Publications by authors named "Peter Minary"

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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, Peter Minary

NAR Genom Bioinform· June 2025

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Learning to quantify uncertainty in off-target activity for CRISPR guide RNAs.
Furkan Özden, Peter Minary

Nucleic Acids Res· October 2024

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Be-dataHIVE: a base editing database.
Lucas Schneider, Peter Minary

BMC Bioinformatics· October 2024

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The Evolution of Nucleic Acid-Based Diagnosis Methods from the (pre-)CRISPR to CRISPR era and the Associated Machine/Deep Learning Approaches in Relevant RNA Design.
Shruti Sarika Chakraborty, Jayati Ray Dutta, Ramakrishnan Ganesan, Peter Minary

Methods Mol Biol· September 2024

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piCRISPR: Physically informed deep learning models for CRISPR/Cas9 off-target cleavage prediction.
Florian Störtz, Jeffrey K Mak, Peter Minary

Artif Intell Life Sci· December 2023

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Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity.
Jeffrey K Mak, Florian Störtz, Peter Minary

BMC Genomics· December 2022

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crisprSQL: a novel database platform for CRISPR/Cas off-target cleavage assays.
Florian Störtz, Peter Minary

Nucleic Acids Res· January 2021

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Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities.
Jeng-Yih Chang, Zhicheng Cui, Kailu Yang, Jianhua Huang, Peter Minary

RNA· December 2020

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Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences.
Hector Zenil, Peter Minary

Nucleic Acids Res· November 2019

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HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.
Samuel Demharter, Bernhard Knapp, Charlotte Deane, Peter Minary

J Chem Inf Model· June 2019

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In silico structural modeling of multiple epigenetic marks on DNA.
Konrad Krawczyk, Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary

Bioinformatics· January 2018

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Tertiary Element Interaction in HIV-1 TAR.
Konrad Krawczyk, Adelene Y L Sim, Bernhard Knapp, Charlotte M Deane, Peter Minary

J Chem Inf Model· September 2016

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Modeling Functional Motions of Biological Systems by Customized Natural Moves.
Samuel Demharter, Bernhard Knapp, Charlotte M Deane, Peter Minary

Biophys J· August 2016

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Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.
Bernhard Knapp, Samuel Demharter, Charlotte M Deane, Peter Minary

Bioinformatics· January 2016

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Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands.
Ignacio Moraga, Gerlinde Wernig, Stephan Wilmes, Vitalina Gryshkova, Christian P Richter, Peter Minary

Cell· March 2015

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Training-free atomistic prediction of nucleosome occupancy.
Peter Minary, Michael Levitt

Proc Natl Acad Sci U S A· April 2014

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Modeling nucleic acids.
Adelene Y L Sim, Peter Minary, Michael Levitt

Curr Opin Struct Biol· June 2012

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Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images.
Junjie Zhang, Peter Minary, Michael Levitt

Proc Natl Acad Sci U S A· June 2012

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Modeling and design by hierarchical natural moves.
Adelene Y L Sim, Michael Levitt, Peter Minary

Proc Natl Acad Sci U S A· February 2012

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Conformational optimization with natural degrees of freedom: a novel stochastic chain closure algorithm.
Peter Minary, Michael Levitt

J Comput Biol· August 2010

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Probing protein fold space with a simplified model.
Peter Minary, Michael Levitt

J Mol Biol· January 2008

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Ab initio molecular dynamics: concepts, recent developments, and future trends.
Radu Iftimie, Peter Minary, Mark E Tuckerman

Proc Natl Acad Sci U S A· May 2005

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Reaction mechanism of cis-1,3-butadiene addition to the Si(100)-2 x 1 surface.
Peter Minary, Mark E Tuckerman

J Am Chem Soc· February 2005

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Long range interactions on wires: a reciprocal space based formalism.
Peter Mináry, Joseph A Morrone, Dawn A Yarne, Mark E Tuckerman, Glenn J Martyna

J Chem Phys· December 2004

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Reaction pathway of the [4 + 2] Diels-Alder adduct formation on Si(100)-2 x 1.
Peter Minary, Mark E Tuckerman

J Am Chem Soc· November 2004

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