Standout Papers
Citation Impact
Citing Papers
Rice Domestication by Reducing Shattering
2006 Science
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
2017 StandoutScienceNobel
Atomic-Level Characterization of the Structural Dynamics of Proteins
2010 StandoutScienceNobel
Cytokinin Oxidase Regulates Rice Grain Production
2005 Science
Single Reconstituted Neuronal SNARE Complexes Zipper in Three Distinct Stages
2012 StandoutScienceNobel
SNARE Proteins: One to Fuse and Three to Keep the Nascent Fusion Pore Open
2012 StandoutScienceNobel
Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations
2002
Pattern of diversity in the genomic region near the maize domestication gene tb1
2003
Computational Thermostabilization of an Enzyme
2005 StandoutScienceNobel
Visualizing Data using t-SNE
2008 StandoutNobel
Expansive discovery of chemically diverse structured macrocyclic oligoamides
2024 StandoutScienceNobel
Improving physical realism, stereochemistry, and side‐chain accuracy in homology modeling: Four approaches that performed well in CASP8
2009 StandoutNobel
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
De novo design of allosterically switchable protein assemblies
2024 StandoutNatureNobel
Cavities and packing at protein interfaces
1994
Structural Mechanisms for Domain Movements in Proteins
1994
Molecular dynamics simulations of biomolecules
2002 Standout
Crystal Structure of lac Repressor Core Tetramer and Its Implications for DNA Looping
1995 StandoutScienceNobel
Glasslike dynamical behavior of the plastocyanin hydration water
2000
The Genetic, Developmental, and Molecular Bases of Fruit Size and Shape Variation in Tomato
2004
Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures
2005 StandoutNobel
Rewiring of the Fruit Metabolome in Tomato Breeding
2018 Standout
Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
1993 StandoutNatureNobel
The ensemble nature of allostery
2014 Nature
Hemoglobin: Structure, Function and Allostery
2020
Design of an optimal Chebyshev‐expanded discrimination function for globular proteins
2002 StandoutNobel
Elbow motion in the immunoglobulins involves a molecular ball-and-socket joint
1988 Nature
A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations
2006
The protein folding ‘speed limit’
2004
The structure of ribosomal protein S5 reveals sites of interaction with 16S rRNA
1992 StandoutNatureNobel
Testing homology modeling on mutant proteins: predicting structural and thermodynamic effects in the Ala98→Val mutants of T4 lysozyme
1996
Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
1994
Irritant-evoked activation and calcium modulation of the TRPA1 receptor
2020 StandoutNatureNobel
MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
2002
A comparison between molecular dynamics and X-ray results for dissociated CO in myoglobin
1997
A Lattice Relaxation Algorithm for Three-Dimensional Poisson-Nernst-Planck Theory with Application to Ion Transport through the Gramicidin A Channel
1999
Folding of a model three-helix bundle protein: a thermodynamic and kinetic analysis 1 1Edited by A. R. Fersht
1999 StandoutNobel
The Molecular Genetics of Crop Domestication
2006 Standout
A fast pairlist‐construction algorithm for molecular simulations under periodic boundary conditions
2004
Simultaneous computation of free energies and kinetics of rare events
2005
Hydrophobic interaction between globin helices
1992
The Amber biomolecular simulation programs
2005 Standout
Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers
2012 StandoutNobel
The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato
2003
The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus
1997
A cryo-electron microscopic study of ribosome-bound termination factor RF2
2003 StandoutNatureNobel
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
2012
Native proteins are surface-molten solids: application of the lindemann criterion for the solid versus liquid state 1 1Edited by A. R. Fersht
1999 StandoutNobel
High-resolution structure prediction and the crystallographic phase problem
2007 StandoutNatureNobel
Mean-field minimization methods for biological macromolecules
1996
Can Morphing Methods Predict Intermediate Structures?
