein folding” on November 22nd, 2010. His thesis committee approved his presentation and accepted his research, making him the first to complete the  Chemical and Physical Biology PhD Program. Congratulations, Steffen!!


Meiler Lab member Steffen Lindert receives NIH travel award to give a presentation in Hawaii. 2010-12-13

Steffen Lindert will give a presentation at the Pacific Symposium on Biocomputing in January on Hawaii (about EM-Fold and our results participating in the cryoEM modeling challenge). He received an NIH travel award to cover the costs associated with the conference.


Liz Dong successfully passed her Qualifying Exam in September 2010-12-13

Congratulations to Liz Dong, an MD/PhD student in the Meiler lab, on her successful completion of qualifying exams on 9/2/2010


Meiler Lab Publication Makes the List of Top 20 Most Downloaded Biochemistry Articles! 2010-12-08

Congratulations to Meiler Lab members Kristian W. Kaufmann, Gordon H. Lemmon, Samuel L. DeLuca, and CSB outreach coordinator, Jonathan H. Sheehan! Their recent publication, "Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You" made the list of the TOP 20 most downloaded articles from the journal Biochemistry