Gregory W. Stull, Michael J. Moore, Venkata S. Mandala, Norman A. Douglas, Heather-Rose Kates, Xinshuai Qi, Samuel F. Brockington, Pamela S. Soltis, Douglas E. Soltis and Matthew A. Gitzendanner. A Targeted Enrichment Strategy for Massively Parallel Sequencing of Angiosperm Plastid… Read More
Power-performance Co-optimization of Throughput Core Architecture using Resistive Memory
Nilanjan Goswami, Bingyi Cao, Tao Li. Power-performance Co-optimization of Throughput Core Architecture using Resistive Memory IEEE International Symposium on High Performance Computer Architecture, 2013-01-25 Abstract: Massively parallel computing on throughput computers such as GPUs requires myriad memory accesses to register… Read More
Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase.
Yang Y, Chakravorty DK, Merz KM Jr.. Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase. Biochemistry. 2010 Nov 9;49(44):9658-66, 2010-10-05 Abstract: Studies aimed at elucidating the unknown Mg2+ binding site… Read More
Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins
Chakravorty DK, Parker TM, Guerra AJ, Sherrill CD, Giedroc DP, Merz KM Jr.. Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins J Am Chem Soc. 2013 Jan 9;135(1):30-3, 2012-12-26 Abstract: A metal-mediated interprotomer hydrogen bond has… Read More
pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4
Natali V. Di Russo, Dario A. Estrin, Marcelo A. Martí mail and Adrian E. Roitberg. pH-Dependent Conformational Changes in Proteins and Their Effect on Experimental pKas: The Case of Nitrophorin 4 PLoS Comput Biol. 2012 November; 8(11): e1002761, 2012-11-01 Abstract:… Read More
pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method
Danial Sabri Dashti, Yilin Meng and Adrian E. Roitberg . pH-Replica Exchange Molecular Dynamics in Proteins Using a Discrete Protonation Method J. Phys. Chem. B, 2012, 116 (30), pp 8805–8811, 2012-06-13 Abstract: Protonation equilibria in biological molecules modulates structure, dynamics,… Read More
Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations
Yilin Meng Danial Sabri Dashti and Adrian E. Roitberg. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations J. Chem. Theory Comput., 2011, 7 (9), pp 2721–2727, 2011-07-28 Abstract: Alchemical free energy calculations play a very important… Read More
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