2008 StandoutNobel
The nature of folded states of globular proteins
1992
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
2011 StandoutNatureNobel
Protein conformational relaxation following photodissociation of carbon monoxide from carbonmonoxymyoglobin: picosecond circular dichroism and absorption studies
1991
Internal Packing and Protein Structural Classes
1987
Theory of protein folding
2004 Standout
Identifying native‐like protein structures using physics‐based potentials
2001
Super-resolution biomolecular crystallography with low-resolution data
2010 StandoutNatureNobel
Crystallographic refinement by simulated annealing
1988
Access of ligands to cavities within the core of a protein is rapid
1996
The energy landscape theory of protein folding: Insights into folding mechanisms and scenarios
2000
Modeling side-chain conformation
1996
Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits
2017
Energy landscape of a native protein: Jumping-among-minima model
1998
Effective energy function for proteins in solution
1999
Improving the performance of rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
2001 StandoutNobel
A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling
1995
Visualizing protein conformational changes on a personal computer – alpha carbon pseudo bonding as a constraint for interpolation in internal coordinate space
2001
A protein-folding reaction under kinetic control
1992 StandoutNatureNobel
Fully Reduced Ribonuclease A Does not Expand at High Denaturant Concentration or Temperature
2007
Identification of structural motifs from protein coordinate data: Secondary structure and first‐level supersecondary structure*
1988
Enzyme Activity below the Dynamical Transition at 220 K
1998
Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11
2011
Documenting domestication: the intersection of genetics and archaeology
2006
MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape
2007
Comparative Sequencing in the Genus Lycopersicon: Implications for the Evolution of Fruit Size in the Domestication of Cultivated Tomatoes
2002
Ligand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombination
1991
Transient Non-native Hydrogen Bonds Promote Activation of a Signaling Protein
2009
A surprising simplicity to protein folding
2000 StandoutNatureNobel
Simulations of ion current in realistic models of ion channels: The KcsA potassium channel
2002 StandoutNobel
Exploring the origin of the ion selectivity of the KcsA potassium channel
2003 StandoutNobel
Multiple copy sampling: Rigid versus flexible protein
1994
Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
1991 StandoutNatureNobel
Building machines with DNA molecules
2019
Domain closure in mitochondrial aspartate aminotransferase
1992
Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core
1991 StandoutNatureNobel
Temperature Dependence of Protein Dynamics: Computer Simulation Analysis of Neutron Scattering Properties
2002
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics
1995
A semi-microscopic Monte Carlo study of permeation energetics in a gramicidin-like channel: the origin of cation selectivity
1996
Toward accurate relative energy predictions of the bioactive conformation of drugs
2008
Conformational substates and motions in myoglobin. External influences on structure and dynamics
1990
Efficient Generation of Feasible Pathways for Protein Conformational Transitions
2002
Discrimination of the native from misfolded protein models with an energy function including implicit solvation
1999
How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences
1998
Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
2006
Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events
2008
Folding funnels and frustration in off-lattice minimalist protein landscapes
1998
PROTEIN FOLDING: The Endgame
1997 StandoutNobel
Retardation of O diffusion through polycrystalline Pt by Be doping
1999
The Flexible Rare Event Sampling Harness System (FRESHS)
2014
Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions
2013
Blue Moon Approach to Rare Events
2004
A method to explore transition paths in macromolecules. Applications to hemoglobin and phosphoglycerate kinase
1995
Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes
2008
Robust and efficient configurational molecular sampling via Langevin dynamics
2013
String method for the study of rare events
2002
Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits
2014
Acid and Thermal Denaturation of Barnase Investigated by Molecular Dynamics Simulations
1995
Computer Simulation of Liquids
2017 Standout
The Debye‐Waller factor: From villain to hero in protein crystallography
1989
Ab Initio Protein Structure Prediction: Progress and Prospects
2001 StandoutNobel
Hydration Dynamics and Time Scales of Coupled Water−Protein Fluctuations
2007
Linkage of Functional and Structural Heterogeneity in Proteins: Dynamic Hole Burning in Carboxymyoglobin
1987 Science
Water as an Active Constituent in Cell Biology
2007 Standout
Characterizing the unfolded states of proteins using single-molecule FRET spectroscopy and molecular simulations
2007
The molecular basis for the chemical denaturation of proteins by urea
