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Protein-ligand docking

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Berichte der deutschen chemischen Gesellschaft

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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Flexible protein–ligand docking by global energy optimization in internal coordinates

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Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization

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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking

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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors

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Einfluss der Configuration auf die Wirkung der Enzyme

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Prediction of Protein—Ligand Interactions. Docking and Scoring: Successes and Gaps

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Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N‐methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic…

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

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Molecular docking using shape descriptors

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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

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Molecular recognition of RNA: challenges for modelling interactions and plasticity

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Including receptor flexibility and induced fit effects into the design of MMP‐2 inhibitors

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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock

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Principles of docking: An overview of search algorithms and a guide to scoring functions

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ConsDock: A new program for the consensus analysis of protein–ligand interactions

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Comparing protein–ligand docking programs is difficult

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CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock

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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

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Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking

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FLIPDock: Docking flexible ligands into flexible receptors

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Molecular dynamics simulation of the docking of substrates to proteins

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Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

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FlexE: efficient molecular docking considering protein structure variations

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The Flexible Pocketome Engine for Structural Chemogenomics

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A fast and efficient method to generate biologically relevant conformations

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LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads

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A good ligand is hard to find: Automated docking methods

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Evaluation of the utility of homology models in high throughput docking

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Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search

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An improved relaxed complex scheme for receptor flexibility in computer-aided drug design

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Improving database enrichment through ensemble docking

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A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)

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How to do an evaluation: pitfalls and traps

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Spatial chemical distance based on atomic property fields

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The interpretation of protein structures: Estimation of static accessibility

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A geometric approach to macromolecule-ligand interactions

inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot

“Soft docking”: Matching of molecular surface cubes

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Current opinion in structural biology

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Comparative Modeling of Drug Target Proteins

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The Process of Structure-Based Drug Design

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A virtual screening study of the acetylcholine binding protein using a relaxed–complex approach

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Fragments, network biology and designing multiple ligands

inferredcites →https://doi.org/10.1016/j.jmb.2004.01.003openalex-snapshot

Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases

inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot

High-resolution protein–protein docking

inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot

Flexible ligand docking to multiple receptor conformations: a practical alternative

inferredcites →https://doi.org/10.1016/j.tips.2007.11.007openalex-snapshot

Novel paradigms for drug discovery: computational multitarget screening

inferredcites →https://doi.org/10.1016/s0009-2614(97)01074-9openalex-snapshot

Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation

inferredcites →https://doi.org/10.1016/s0022-2836(05)80038-5openalex-snapshot

Ligand docking to proteins with discrete side-chain flexibility

inferredcites →https://doi.org/10.1016/s0026-895x(24)23192-8openalex-snapshot

Accommodating Protein Flexibility in Computational Drug Design,

inferredcites →https://doi.org/10.1016/s0065-7743(04)39020-2openalex-snapshot

Comparative Protein Structure Modeling and its Applications to Drug Discovery

inferredcites →https://doi.org/10.1016/s0167-7799(00)89015-0openalex-snapshot

Genetic algorithms in molecular recognition and design

inferredcites →https://doi.org/10.1016/s0959-440x(00)00195-0openalex-snapshot

Statistical potentials and scoring functions applied to protein–ligand binding

inferredcites →https://doi.org/10.1016/s1074-5521(96)90093-9openalex-snapshot

Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites

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From magic bullets to designed multiple ligands

inferredcites →https://doi.org/10.1016/s1367-5931(00)00217-9openalex-snapshot

High-throughput docking for lead generation

inferredcites →https://doi.org/10.1016/s1367-5931(02)00339-3openalex-snapshot

Lead discovery using molecular docking

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Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models

inferredcites →https://doi.org/10.1021/ar010030mopenalex-snapshot

Free Energy Simulations Come of Age: Protein−Ligand Recognition

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Efficient Drug Lead Discovery and Optimization

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JOURNAL OF CHEMICAL INFORMATION AND MODELING

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How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment

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A Comparative Study on the Application of Hierarchical−Agglomerative Clustering Approaches to Organize Outputs of Reiterated Docking Runs

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Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints

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Investigation of MM-PBSA Rescoring of Docking Poses

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Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes

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Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs

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Comparative Assessment of Scoring Functions on a Diverse Test Set

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Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy

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Molecular Docking Screens Using Comparative Models of Proteins

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Free energy calculations: Applications to chemical and biochemical phenomena

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Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme

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Flexible Docking in Solution Using Metadynamics

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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design

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VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands

inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot

Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations

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A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

inferredcites →https://doi.org/10.1021/jm0200299openalex-snapshot

Simple, Intuitive Calculations of Free Energy of Binding for Protein−Ligand Complexes. 1. Models without Explicit Constrained Water

