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A good ligand is hard to find: Automated docking methods
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/9780470125786.ch6openalex-snapshot
Searching Databases of Three‐Dimensional Structures
inferredcites →https://doi.org/10.1002/bip.360260602openalex-snapshot
A new approach to the problem of docking two molecules: The ellipsoid algorithm
inferredcites →https://doi.org/10.1002/chin.199132317openalex-snapshot
ChemInform Abstract: Computer Graphics and Molecular Modeling in the Analysis of Synthetic Targets
inferredcites →https://doi.org/10.1002/jcc.540060510openalex-snapshot
Computer graphics in real‐time docking with energy calculation and minimization
inferredcites →https://doi.org/10.1002/jcc.540130311openalex-snapshot
Molecular docking using shape descriptors
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
inferredcites →https://doi.org/10.1002/jcc.540130608openalex-snapshot
Conformational analysis of flexible ligands in macromolecular receptor sites
inferredcites →https://doi.org/10.1002/pro.5560010204openalex-snapshot
Atomic solvation parameters applied to molecular dynamics of proteins in solution
inferredcites →https://doi.org/10.1002/prot.340080302openalex-snapshot
Automated docking of substrates to proteins by simulated annealing
inferredcites →https://doi.org/10.1002/prot.340110409openalex-snapshot
Computer design of bioactive molecules: A method for receptor‐based de novo ligand design
inferredcites →https://doi.org/10.1002/prot.340120105openalex-snapshot
CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure
inferredcites →https://doi.org/10.1002/prot.340130304openalex-snapshot
A multiple‐start Monte Carlo docking method
inferredcites →https://doi.org/10.1002/prot.340160306openalex-snapshot
Surface motifs by a computer vision technique: Searches, detection, and implications for protein–ligand recognition
inferredcites →https://doi.org/10.1002/prot.340170104openalex-snapshot
Automated docking in crystallography: Analysis of the substrates of aconitase
inferredcites →https://doi.org/10.1007/978-3-662-09438-9openalex-snapshot
Principles of Artificial Intelligence
inferredcites →https://doi.org/10.1007/978-94-011-1472-1_98openalex-snapshot
Flexible docking of ligands to receptor sites using genetic algorithms
inferredcites →https://doi.org/10.1007/bf00125505openalex-snapshot
An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes
inferredcites →https://doi.org/10.1007/bf00126217openalex-snapshot
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
inferredcites →https://doi.org/10.1007/bf00141573openalex-snapshot
GenStar: A method for de novo drug design
inferredcites →https://doi.org/10.1016/0014-5793(88)81394-2openalex-snapshot
Molecular foundations of drug—receptor interaction
inferredcites →https://doi.org/10.1016/0022-2836(79)90308-5openalex-snapshot
Gene duplications in the structural evolution of chymotrypsin
inferredcites →https://doi.org/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0022-2836(91)80222-gopenalex-snapshot
Protein docking and complementarity
inferredcites →https://doi.org/10.1016/0022-2836(91)90859-5openalex-snapshot
“Soft docking”: Matching of molecular surface cubes
inferredcites →https://doi.org/10.1016/0022-2836(92)90405-9openalex-snapshot
Docking by least-squares fitting of molecular surface patterns
inferredcites →https://doi.org/10.1016/0022-2836(92)90506-fopenalex-snapshot
New algorithm to model protein-protein recognition based on surface complementarity
inferredcites →https://doi.org/10.1016/0898-5529(90)90169-9openalex-snapshot
DOCKing ligands into receptors: The test case of α-chymotrypsin
inferredcites →https://doi.org/10.1016/0968-0004(84)90122-1openalex-snapshot
Basis of biological specificity
inferredcites →https://doi.org/10.1016/s0021-9258(18)33497-5openalex-snapshot
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
inferredcites →https://doi.org/10.1016/s0021-9258(18)82261-xopenalex-snapshot
Structure of a non-peptide inhibitor complexed with HIV-1 protease. Developing a cycle of structure-based drug design
inferredcites →https://doi.org/10.1016/s0022-2836(75)80005-2openalex-snapshot
The refined crystal structure of bovine β-trypsin at 1·8 Å resolution
inferredcites →https://doi.org/10.1016/s0022-2836(77)80200-3openalex-snapshot
The protein data bank: A computer-based archival file for macromolecular structures
inferredcites →https://doi.org/10.1021/bi00063a007openalex-snapshot
Inhibition of the fusion-inducing conformational change of influenza hemagglutinin by benzoquinones and hydroquinones