2003
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
1987
Free energy from simulations
1991
Toward High-Resolution de Novo Structure Prediction for Small Proteins
2005 StandoutScienceNobel
Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space
2013
A cytochrome P450 regulates a domestication trait in cultivated tomato
2013
A practical perspective on the implementation of hyperdynamics for accelerated simulation
2014
The Energy Landscapes and Motions of Proteins
1991 StandoutScience
Anatomy of a Conformational Change: Hinged "Lid" Motion of the Triosephosphate Isomerase Loop
1990 Science
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
2007 Standout
Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared‐memory computers
1991
Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration
2000
Self-guided enhanced sampling methods for thermodynamic averages
2003
Adsorption and dissociation of O2 on Cu(): thermochemistry, reaction barrier and the effect of strain
2001
Large‐scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
2015
An evaluvation of discrete and continuum search techniques for conformational analysis of side chains in proteins
1995
Funnel sculpting for in silico assembly of secondary structure elements of proteins
2003 StandoutNobel
Roles of mutation and recombination in the evolution of protein thermodynamics
2002 StandoutNobel
Simulation of activation free energies in molecular systems
1996
Predicting slow structural transitions in macromolecular systems: Conformational flooding
1995
High thermodynamic stability of parametrically designed helical bundles
2014 StandoutScienceNobel
Solvent dependence of dynamic transitions in protein solutions
2000
Sprouting side chain conformations in X‐PLOR simulations of peptides
1993
Improved recognition of native-like protein structures using a family of designed sequences
2002 StandoutNobel
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
2008
Rare events via multiple reaction channels sampled by path replica exchange
2008
Investigating rare events by transition interface sampling
2004
Through the Channel and around the Channel: Validating and Comparing Microscopic Approaches for the Evaluation of Free Energy Profiles for Ion Penetration through Ion Channels
2005 StandoutNobel
Molecular Dynamics Simulation on the Connection Machine
1991
Progress in Modeling of Protein Structures and Interactions
2005 StandoutScienceNobel
Crystal Structure of a CAP-DNA Complex: the DNA Is Bent by 90°
1991 StandoutScienceNobel
Computational design of mechanically coupled axle-rotor protein assemblies
2022 StandoutScienceNobel
Protein Structure Prediction and Structural Genomics
2001 StandoutScienceNobel
Finite Temperature String Method for the Study of Rare Events
2005
Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin
1996
Rebinding and relaxation in the myoglobin pocket
1987
Shadowing, rare events, and rubber bands. A variational Verlet algorithm for molecular dynamics
1992
MBO(N)D: A multibody method for long-time molecular dynamics simulations
2000
Oscillatory Thermomechanical Instability of an Ultrathin Catalyst
2003 StandoutScienceNobel
Combining MONSSTER and LES/PME to Predict Protein Structure from Amino Acid Sequence: Application to the Small Protein CMTI-1
2000
The Role of Dynamics in Enzyme Activity
2003
Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing
2001
Molecular dynamics in the endgame of protein structure prediction
2001 StandoutNobel
A self-learning algorithm for biased molecular dynamics
2010
Determination of reaction coordinates via locally scaled diffusion map
2011
Fast Parallel Algorithms for Short-Range Molecular Dynamics
1995 Standout
Glassy behavior of a protein
1989
Identification and Mode of Inheritance of Quantitative Trait Loci for Secondary Metabolite Abundance in Tomato
2015
Effects of Lipid Composition on Bilayer Membranes Quantified by All-Atom Molecular Dynamics
2015
Simulating rare events in equilibrium or nonequilibrium stochastic systems
2006
Design and control of gas diffusion process in a nanoporous soft crystal
2019 StandoutScienceNobel
A Large-Scale Screen for Artificial Selection in Maize Identifies Candidate Agronomic Loci for Domestication and Crop Improvement
2005
Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNA Gln and ATP at 2.8 Å Resolution
1989 StandoutScienceNobel
Adaptive nudged elastic band approach for transition state calculation
2002
Atomistic Determination of Cross-Slip Pathway and Energetics
1997
Dynamical simulation of rate constants in protein-ligand interactions
1988
2.1 and 1.8 Å Average Cα RMSD Structure Predictions on Two Small Proteins, HP-36 and S15
2001 StandoutNobel
Transient behavior of a model fluid under applied shear
2013
Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics
2014
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
2003
Molecular Dynamics of Water at the Protein−Solvent Interface
2002
Computing aspects of molecular dynamics simulation
1992
Overcoming barriers in trajectory space: Mechanism and kinetics of rare events via Wang–Landau enhanced transition path sampling
2010
Does Urea Denature Hydrophobic Interactions?
