Standout Papers
Citation Impact
Citing Papers
Protein interaction networks revealed by proteome coevolution
2019 StandoutScienceNobel
A defined structural unit enables de novo design of small-molecule–binding proteins
2020 Science
DNA capture by a CRISPR-Cas9–guided adenine base editor
2020 StandoutScienceNobel
Membrane-tethered mucin-like polypeptides sterically inhibit binding and slow fusion kinetics of influenza A virus
2020 StandoutNobel
Origins of coevolution between residues distant in protein 3D structures
2017 StandoutNobel
Directed Evolution Mimics Allosteric Activation by Stepwise Tuning of the Conformational Ensemble
2018 StandoutNobel
Exploiting conformational dynamics to modulate the function of designed proteins
2023 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
Property‐Driven Development of Passively Permeable Macrocyclic Scaffolds Using Heterocycles**
2022
Modelling proteins’ hidden conformations to predict antibiotic resistance
2016
Target-conditioned diffusion generates potent TNFR superfamily antagonists and agonists
2024 StandoutScienceNobel
Expansive discovery of chemically diverse structured macrocyclic oligoamides
2024 StandoutScienceNobel
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice
2023 StandoutNobel
Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation
2009
Computational design of soluble and functional membrane protein analogues
2024 StandoutNatureNobel
Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations
2018
De novo design of allosterically switchable protein assemblies
2024 StandoutNatureNobel
Microenvironmental modulation breaks intrinsic pH limitations of nanozymes to boost their activities
2024 StandoutNobel
LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales
2021 Standout
The promise and challenge of therapeutic genome editing
2020 StandoutNatureNobel
Mechanisms of SARS-CoV-2 entry into cells
2021 Standout
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview
2018
Multistate and functional protein design using RoseTTAFold sequence space diffusion
2024 StandoutNobel
Phage-assisted evolution of an adenine base editor with improved Cas domain compatibility and activity
2020 StandoutNobel
Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
2018
Hydrophobic mismatch drives self-organization of designer proteins into synthetic membranes
2024 StandoutNobel
The ensemble nature of allostery
2014 Nature
A challenging system: Free energy prediction for factor Xa
2011
A cross docking pipeline for improving pose prediction and virtual screening performance
2017
Influenza A penetrates host mucus by cleaving sialic acids with neuraminidase
2013
CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification
2019 StandoutNobel
Effect of atomic charge, solvation, entropy, and ligand protonation state on MM‐PB(GB)SA binding energies of HIV protease
2012
Using Ligand‐Mapping Simulations to Design a Ligand Selectively Targeting a Cryptic Surface Pocket of Polo‐Like Kinase 1
2012
Computational Methods in Drug Discovery
2014
Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016
2021
Molecular Dynamics Simulation for All
2018 Standout
Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage
2017 StandoutNature
Role of computer-aided drug design in modern drug discovery
2015
Engineering allostery
2014
A Brief History of De Novo Protein Design: Minimal, Rational, and Computational
2021
mRNA vaccines for infectious diseases: principles, delivery and clinical translation
2021 StandoutNobel
Enhanced proofreading governs CRISPR–Cas9 targeting accuracy
2017 StandoutNatureNobel
Capsaicin Interaction with TRPV1 Channels in a Lipid Bilayer: Molecular Dynamics Simulation
2015
Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies
2021
Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
2010
Vulnerabilities in coronavirus glycan shields despite extensive glycosylation
2020
Recent Developments and Applications of the MMPBSA Method
2018
Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge
2014
Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations
2016
Molecular dynamics simulations and drug discovery
2011
Search-and-replace genome editing without double-strand breaks or donor DNA
2019 StandoutNature
Scalable molecular dynamics with NAMD
2005 Standout
Improved protein structure prediction using potentials from deep learning
2020 StandoutNatureNobel
TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action
2016 StandoutNatureNobel
Molecular dynamics simulations reveal ligand-controlled positioning of a peripheral protein complex in membranes
2017
De novo design of bioactive protein switches
2019 StandoutNatureNobel
Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis
2019 Nature
Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach
2014
The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities
2015 Standout
SARS-CoV-2 variants, spike mutations and immune escape
2021 Standout
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis
2009
Emerging Topics in Structure-Based Virtual Screening
2013
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
2017 Standout
Allosteric regulation and catalysis emerge via a common route
2008
Structural Prediction of Peptide–MHC Binding Modes
2022
Improving binding mode and binding affinity predictions of docking by ligand-based search of protein conformations: evaluation in D3R grand challenge 2015
2017
Molecular Architecture of the SARS-CoV-2 Virus
2020
Tools to cut the sweet layer-cake that is glycoproteomics
2021
The role of protein dynamics in the evolution of new enzyme function
2016
Predicting drug metabolism: experiment and/or computation?
