Peter Minary : Publications
Journal papers
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[1]
Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR–Cas9 off−target activity
Jeffrey Kelvin Mak‚ Artemi Bendandi‚ José Augusto Salim‚ Ivan Mazoni‚ Fabio Rogerio de Moraes‚ Luiz Borro‚ Florian Störtz‚ Walter Rocchia‚ Goran Neshich and Peter Minary
In NAR Genomics and Bioinformatics. Vol. 7. No. 2. Pages lqaf054. 2025.
Details about Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR–Cas9 off−target activity | BibTeX data for Learning to utilize internal protein 3D nanoenvironment descriptors in predicting CRISPR–Cas9 off−target activity
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[2]
Learning to quantify uncertainty in off−target activity for CRISPR guide RNAs
Furkan Ozden and Peter Minary
In Nucleic Acids Research. Vol. 52. No. 18. Pages e87. October, 2024.
Details about Learning to quantify uncertainty in off−target activity for CRISPR guide RNAs | BibTeX data for Learning to quantify uncertainty in off−target activity for CRISPR guide RNAs | DOI (10.1093/nar/gkae759) | Link to Learning to quantify uncertainty in off−target activity for CRISPR guide RNAs
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[3]
piCRISPR: physically informed deep learning models for CRISPR/Cas9 off−target cleavage prediction
Florian Störtz‚ Jeffrey K Mak and Peter Minary
In Artificial Intelligence in the Life Sciences. Vol. 3. Pages 100075. 2023.
Details about piCRISPR: physically informed deep learning models for CRISPR/Cas9 off−target cleavage prediction | BibTeX data for piCRISPR: physically informed deep learning models for CRISPR/Cas9 off−target cleavage prediction
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[4]
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo
Bernhard Knapp‚ Samuel Demharter‚ Charlotte M Deane and Peter Minary
In Bioinformatics. Pages btv502. 2015.
Details about Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo | BibTeX data for Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo
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[5]
Training−free atomistic prediction of nucleosome occupancy
Peter Minary and Michael Levitt
In Proceedings of the National Academy of Sciences. Vol. 111. No. 17. Pages 6293–6298. 2014.
Details about Training−free atomistic prediction of nucleosome occupancy | BibTeX data for Training−free atomistic prediction of nucleosome occupancy
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[6]
Modeling and design by hierarchical natural moves
Adelene YL Sim‚ Michael Levitt and Peter Minary
In Proceedings of the National Academy of Sciences. Vol. 109. No. 8. Pages 2890–2895. 2012.
Details about Modeling and design by hierarchical natural moves | BibTeX data for Modeling and design by hierarchical natural moves
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[7]
Multiscale natural moves refine macromolecules using single−particle electron microscopy projection images
Junjie Zhang‚ Peter Minary and Michael Levitt
In Proceedings of the National Academy of Sciences. Vol. 109. No. 25. Pages 9845–9850. 2012.
Details about Multiscale natural moves refine macromolecules using single−particle electron microscopy projection images | BibTeX data for Multiscale natural moves refine macromolecules using single−particle electron microscopy projection images
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[8]
Modeling nucleic acids
Adelene YL Sim‚ Peter Minary and Michael Levitt
In Current Opinion in Structural Biology. 2012.
Details about Modeling nucleic acids | BibTeX data for Modeling nucleic acids
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[9]
Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm
Peter Minary and Michael Levitt
In Journal of Computational Biology. Vol. 17. No. 8. Pages 993–1010. 2010.
Details about Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm | BibTeX data for Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm
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[10]
Probing protein fold space with a simplified model
Peter Minary and Michael Levitt
In Journal of molecular biology. Vol. 375. No. 4. Pages 920. 2008.
Details about Probing protein fold space with a simplified model | BibTeX data for Probing protein fold space with a simplified model
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[11]
Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure
Peter Minary‚ Mark E Tuckerman and Glenn J Martyna
In SIAM Journal on Scientific Computing. Vol. 30. No. 4. Pages 2055–2083. 2008.
