Citation Impact
Citing Papers
Expanded therapeutic potential in activity space of next-generation 5-nitroimidazole antimicrobials with broad structural diversity
2013 StandoutNobel
The 2.6 Angstrom Crystal Structure of a Human A 2A Adenosine Receptor Bound to an Antagonist
2008 StandoutScience
The Cambridge Structural Database
2016 Standout
What do we know and when do we know it?
2008
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
2008
Scoring functions for protein–protein interactions
2013 StandoutNobel
Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes
2010
Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions
2010 StandoutNobel
Rapid Calculation of Protein pKa Values Using Rosetta
2012
Protein-Protein Docking with Dynamic Residue Protonation States
2014
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
2011 StandoutNobel
Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis
2012 StandoutNobel
Open Babel: An open chemical toolbox
2011 Standout
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
2011
In Silico Target Prediction for Small Molecules
2018
Software for molecular docking: a review
2017
New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays
2010 Standout
Discovery and biological evaluation of novel α-glucosidase inhibitors with in vivo antidiabetic effect
2008
Generation of Receptor Structural Ensembles for Virtual Screening Using Binding Site Shape Analysis and Clustering
2012
Electrostatic effects play a central role in cold adaptation of trypsin
2001
Using RosettaLigand for Small Molecule Docking into Comparative Models
2012
Molecular Dynamics Simulation for All
2018 Standout
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
2003
Blind docking of pharmaceutically relevant compounds using RosettaLigand
2009 StandoutNobel
Engineering an allosteric transcription factor to respond to new ligands
2015 StandoutNobel
Novel inhibitors of anthrax edema factor
2008
GalaxyDock BP2 score: a hybrid scoring function for accurate protein–ligand docking
2017
A structure-based computational workflow to predict liability and binding modes of small molecules to hERG
2020 StandoutNobel
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
2013 Standout
Towards Accurate Free Energy Calculations in Ligand Protein-Binding Studies
2010
Designing antimicrobial peptides: form follows function
2011 Standout
Structure-based drug screening for G-protein-coupled receptors
2012 StandoutNobel
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
2007
Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites
2021 StandoutNobel
Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”
2009
Drug repurposing: progress, challenges and recommendations
2018 Standout
Methods of Protein Structure Comparison
2011
Q‐Dock: Low‐resolution flexible ligand docking with pocket‐specific threading restraints
2008
Discovery of VHR Phosphatase Inhibitors with Micromolar Activity based on Structure‐Based Virtual Screening
2008
PubChem Substance and Compound databases
2015 Standout
Psychrophilic enzymes: hot topics in cold adaptation
2003 Standout
Surflex-Dock: Docking benchmarks and real-world application
2012
A Pareto-Optimal Refinement Method for Protein Design Scaffolds
2013 StandoutNobel
Recent Developments in Fragment-Based Drug Discovery
2008
De novo design of a fluorescence-activating β-barrel
2018 StandoutNatureNobel
Hit finding: towards ‘smarter’ approaches
2009
Calculations of protein-ligand binding entropy of relative and overall molecular motions
2007
RosettaLigand Docking with Full Ligand and Receptor Flexibility
2008 StandoutNobel
Evolutionary Optimization of Computationally Designed Enzymes: Kemp Eliminases of the KE07 Series
2009 StandoutNobel
A fragment-based approach to the SAMPL3 Challenge
2012
Crystal structure of the µ-opioid receptor bound to a morphinan antagonist
2012 StandoutNatureNobel
Binding MOAD (Mother Of All Databases)
2005
Molecular modeling of A1and A2Aadenosine receptors: Comparison of rhodopsin‐ and β2‐adrenergic‐based homology models through the docking studies
2008
I-TASSER: a unified platform for automated protein structure and function prediction
2010 Standout
A computational approach for predicting off-target toxicity of antiviral ribonucleoside analogues to mitochondrial RNA polymerase
2018 StandoutNobel
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules
2017 Standout
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
2009 Standout
Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry
2010
Cryo-EM structure of a type IV secretion system
2022 StandoutNatureNobel
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
2009 Standout
Predicting drug metabolism: experiment and/or computation?