2006
The Genetics of Maize Evolution
2004
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
2000 Standout
A climbing image nudged elastic band method for finding saddle points and minimum energy paths
2000 Standout
Works of Ron Elber being referenced
New Algorithms for Macromolecular Simulation (Lecture Notes in Computational Science and Engineering)
2006
How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations
2012
On the design and analysis of protein folding potentials
2000
A Milestoning Study of the Kinetics of an Allosteric Transition: Atomically Detailed Simulations of Deoxy Scapharca Hemoglobin
2007
Ligand diffusion in globins: simulations versus experiment
2010
Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin
1990
Sodium in gramicidin: an example of a permion
1995
Molecular machines
2013
Computational studies of ligand diffusion in globins: I. Leghemoglobin
1991
Nitric Oxide Recombination to Double Mutants of Myoglobin: Role of Ligand Diffusion in a Fluctuating Heme Pocket
1994
Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction
1997
The dominant interaction between peptide and urea is electrostatic in nature: A molecular dynamics simulation study
2003
Simulations of allosteric transitions
2011
Novel methods for molecular dynamics simulations
1996
Long-timescale simulation methods
2005
Atomically Detailed Simulations of Helix Formation with the Stochastic Difference Equation
2003
SSALN: An alignment algorithm using structure‐dependent substitution matrices and gap penalties learned from structurally aligned protein pairs
2005
A new technique to calculate steepest descent paths in flexible polyatomic systems
1990
Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
2007
Calculations of a list of neighbors in Molecular Dynamics simulations
1989
On the assumptions underlying milestoning
2008
The thermal equilibrium aspects of the time dependent Hartree and the locally enhanced sampling approximations: Formal properties, a correction, and computational examples for rare gas clusters
1993
Reaction path study of conformational transitions and helix formation in a tetrapeptide.
1989
Computing time scales from reaction coordinates by milestoning
2004
Molecular dynamics simulation of NO recombination to myoglobin mutants.
1993
Stochastic Path Approach to Compute Atomically Detailed Trajectories: Application to the Folding of C Peptide
1999
Parallel computations of molecular dynamics trajectories using the stochastic path approach
2000
Ligand binding and conformation change in the dimeric hemoglobin of the clam Scapharca inaequivalvis.
1993
Anharmonic Wave Functions of Proteins: Quantum Self-Consistent Field Calculations of BPTI
1995 Science
Hydrophobic "Collapse" in a Cyclic Hexapeptide: Computer Simulations of CHDLFC and CAAAAC in Water
1994
Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants.
1992
Multiphoton Absorption of Myoglobin–Nitric Oxide Complex: Relaxation by D-NEMD of a Stationary State
2012
Long Time Dynamics of Complex Systems
2002
Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems
1990
Application of the locally enhanced sampling (LES) and a mean field with a binary collision correction (cLES) to the simulation of argon diffusion and nitric oxide recombination in myoglobin
1994
A method for determining reaction paths in large molecules: Application to myoglobin
1987
Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
1987 Science
Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories
1999
fw2.2 : A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size
2000 StandoutScience
Milestoning without a Reaction Coordinate
2010
Fractal analysis of protein potential energy landscapes
1999
Coupling the folding of homologous proteins
1998
Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
1990 Standout
Calculation of the potential of mean force using molecular dynamics with linear constraints: An application to a conformational transition in a solvated dipeptide
1990
Distance-dependent, pair potential for protein folding: Results from linear optimization
2000
Revisiting and Computing Reaction Coordinates with Directional Milestoning
2011
Measurement of the Membrane Dipole Electric Field in DMPC Vesicles Using Vibrational Shifts of p-Cyanophenylalanine and Molecular Dynamics Simulations
2015
Reaction path study of conformational transitions in flexible systems: Applications to peptides
1990
Revisiting and parallelizing SHAKE
2005
Modeling side chains in peptides and proteins: Application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations
1991
New Algorithms for Macromolecular Simulation
2006
Unassisted Transport of N-Acetyl-l -tryptophanamide through Membrane: Experiment and Simulation of Kinetics
2012
Yet another look at the steepest descent path
1997
Microscopic modeling of ligand diffusion through the protein leghemoglobin: computer simulations and experiments
1992
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
2002
Calculation of classical trajectories with a very large time step: Formalism and numerical examples
1996