Standout Papers
Citation Impact
Citing Papers
On the relationship between folding and chemical landscapes in enzyme catalysis
2008 StandoutNobel
Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation
2014 StandoutScienceNobel
DNA capture by a CRISPR-Cas9–guided adenine base editor
2020 StandoutScienceNobel
Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage
2016 StandoutScienceNobel
Ion motions in molecular dynamics simulations on DNA
2004
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Comprehensive computational design of ordered peptide macrocycles
2017 StandoutScienceNobel
Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O 2 activation
2019 StandoutNobel
Origins of coevolution between residues distant in protein 3D structures
2017 StandoutNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
Protein structure determination using metagenome sequence data
2017 StandoutScienceNobel
Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich era
2013 StandoutNobel
Hallucinating symmetric protein assemblies
2022 StandoutScienceNobel
Allosteric transcriptional regulation via changes in the overall topology of the core promoter
2015 Science
High‐accuracy refinement using Rosetta in CASP13
2019 StandoutNobel
Structures of the RNA-guided surveillance complex from a bacterial immune system
2011 StandoutNatureNobel
De novo design of allosterically switchable protein assemblies
2024 StandoutNatureNobel
Structure-based protein design with deep learning
2021
Endonuclease V cleaves at inosines in RNA
2013
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
2013
Tuning in to Interference: R-Loops and Cascade Complexes in CRISPR Immunity
2012
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
2010 Standout
Molecular dynamics simulations and their application to four-stranded DNA
2007
Long-Residency Hydration, Cation Binding, and Dynamics of Loop E/Helix IV rRNA-L25 Protein Complex
2004
Elbow Flexibility of the kt38 RNA Kink-Turn Motif Investigated by Free-Energy Molecular Dynamics Simulations
2009
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch
2009
Molecular Dynamics Simulation for All
2018 Standout
Exploring the role of large conformational changes in the fidelity of DNA polymerase β
2007 StandoutNobel
ACPYPE - AnteChamber PYthon Parser interfacE
2012 Standout
Protein folding and de novo protein design for biotechnological applications
2013
Molecular dynamics simulations of RNA: An in silico single molecule approach
2006
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy
2017 StandoutNatureNobel
The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA
2016 StandoutNatureNobel
Crystal structure of a monomeric retroviral protease solved by protein folding game players
2011 StandoutNobel
The coming of age of de novo protein design
2016 StandoutNatureNobel
Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge
2004
RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics
2006
Oncogenic Mutations Counteract Intrinsic Disorder in the EGFR Kinase and Promote Receptor Dimerization
2012 StandoutNobel
RNA-guided genetic silencing systems in bacteria and archaea
2012 StandoutNatureNobel
Nucleic acid solvation: from outside to insight
2007
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
Long-timescale molecular dynamics simulations of protein structure and function
2009
A short guide for molecular dynamics simulations of RNA systems
2008
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
2006 Standout
Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM
2009 StandoutNobel
Biomolecular modeling and simulation: a field coming of age
2011
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps
2018
Structural basis for CRISPR RNA-guided DNA recognition by Cascade
2011 StandoutNobel
Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering
2016 StandoutNobel
KoBaMIN: a knowledge-based minimization web server for protein structure refinement
2012 StandoutNobel
A computational approach for predicting off-target toxicity of antiviral ribonucleoside analogues to mitochondrial RNA polymerase
2018 StandoutNobel
Refinement of protein structure homology models via long, all‐atom molecular dynamics simulations
2012
Tertiary Structural Propensities Reveal Fundamental Sequence/Structure Relationships
2015
The Biology of CRISPR-Cas: Backward and Forward
2018 StandoutNobel
Why nature really chose phosphate
2013 StandoutNobel
Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics
2007
Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing
2012
Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps
2005
Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations
2005
Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA
2007
RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions
2011 StandoutNobel
Quantitative exploration of the molecular origin of the activation of GTPase
2013 StandoutNobel
The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals
2007 Standout
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
2007
Converting structural information into an allosteric-energy-based picture for elongation factor Tu activation by the ribosome
2011 StandoutNobel
Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields
2009
Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations
2006
Molecular Dynamics and Free Energy Study of the Conformational Equilibria in the UUUU RNA Hairpin
2007
Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase
2018 StandoutNobel
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
2015 Standout
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
2013 Standout
Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning
2015 StandoutScienceNobel
Evaluation of template‐based modeling in CASP13
2019
Ion-dependent protein–surface interactions from intrinsic solvent response
2021 StandoutNobel
2015 StandoutNobel
Critical assessment of methods of protein structure prediction (CASP)—Round XIII
2019
Significant Refinement of Protein Structure Models Using a Residue-Specific Force Field
2015
A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations
2020
CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference
2014 StandoutNobel
Modeling and design by hierarchical natural moves
2012 StandoutNobel
Algorithm discovery by protein folding game players
2011 StandoutNobel
De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
2017 StandoutNobel
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
2017
Protein Structure Refinement through Structure Selection and Averaging from Molecular Dynamics Ensembles
2012
Modular repeat protein sculpting using rigid helical junctions
2020 StandoutNobel
A consistent and accurateab initioparametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
2010 Standout
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
2018
Computational protein structure refinement: almost there, yet still so far to go
2017
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
Designing and defining dynamic protein cage nanoassemblies in solution
2016
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
2019
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters
2013
Assessment of the model refinement category in CASP12
2017
Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
2014
Assessment of refinement of template‐based models in CASP11
2016
Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles
2011
Physics‐based protein structure refinement through multiple molecular dynamics trajectories and structure averaging
2013
Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations
2016
Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases
2009 StandoutNobel
Reconfigurable asymmetric protein assemblies through implicit negative design
2022 StandoutScienceNobel
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
2013 Standout
Evaluation of model refinement in CASP13
2019
Simulating the Effect of DNA Polymerase Mutations on Transition-State Energetics and Fidelity: Evaluating Amino Acid Group Contribution and Allosteric Coupling for Ionized Residues in Human Pol β
2006 StandoutNobel
Molecular dynamics simulation of triclinic lysozyme in a crystal lattice
2015
Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors
2020
Works of Alberto Pérez being referenced
Accelerating molecular simulations of proteins using Bayesian inference on weak information
2015
Theoretical methods for the simulation of nucleic acids
2003
Toward a Consensus View of Duplex RNA Flexibility
2010
Relative Flexibility of DNA and RNA: a Molecular Dynamics Study
2004
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
2007 Standout
Recent advances in the study of nucleic acid flexibility by molecular dynamics
2008
Data Mining of Molecular Dynamics Trajectories of Nucleic Acids
2006
Towards a molecular dynamics consensus view of B-DNA flexibility
2008
A consensus view of protein dynamics
2007
The relative flexibility of B-DNA and A-RNA duplexes: database analysis
2004
Exploring polymorphisms in B-DNA helical conformations
2012
A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA
2009
Theoretical study of large conformational transitions in DNA: the B↔A conformational change in water and ethanol/water
2007
Assessment of protein structure refinement in CASP9
2011
Parmbsc1: a refined force field for DNA simulations
2015
Advances in free-energy-based simulations of protein folding and ligand binding
2016
Are the Hydrogen Bonds of RNA (A⋅U) Stronger Than those of DNA (A⋅T)? A Quantum Mechanics Study
2005
FlexE: Using Elastic Network Models to Compare Models of Protein Structure
2012
Integrative Modeling of Protein Conformational Ensembles using Limited Data
2013
Blind protein structure prediction using accelerated free-energy simulations
2016
NMR‐assisted protein structure prediction with MELDxMD
2019
Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer
2012
Dynamics of B-DNA on the Microsecond Time Scale
2007
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference
2015
MELD × MD Folds Nonthreadables, Giving Native Structures and Populations
2018
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
2015
Geometrical and Electronic Structure Variability of the Sugar−phosphate Backbone in Nucleic Acids
2008
Structure, Recognition Properties, and Flexibility of the DNA·RNA Hybrid
2005
Frontiers in Molecular Dynamics Simulations of DNA
2011