Biosciences Graduate Program

Michael J. Schnieders, PhD


Assistant Professor
Assistant Professor of Biochemistry
Assistant Professor of Biomedical Engineering

Contact Information

Primary Office: 4-516 Bowen Science Building
Iowa City, IA 52242
Phone: 319-335-7891

Office: 5013 Seamans Center for the Engineering Arts and Sciences
Iowa City, IA 52242

Lab: 4-508 Bowen Science Building
Iowa City, IA 52242
Phone: 319-335-6723

Web: Schnieders Laboratory
Web: Biomedical Engineering Department Profile
Web: Force Field X Software


BS, Biomedical Engineering , The University of Iowa
PhD, Biomedical Engineering, Washington University in St. Louis

Post Doctorate, Chemistry, Stanford University
Post Doctorate, Biomedical Engineering, The University of Texas

Education/Training Program Affiliations

Biosciences Graduate Program
Department of Biochemistry PhD
Department of Pharmacology Graduate Program
Interdisciplinary Graduate Program in Informatics
Medical Scientist Training Program

Research Summary

Our lab is focused on molecular biophysics theory and high performance computational algorithms that are needed to reduce the time and cost of engineering drugs and organic biomaterials. A complementary goal is to help open the door to personalized medicine by developing tools to map genetic information onto molecular phenotypes.

1. Next Generation Macromolecular X-ray Crystallography X-ray crystallography is a critical experimental method used by biochemists to determine the structure and function of the biomolecular foundations of medicine. We have recently demonstrated that the chemical information contained in a polarizable force field called AMOBEA significantly improves DNA and protein structures compared to X-ray refinements done with previous generation theory. We are now working to model experimental X-ray diffraction data as an ensemble using Bayesian inference.

2. Prediction of the Structure, Thermodynamics and Solubility of Drug Tablets Important unsolved problems for the engineering of organic biomaterials include prediction of their structure, thermodynamic stability and solubility from first principles. Solubility is the saturating concentration of a molecule within a liquid solvent, where the physical process consists of solvated molecules in equilibrium with their solid phase. We have developed the first consistent procedure for the prediction of the structure, thermodynamic stability, and solubility of organic crystals using molecular dynamics simulations. Currently the methodology is being extended to predict the properties for a range of organic crystals, including both pharmaceuticals and peptide models of neurological aggregation diseases.

3. Personalized Medicine: From Genome Sequencing to Molecular Phenotypes Since 2001, the cost to sequence a patient’s genome has fallen from $100 million to approximately $1,000. The rapid achievement of affordable genetic information is outpacing our ability to fully capitalize on opportunities to provide personalized healthcare. To help address this challenge, we are collaborating with The University of Iowa Center for Bioinformatics and Computational Biology to develop tools that tightly couple bioinformatics to the computational prediction of biomolecular structure, thermodynamics and kinetics.

4. Biomolecular Electrostatics and High-Performance Computing Application such as X-ray crystallography refinement, biomaterials thermodynamics and personalized medicine depend on an accurate, efficient description of molecular energetics. Our lab contributes a parallelized molecular biophysics computer code called Force Field X that includes novel biomolecular electrostatics algorithms such as particle-mesh Ewald with support for space group symmetry and the generalized Kirkwood implicit solvent model.

Center, Program and Institute Affiliations

Center for Biocatalysis and Bioprocessing
Center for Bioinformatics and Computational Biology
Holden Comprehensive Cancer Center
Iowa Initiative in Human Genetics
Stephen A. Wynn Institute for Vision Research

Selected Publications

Show All

Booth K, Azaiez H, Kahrizi K, Simpson A, Tollefson W, Sloan C, Meyer N, Schnieders M, Najmabadi H, Smith R.  PDZD7 and Hearing Loss: More Than Just a Modifier.  American Journal of Medical Genetics Part A.  2015 September 29. 

LuCore S, Litman J, Powers K, Gao S, Lynn A, Tollefson W, Fenn T, Washington M, Schnieders M.  Dead-End Elimination with a Polarizable Force Field Repacks PCNA Structures.  Biophysical Journal.  2015 August 18. 109(4):816-826.

Bu F, Borsa N, Jones M, Takanami E, Nishimura C, Hauer J, Azaiez H, Black-Ziegelbein E, Meyer N, Kolbe D, Li Y, Frees K, Schnieders M, Thomas C, Nester C, Smith R.  High-throughput Genetic Testing for the Thrombotic Microangiopathies and C3 Glomerulopathies.  Journal of the American Society of Nephrology.  2015 August 17. 

Lagardère L, Lipparini F, Stamm B, Schnieders M, Cances E, Ren P, Maday Y, Piquemal J.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations Using Smooth Particle Mesh Ewald.  Journal of Chemical Theory and Computation.  2015 May 21. 11(6):2589–2599.

Shi Y, Schnieders M, Piquemal J, Ren P.  Polarizable Force Fields for Biomolecular Modeling.  Reviews in Computational Chemistry.  2015 May 1. 28:51-86.

Lipparini F, Lagardère L, Raynaud C, Stamm B, Cancès E, Mennucci B, Schnieders M, Ren P, Maday Y, Piquemal J.  Polarizable Molecular Dynamics in a Polarizable Continuum Solvent.  Journal of Chemical Theory and Computation.  2015 January. 11(2):623–634.

Park J, Nessler I, McClain B, Macikenas D, Baltrusaitis J, Schnieders M.  Absolute Organic Crystal Thermodynamics: Growth of the Asymmetric Unit into a Crystal via Alchemy.  Journal of Chemical Theory and Computation.  2014 May 20. 10(7):2781–2791.

Lipparini F, Lagardère L, Stamm B, Cancès E, Schnieders M, Ren P, Maday Y, Piquemal J.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: I. Toward Massively Parallel Direct Space Computations.  Journal of Chemical Theory and Computation.  2014 February 28. 10(4):1638–1651.

Schnieders M, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P.  The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field.  Journal of Chemical Theory and Computation.  2012 May. 8(5):1721-1736.

Schnieders M, Kaoud T, Yan C, Dalby K, Ren P.  Computational insights for the discovery of non-ATP competitive inhibitors of MAP kinases.  Current Pharmaceutical Design.  2012. 18(9):1173-1185.

Date Last Modified: 09/17/2015 - 08:59:05