Standout Papers
- SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations (2012)
- An overview of the Amber biomolecular simulation package (2012)
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born (2012)
- Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald (2013)
- Advances in Rosetta protein structure prediction on massively parallel systems (2008)
Citation Impact
Citing Papers
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
2014 StandoutNobel
DNA capture by a CRISPR-Cas9–guided adenine base editor
2020 StandoutScienceNobel
CRISPR–Cas9 Structures and Mechanisms
2017 StandoutNobel
Global analysis of protein folding using massively parallel design, synthesis, and testing
2017 StandoutScienceNobel
Protein homology model refinement by large-scale energy optimization
2018 StandoutNobel
Comprehensive computational design of ordered peptide macrocycles
2017 StandoutScienceNobel
A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9
2017 StandoutNobel
Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble
2018 StandoutNobel
Improved protein structure prediction using predicted interresidue orientations
2020 StandoutNobel
De novo design of transmembrane β barrels
2021 StandoutScienceNobel
Computational design of closely related proteins that adopt two well-defined but structurally divergent folds
2020 StandoutNobel
Structures of the CRISPR genome integration complex
2017 StandoutScienceNobel
Accurate computational design of multipass transmembrane proteins
2018 StandoutScienceNobel
De novo design of picomolar SARS-CoV-2 miniprotein inhibitors
2020 StandoutScienceNobel
Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2
2020 StandoutScience
High‐accuracy refinement using Rosetta in CASP13
2019 StandoutNobel
CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity
2018 StandoutScienceNobel
Incorporation of sensing modalities into de novo designed fluorescence-activating proteins
2021 StandoutNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Structural insights into µ-opioid receptor activation
2015 NatureNobel
Aromatic Rings in Chemical and Biological Recognition: Energetics and Structures
2011
Supramolecular Binding Thermodynamics by Dispersion‐Corrected Density Functional Theory
2012 Standout
QM/MM Methods for Biomolecular Systems
2009 Standout
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
2015
Structural mechanisms of selectivity and gating in anion channelrhodopsins
2018 NatureNobel
Channel opening and gating mechanism in AMPA-subtype glutamate receptors
2017 StandoutNatureNobel
Structure of the µ-opioid receptor–Gi protein complex
2018 NatureNobel
The road to fully programmable protein catalysis
2022 StandoutNatureNobel
Molecular Dynamics Simulation for All
2018 Standout
A single residue switch reveals principles of antibody domain integrity
2018
Why copper is preferred over iron for oxygen activation and reduction in haem-copper oxidases
2016
Mechanisms of improved specificity of engineered Cas9s revealed by single-molecule FRET analysis
2018
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy
2017 StandoutNatureNobel
A Broad-Spectrum Inhibitor of CRISPR-Cas9
2017 StandoutNobel
Mechanism of Substrate Translocation in an Alternating Access Transporter
2017
Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue GltTk
2016
To milliseconds and beyond: challenges in the simulation of protein folding
2012
Integrating protein structural dynamics and evolutionary analysis with Bio3D
2014
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Structural snapshots of TRPV1 reveal mechanism of polymodal functionality
2021 StandoutNobel
Role of the Ion Channel Extracellular Collar in AMPA Receptor Gating
2017
Enhanced sampling techniques in molecular dynamics simulations of biological systems
2014
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
2015
Molecular mechanism of GPCR-mediated arrestin activation
2018 Nature
Biomembranes in atomistic and coarse-grained simulations
2015
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
2017 Standout
The Biology of CRISPR-Cas: Backward and Forward
2018 StandoutNobel
A Catenane Assembled through a Single Charge‐Assisted Halogen Bond
2013
CasX enzymes comprise a distinct family of RNA-guided genome editors
2019 StandoutNatureNobel
Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane
2020
Flexibility and Design: Conformational Heterogeneity along the Evolutionary Trajectory of a Redesigned Ubiquitin
2017
De novo protein design by deep network hallucination
2021 StandoutNatureNobel
Quantitative exploration of the molecular origin of the activation of GTPase
2013 StandoutNobel
A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems: Application to Chorismate Mutase
2003
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
2015
A charge-modified general amber force field for phospholipids: improved structural properties in the tensionless ensemble
2014
Antibiotic Deactivation by a Dizinc β-Lactamase: Mechanistic Insights from QM/MM and DFT Studies
2007
Computer Simulation of Liquids
2017 Standout
Blind protein structure prediction using accelerated free-energy simulations
2016
The emerging role of computational design in peptide macrocycle drug discovery
2020
Perspective: Markov models for long-timescale biomolecular dynamics
2014
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity
2014
Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools
2016
The ONIOM Method and Its Applications
2015
Catalytic iron-carbene intermediate revealed in a cytochrome c carbene transferase
2018 StandoutNobel
QTY code enables design of detergent-free chemokine receptors that retain ligand-binding activities
2018
More bang for your buck: Improved use of GPU nodes for GROMACS 2018