inferredcites →https://doi.org/10.1021/ci00003a004openalex-snapshot
Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads
inferredcites →https://doi.org/10.1021/ja00315a051openalex-snapshot
A new force field for molecular mechanical simulation of nucleic acids and proteins
inferredcites →https://doi.org/10.1021/ja00387a046openalex-snapshot
Molecular mechanics simulation of protein-ligand interactions: binding of thyroid hormone analogs to prealbumin
inferredcites →https://doi.org/10.1021/jm00064a003openalex-snapshot
GroupBuild: a fragment-based method for de novo drug design
inferredcites →https://doi.org/10.1021/jm00088a002openalex-snapshot
Definition and display of steric, hydrophobic, and hydrogen bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design
inferredcites →https://doi.org/10.1021/jm00090a001openalex-snapshot
3D database searching in drug design
inferredcites →https://doi.org/10.1021/jm00111a001openalex-snapshot
Design of enzyme inhibitors using iterative protein crystallographic analysis
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm00161a004openalex-snapshot
Docking flexible ligands to macromolecular receptors by molecular shape
inferredcites →https://doi.org/10.1021/jm00399a006openalex-snapshot
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
inferredcites →https://doi.org/10.1038/314235a0openalex-snapshot
Hydrogen bonding and biological specificity analysed by protein engineering
inferredcites →https://doi.org/10.1038/319199a0openalex-snapshot
Solvation energy in protein folding and binding
inferredcites →https://doi.org/10.1038/356539a0openalex-snapshot
The dead-end elimination theorem and its use in protein side-chain positioning
inferredcites →https://doi.org/10.1038/358774a0openalex-snapshot
Prediction of the structure of a receptor–protein complex using a binary docking method
inferredcites →https://doi.org/10.1038/363418a0openalex-snapshot
Rational design of potent sialidase-based inhibitors of influenza virus replication
inferredcites →https://doi.org/10.1063/1.1699114openalex-snapshot
Equation of State Calculations by Fast Computing Machines
inferredcites →https://doi.org/10.1073/pnas.71.11.4298openalex-snapshot
The Three-Dimensional Structure of a Phosphorylcholine-Binding Mouse Immunoglobulin Fab and the Nature of the Antigen Binding Site
inferredcites →https://doi.org/10.1073/pnas.84.10.3086openalex-snapshot
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides.
inferredcites →https://doi.org/10.1073/pnas.87.17.6644openalex-snapshot
Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease.
inferredcites →https://doi.org/10.1073/pnas.88.24.11540openalex-snapshot
Application of crystallographic and modeling methods in the design of purine nucleoside phosphorylase inhibitors.
inferredcites →https://doi.org/10.1073/pnas.90.4.1146openalex-snapshot
Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli.
inferredcites →https://doi.org/10.1073/pnas.90.8.3583openalex-snapshot
Structure-based inhibitor design by using protein models for the development of antiparasitic agents.
inferredcites →https://doi.org/10.1093/protein/4.2.177openalex-snapshot
Distance-constrained molecular docking by simulated annealing
inferredcites →https://doi.org/10.1093/protein/5.1.69openalex-snapshot
A robust and efficient automated docking algorithm for molecular recognition
inferredcites →https://doi.org/10.1093/protein/6.7.723openalex-snapshot
Matching chemistry and shape in molecular docking
inferredcites →https://doi.org/10.1107/s0567740879009249openalex-snapshot
The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information
inferredcites →https://doi.org/10.1111/j.1476-5381.1976.tb07468.xopenalex-snapshot
COMPOUNDS DESIGNED TO FIT A SITE OF KNOWN STRUCTURE IN HUMAN HAEMOGLOBIN
inferredcites →https://doi.org/10.1126/science.256.5054.213openalex-snapshot
An SCF Solvation Model for the Hydrophobic Effect and Absolute Free Energies of Aqueous Solvation
inferredcites →https://doi.org/10.1126/science.257.5073.1078openalex-snapshot
Structure-Based Strategies for Drug Design and Discovery
inferredcites →https://doi.org/10.1126/science.3810155openalex-snapshot
Evaluation of Intrinsic Binding Energy from a Hydrogen Bonding Group in an Enzyme Inhibitor
inferredcites →https://doi.org/10.1126/science.6879170openalex-snapshot
Solvent-Accessible Surfaces of Proteins and Nucleic Acids
inferredcites →https://doi.org/10.1126/science.8451640openalex-snapshot
Structure-Based Discovery of Inhibitors of Thymidylate Synthase
inferredcites →https://doi.org/10.1248/cpb.41.1200openalex-snapshot
Development of an efficient automated docking method.