2015
Free Energy Calculations and Ligand Binding
2003
ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
2006 StandoutNobel
Healthy skepticism: assessing realistic model performance
2009
Click Chemistry for Drug Development and Diverse Chemical–Biology Applications
2013 Standout
Improvements, trends, and new ideas in molecular docking: 2012–2013 in review
2015
A Simple QM/MM Approach for Capturing Polarization Effects in Protein−Ligand Binding Free Energy Calculations
2011
CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge
2015 StandoutNobel
The scientific impact of the Cambridge Structural Database: a citation-based study
2010
Knowledge Based Identification of Potent Antitubercular Compounds Using Structure Based Virtual Screening and Structure Interaction Fingerprints
2008
Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
2010
Using AutoDock for Ligand‐Receptor Docking
2008
DSX: A Knowledge-Based Scoring Function for the Assessment of Protein–Ligand Complexes
2011
MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening
2008
CSAR Benchmark Exercise of 2010: Selection of the Protein–Ligand Complexes
2011
Comparison of Topological, Shape, and Docking Methods in Virtual Screening
2007
Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
2009
Rationalizing Tight Ligand Binding through Cooperative Interaction Networks
2011
Predicting New Indications for Approved Drugs Using a Proteochemometric Method
2012
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
2012 Standout
Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment
2012 StandoutNobel
Chemical space as a source for new drugs
2010
Lead Finder: An Approach To Improve Accuracy of Protein−Ligand Docking, Binding Energy Estimation, and Virtual Screening
2008
Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise
2013
CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
2011
Click Chemistry Approach to New N-Substituted Aminocyclitols as Potential Pharmacological Chaperones for Gaucher Disease
2010
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules
2019 Standout
Comparison of Shape-Matching and Docking as Virtual Screening Tools
2006
Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps
2006
Force Field Optimization Guided by Small Molecule Crystal Lattice Data Enables Consistent Sub-Angstrom Protein–Ligand Docking
2021 StandoutNobel
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
2009
Enhancement of Hydrophobic Interactions and Hydrogen Bond Strength by Cooperativity: Synthesis, Modeling, and Molecular Dynamics Simulations of a Congeneric Series of Thrombin Inhibitors
2010
CSAR Benchmark Exercise 2011–2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
2013
Target Flexibility: An Emerging Consideration in Drug Discovery and Design
2008
Computational design of environmental sensors for the potent opioid fentanyl
2017 StandoutNobel
Biochemical Properties and Crystal Structure of a β-Phenylalanine Aminotransferase from Variovorax paradoxus
2012 StandoutNobel
Lessons in Molecular Recognition. 2. Assessing and Improving Cross-Docking Accuracy
2007
QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors
2009
Thermodynamic and Structural Effects of Conformational Constraints in Protein−Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization
2009
Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
2010
Protein–protein binding affinity prediction on a diverse set of structures
2011
Calculation of Protein-Ligand Binding Affinities
2007
Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects
2009 StandoutNobel
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
2017 StandoutNobel
Improving the Catalytic Performance of an Artificial Metalloenzyme by Computational Design
2015 StandoutNobel
Efficient and Accurate Free Energy Calculations on Trypsin Inhibitors
2012
Assessing hERG Pore Models As Templates for Drug Docking Using Published Experimental Constraints: The Inactivated State in the Context of Drug Block
2014
Update 1 of: Computational Modeling Approaches to Structure–Function Analysis of G Protein-Coupled Receptors
2011
Exploring, Refining, and Validating the Paradynamics QM/MM Sampling
2012 StandoutNobel
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database
2010
Automating human intuition for protein design
2013 StandoutNobel
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets
2020 Standout
Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes
2013
Principles and Applications of Halogen Bonding in Medicinal Chemistry and Chemical Biology
2012 Standout
Reverse Docking: A Powerful Tool for Drug Repositioning and Drug Rescue
2014
Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations
2019 StandoutNobel
Works of Ian D. Wall being referenced
Bioinformatics and molecular modelling approaches to GPCR oligomerization
2009
Modeling GPCR active state conformations: The β2‐adrenergic receptor
2011
A Critical Assessment of Docking Programs and Scoring Functions
2005
Binding Constants of Neuraminidase Inhibitors: An Investigation of the Linear Interaction Energy Method
1999