Details about Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure | BibTeX data for Dynamical spatial warping: A novel method for the conformational sampling of biophysical structure
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[12]
Discussion of" EQUI−energy sampler" by Kou‚ Zhou and Wong
P Minary and M Levitt
In Ann. Stat.. Vol. 34. No. math. ST/0611221. Pages 1636–1641. 2006.
Details about Discussion of" EQUI−energy sampler" by Kou‚ Zhou and Wong | BibTeX data for Discussion of" EQUI−energy sampler" by Kou‚ Zhou and Wong
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[13]
Reaction Mechanism of cis−1‚ 3−Butadiene Addition to the Si (100)−2 1 Surface
Peter Minary and Mark E Tuckerman
In Journal of the American Chemical Society. Vol. 127. No. 4. Pages 1110–1111. 2005.
Details about Reaction Mechanism of cis−1‚ 3−Butadiene Addition to the Si (100)−2 1 Surface | BibTeX data for Reaction Mechanism of cis−1‚ 3−Butadiene Addition to the Si (100)−2 1 Surface
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[14]
Ab initio molecular dynamics: Concepts‚ recent developments‚ and future trends
Radu Iftimie‚ Peter Minary and Mark E Tuckerman
In Proceedings of the National Academy of Sciences of the United States of America. Vol. 102. No. 19. Pages 6654–6659. 2005.
Details about Ab initio molecular dynamics: Concepts‚ recent developments‚ and future trends | BibTeX data for Ab initio molecular dynamics: Concepts‚ recent developments‚ and future trends
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[15]
Long range interactions on wires: A reciprocal space based formalism
Peter Mináry‚ Joseph A Morrone‚ Dawn A Yarne‚ Mark E Tuckerman and Glenn J Martyna
In The Journal of chemical physics. Vol. 121. Pages 11949. 2004.
Details about Long range interactions on wires: A reciprocal space based formalism | BibTeX data for Long range interactions on wires: A reciprocal space based formalism
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[16]
Reaction Pathway of the [4+ 2] Diels−Alder Adduct Formation on Si (100)−2 1
Peter Minary and Mark E Tuckerman
In Journal of the American Chemical Society. Vol. 126. No. 43. Pages 13920–13921. 2004.
Details about Reaction Pathway of the [4+ 2] Diels−Alder Adduct Formation on Si (100)−2 1 | BibTeX data for Reaction Pathway of the [4+ 2] Diels−Alder Adduct Formation on Si (100)−2 1
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[17]
Long time molecular dynamics for enhanced conformational sampling in biomolecular systems
P Minary‚ ME Tuckerman and GJ Martyna
In Physical review letters. Vol. 93. No. 15. Pages 150201. 2004.
Details about Long time molecular dynamics for enhanced conformational sampling in biomolecular systems | BibTeX data for Long time molecular dynamics for enhanced conformational sampling in biomolecular systems
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[18]
Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics
Peter Minary‚ Glenn J Martyna and Mark E Tuckerman
In The Journal of chemical physics. Vol. 118. Pages 2527. 2003.
Details about Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics | BibTeX data for Algorithms and novel applications based on the isokinetic ensemble. II. Ab initio molecular dynamics
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[19]
Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics
Peter Minary‚ Glenn J Martyna and Mark E Tuckerman
In The Journal of chemical physics. Vol. 118. Pages 2510. 2003.
Details about Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics | BibTeX data for Algorithms and novel applications based on the isokinetic ensemble. I. Biophysical and path integral molecular dynamics
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[20]
A new reciprocal space based treatment of long range forces on surfaces
ME Tuckerman‚ P Minary‚ K Pihakari and GJ Martyna
In J. Chem. Phys. Vol. 116. Pages 5351. 2002.
Details about A new reciprocal space based treatment of long range forces on surfaces | BibTeX data for A new reciprocal space based treatment of long range forces on surfaces