2015
Antibacterial drug discovery in the resistance era
2016 StandoutNature
Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins
2023 Nobel
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
2015
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
2011
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
2015 StandoutNobel
Fluorine in Pharmaceutical Industry: Fluorine-Containing Drugs Introduced to the Market in the Last Decade (2001–2011)
2013 Standout
Allosteric pathways in imidazole glycerol phosphate synthase
2012
Computer Simulation of Liquids
2017 Standout
A Water-Based Mechanism of Specificity and Resistance for Lapatinib with ErbB Family Kinases
2012
Binding Affinity via Docking: Fact and Fiction
2018
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings
2021 Standout
Nanozymes: Classification, Catalytic Mechanisms, Activity Regulation, and Applications
2019 Standout
Correction: Binding of Protein Kinase Inhibitors to Synapsin I Inferred from Pair-Wise Binding Site Similarity Measurements
2010
Lysosomal cathepsin D mediates endogenous mucin glycodomain catabolism in mammals
2022 StandoutNobel
Redox-Controlled Selective Docking in a [2]Catenane Host
2013 StandoutNobel
Peptide-binding specificity prediction using fine-tuned protein structure prediction networks
2023 StandoutNobel
Molecular Docking: Shifting Paradigms in Drug Discovery
2019 Standout
Inhibition of SARS-CoV-2 viral entry upon blocking N- and O-glycan elaboration
2020
Metal–ligand interactions in drug design
2018
Design and optimization of enzymatic activity in a de novo β‐barrel scaffold
2022 StandoutNobel
Evolutionary-scale prediction of atomic-level protein structure with a language model
2023 StandoutScience
Dynamic Docking: A Paradigm Shift in Computational Drug Discovery
2017
Reactive Oxygen Species (ROS)-Based Nanomedicine
2019 Standout
Controlling Allosteric Networks in Proteins
2016
Role of Molecular Dynamics and Related Methods in Drug Discovery
2016
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
2015
A Panel of TrpB Biocatalysts Derived from Tryptophan Synthase through the Transfer of Mutations that Mimic Allosteric Activation
2016 StandoutNobel
Calculating potentials of mean force from steered molecular dynamics simulations
2004
Conformational Effects on the Passive Membrane Permeability of Synthetic Macrocycles
2022
Addressing Selective Polypharmacology of Antipsychotic Drugs Targeting the Bioaminergic Receptors through Receptor Dynamic Conformational Ensembles
2013
Allosteric Modulation of Substrate Binding within a Tetracationic Molecular Receptor
2015 StandoutNobel
CRISPR-Cas guides the future of genetic engineering
2018 StandoutScienceNobel
Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations
2016
Challenges of Antibacterial Discovery
2011
Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality
2003
Redox Control of the Binding Modes of an Organic Receptor
2015 StandoutNobel
Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics
2013
Computer simulations explain mutation-induced effects on the DNA editing by adenine base editors
2020
Works of Rommie E. Amaro being referenced
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
2008
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
2021
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
2013
Incorporation of sensing modalities into de novo designed fluorescence-activating proteins
2021 StandoutNobel
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
2008
Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?
2012
Teach–Discover–Treat (TDT): Collaborative computational drug discovery for neglected diseases
2012
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
2015
Ensemble Docking in Drug Discovery
2018
Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin
2015
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
2016
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
2016
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology
2010
Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
2010
Architecture and self-assembly of the jumbo bacteriophage nuclear shell
2022 Nature
Emerging Methods for Ensemble-Based Virtual Screening
2010
D3R grand challenge 4: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
2020
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry
2014
Structural Elements in IGP Synthase Exclude Water to Optimize Ammonia Transfer
2005
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
2015
Rational Prediction with Molecular Dynamics for Hit Identification
2012
Modeling the pharmacodynamics of passive membrane permeability
2011
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
2017
Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B
2017
Computational approaches to mapping allosteric pathways
2014
Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble
2008
Ensemble-Based Virtual Screening Reveals Potential Novel Antiviral Compounds for Avian Influenza Neuraminidase
2008
A multiscale coarse-grained model of the SARS-CoV-2 virion
2020
Multiscale methods in drug design bridge chemical and biological complexity in the search for cures
2018
Exploring Residue Component Contributions to Dynamical Network Models of Allostery
2012
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
2016
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding
2017
Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein
2020
Developing an energy landscape for the novel function of a (β/α)8barrel: Ammonia conduction through HisF
2003
MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein−Protein Interface
2009
Molecular dynamics simulations of substrate channeling through an α–β barrel protein
2004
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis
2014
Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit
2019
A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase
2007
Reaction Coupling through Interdomain Contacts in Imidazole Glycerol Phosphate Synthase
2005
Role of Secondary Sialic Acid Binding Sites in Influenza N1 Neuraminidase
2010
Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations
2019 StandoutNobel