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Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

inferredcites →https://doi.org/10.1021/jm0300330openalex-snapshot

Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes

inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot

Evaluation of Docking Performance: Comparative Data on Docking Algorithms

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Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding

inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot

Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy

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Discovery of a Novel Binding Trench in HIV Integrase

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A Computational Study of the Binding of Propidium to the Peripheral Anionic Site of Human Acetylcholinesterase

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Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures

inferredcites →https://doi.org/10.1021/jm050043wopenalex-snapshot

M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects

inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot

Modeling Water Molecules in Protein−Ligand Docking Using GOLD

inferredcites →https://doi.org/10.1021/jm060236zopenalex-snapshot

A Combination of Docking/Dynamics Simulations and Pharmacophoric Modeling To Discover New Dual c-Src/Abl Kinase Inhibitors

inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot

Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance

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Recent Developments in Fragment-Based Drug Discovery

inferredcites →https://doi.org/10.1021/jm8009958openalex-snapshot

Four-Dimensional Docking: A Fast and Accurate Account of Discrete Receptor Flexibility in Ligand Docking

inferredcites →https://doi.org/10.1021/jm8010096openalex-snapshot

Discovery of Multitarget Inhibitors by Combining Molecular Docking with Common Pharmacophore Matching

inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot

A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach

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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins

inferredcites →https://doi.org/10.1021/jp803936qopenalex-snapshot

Exploring Complex Protein−Ligand Recognition Mechanisms with Coarse Metadynamics

inferredcites →https://doi.org/10.1038/nchembio.155openalex-snapshot

Molecular docking and ligand specificity in fragment-based inhibitor discovery

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The role of dynamic conformational ensembles in biomolecular recognition

inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot

Implications of protein flexibility for drug discovery

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Paul Ehrlich: Magister Mundi

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Docking and scoring in virtual screening for drug discovery: methods and applications

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Computer-based de novo design of drug-like molecules

inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot

Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go

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Statistical Mechanics of Fluid Mixtures

inferredcites →https://doi.org/10.1073/pnas.202427399openalex-snapshot

Escaping free-energy minima

inferredcites →https://doi.org/10.1073/pnas.221290398openalex-snapshot

Structure of the interferon-receptor complex determined by distance constraints from double-mutant cycles and flexible docking

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Application of a Theory of Enzyme Specificity to Protein Synthesis

inferredcites →https://doi.org/10.1089/106652702760277336openalex-snapshot

A Combinatorial Approach to Protein Docking with Flexible Side Chains

inferredcites →https://doi.org/10.1093/bioinformatics/btl212openalex-snapshot

AClAP, Autonomous hierarchical agglomerative Cluster Analysis based protocol to partition conformational datasets

inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot

A new method for predicting binding affinity in computer-aided drug design

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Efficient molecular docking of NMR structures: Application to HIV‐1 protease

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Atomic Property Fields: Generalized 3D Pharmacophoric Potential for Automated Ligand Superposition, Pharmacophore Elucidation and 3D QSAR

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The Many Roles of Computation in Drug Discovery

inferredcites →https://doi.org/10.1126/science.6879170openalex-snapshot

Solvent-Accessible Surfaces of Proteins and Nucleic Acids

inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot

Molecular Recognition and Docking Algorithms

inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot

Calculation of Protein-Ligand Binding Affinities

inferredcites →https://doi.org/10.1371/journal.pcbi.1000648openalex-snapshot

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

inferredcites →https://doi.org/10.1529/biophysj.105.071589openalex-snapshot

Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches

inferredcites →https://doi.org/10.2172/4390578openalex-snapshot

Equation of state calculations by fast computing machines

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Targeted Drugs in Chronic Myeloid Leukemia

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Molecular Descriptors and Methods for Ligand Based Virtual High Throughput Screening in Drug Discovery

inferredcites →https://doi.org/10.2174/138161206777585256openalex-snapshot

Development, Validation, and Applications of Anisotropic Polarizable Molecular Mechanics to Study Ligand and Drug-Receptor Interactions

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Methods for the Prediction of Protein-Ligand Binding Sites for Structure-Based Drug Design and Virtual Ligand Screening.

inferredcites →https://doi.org/10.2174/138920308783565741openalex-snapshot

Recent Progress and Future Directions in Protein-Protein Docking

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Last Findings on Dual Inhibitors of Abl and Src Tyrosine-Kinases

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Targeting the Kinase Activity of the BCR-ABL Fusion Protein in Patients with Chronic Myeloid Leukemia

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Ligand-Based Drug Design Methodologies in Drug Discovery Process: An Overview

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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