2019
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
2015 Standout
The atom, the molecule, and the covalent organic framework
2017 StandoutScienceNobel
The chemistry of Cas9 and its CRISPR colleagues
2017 StandoutNobel
Unveiling the Delicate Balance of Steric and Dispersion Interactions in Organocatalysis Using High-Level Computational Methods
2020 StandoutNobel
Ion-dependent protein–surface interactions from intrinsic solvent response
2021 StandoutNobel
Folding of Oligoviologens Induced by Radical–Radical Interactions
2014 StandoutNobel
Driven to near‐experimental accuracy by refinement via molecular dynamics simulations
2019
Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
2015
Molecular-Level Characterization of the Breathing Behavior of the Jungle-Gym-type DMOF-1 Metal–Organic Framework
2012
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes
2018 StandoutScienceNobel
Simultaneous Optimization of Biomolecular Energy Functions on Features from Small Molecules and Macromolecules
2016 StandoutNobel
Efficiency and Accuracy of the Generalized Solvent Boundary Potential for Hybrid QM/MM Simulations: Implementation for Semiempirical Hamiltonians
2008
Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs
2017
An efficient and extensible format, library, and API for binary trajectory data from molecular simulations
2013
Correlation as a Determinant of Configurational Entropy in Supramolecular and Protein Systems
2014
A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)
2017 Standout
Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1
2021 StandoutNobel
Target Specificity of Cas9 Nuclease via DNA Rearrangement Regulated by the REC2 Domain
2018
New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions
2018
Structural basis for chemokine recognition and activation of a viral G protein–coupled receptor
2015 Science
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
Structures of Metal–Organic Frameworks with Rod Secondary Building Units
2016 StandoutNobel
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution
2019
Polarizable force fields for molecular dynamics simulations of biomolecules
2015
Molecular Dynamics Explorations of Active Site Structure in Designed and Evolved Enzymes
2015
Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2
2016 Standout
Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling
2020 StandoutNobel
Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent
2014
Effect of Redox Partner Binding on Cytochrome P450 Conformational Dynamics
2017
Neoantigens in cancer immunotherapy
2015 StandoutScience
Accelerated molecular dynamics simulations of protein folding
2015
Quantum Mechanical Continuum Solvation Models
2005 Standout
Combined quantum mechanical and molecular mechanical method for metal–organic frameworks: proton topologies of NU-1000
2017
Fast Parallel Algorithms for Short-Range Molecular Dynamics
1995 Standout
Theoretical Insight into Gate-Opening Adsorption Mechanism and Sigmoidal Adsorption Isotherm into Porous Coordination Polymer
2018 StandoutNobel
Alternate Heme Ligation Steers Activity and Selectivity in Engineered Cytochrome P450-Catalyzed Carbene-Transfer Reactions
2018 StandoutNobel
CRISPR-Cas guides the future of genetic engineering
2018 StandoutScienceNobel
Long-ranged contributions to solvation free energies from theory and short-ranged models
2016
Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors
2020
Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems
2016
A smooth particle mesh Ewald method
1995 Standout
Works of Ross C. Walker being referenced
Comparison of basis set effects and the performance of ab initio and DFT methods for probing equilibrium fluctuations
2006
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation
2014
Assessment of standard force field models against high‐qualityab initiopotential curves for prototypes of π–π, CH/π, and SH/π interactions
2009
Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations
2015
CHAMBER: Comprehensive support for CHARMM force fields within the AMBER software
2009
Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning
2015
Lipid14: The Amber Lipid Force Field
2014
Linking Chemical Electron–Proton Transfer to Proton Pumping in Cytochrome c Oxidase: Broken-Symmetry DFT Exploration of Intermediates along the Catalytic Reaction Pathway of the Iron–Copper Dinuclear Complex
2014
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born
2012 Standout
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald
2013 Standout
Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package
2007
Fast and flexible gpu accelerated binding free energy calculations within the amber molecular dynamics package
2018
Large and Fast Relaxations inside a Protein: Calculation and Measurement of Reorganization Energies in Alcohol Dehydrogenase
2002
Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics
2012
SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations
2012 Standout
GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid
2012
Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation
2015
Application of Adaptive QM/MM Methods to Molecular Dynamics Simulations of Aqueous Systems
2012
Are Current Semiempirical Methods Better Than Force Fields? A Study from the Thermodynamics Perspective
2009
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
2017
The implementation of a fast and accurate QM/MM potential method in Amber
2007
Paramfit: Automated optimization of force field parameters for molecular dynamics simulations
2014
An overview of the Amber biomolecular simulation package
2012 Standout
Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations
2016
LIPID11: A Modular Framework for Lipid Simulations Using Amber
2012