inferredcites →https://doi.org/10.1248/cpb.41.1203openalex-snapshot
Application and evaluation of the automated docking method.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
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Mapping of proteinase active sites by projection of surface-derived correlation vectors
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Statistical analysis of computational docking of large compound data bases to distinct protein binding sites
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Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes
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Evaluation of the CASP2 docking section
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CASP2 experiences with docking flexible ligands using FLEXX
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Mean field analysis of FKBP12 complexes with FK506 and rapamycin: Implications for a role of crystallographic water molecules in molecular recognition and specificity
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Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin
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Flexible docking using tabu search and an empirical estimate of binding affinity
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Flexible ligand docking: A multistep strategy approach
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Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
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Efficacy and selectivity in flexible database docking
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Dynamic ligand design and combinatorial optimization: Designing inhibitors to endothiapepsin
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Low-resolution docking: Prediction of complexes for underdetermined structures
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Automated docking of flexible ligands: Applications of autodock
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Molecular docking towards drug discovery
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High‐throughput ‘Virtual’ Chemistry
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Genetic Algorithms: Introduction and Applications
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Molecular Modeling in Drug Design
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Docking and Scoring in Drug Discovery
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Docking, Scoring, and Virtual Screening in Drug Discovery
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Similarity-driven flexible ligand docking
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Mapping of stereoselective recognition sites on human serum transferrin by capillary electrophoresis and molecular modelling
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Similarity Searching in Databases of Chemical Structures
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Current Issues in De Novo Molecular Design
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Approaches to Three‐Dimensional Quantitative Structure‐Activity Relationships
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Structure‐Based Design: From Renin to HIV‐1 Protease
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New Computational Approaches to Predict Protein‐Ligand Interactions
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3D—Segmentierungstechniken und vektorwertige Bewertungsfunktionen für symbolisches Protein—Protein—Docking
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Was läßt sich aus der molekularen Erkennung in Protein‐Ligand‐Komplexen für das Design neuer Wirkstoffe lernen?
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What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs?
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THE ROLE OF LIGAND FLEXIBILITY IN PREDICTING BIOLOGICAL ACTIVITY: STRUCTURE–ACTIVITY RELATIONSHIPS FOR ARYL HYDROCARBON, ESTROGEN, AND ANDROGEN RECEPTOR BINDING AFFINITY
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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Docking of small ligands to low‐resolution and theoretically predicted receptor structures
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An efficient molecular docking using conformational space annealing
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A distance geometry heuristic for expanding the range of geometries sampled during conformational search
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Searching for pharmacophoric patterns in databases of three‐dimensional chemical structures
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Biophysical and structural characterization of tetramethrin serum protein complex and its toxicological implications
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Stochastic Proximity Embedding: Methods and Applications
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Investigation of Active Compounds of Brucea Javanica In Treating Hypertension Using A Network Pharmacology‐Based Analysis Combined with Homology Modeling, Molecular Docking and Molecular Dynamics Simulation
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Molecular interaction fields in drug discovery: recent advances and future perspectives
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen
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3D QSAR: Current State, Scope, and Limitations
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Similarity versus docking in 3D virtual screening
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A recursive algorithm for efficient combinatorial library docking
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Smooth surfaces for multi-scale shape representation
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Gaussian-Based Approaches to Protein-Structure Similarity
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Molecular Docking with a View: The Integration of a Monte Carlo Docking Program into a Virtual Reality Environment
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Protein Docking in the Absence of Detailed Molecular Structures
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Computational Approaches to Understand Cleavage Mechanism of Amyloid Beta (Aβ) Peptide
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Docking Methods for Structure-Based Library Design
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Chances and Risks of Modeling in Industry
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On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
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Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
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Evolutionary algorithms in computer-aided molecular design
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Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal
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Computational Approaches to Drug Design
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Molecular structures of some D-homo-6-oxa-8α analogs of steroidal estrogens
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Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor
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Docking small-molecule ligands into active sites
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Ligand—protein docking and rational drug design
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Structure-affinity relationships of baclofen and 3-heteroaromatic analogues
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Computer-based screening of compound databases for the identification of novel leads
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Ascorbic Acid Is a Potential Inhibitor of Collagenases—In Silico and In Vitro Biological Studies
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Modeling Drug–Receptor Interactions
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Genetic Algorithms for Chemical Structure Handling and Molecular Recognition
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Genetic programming for QSAR investigation of docking energy
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In silico identification and biochemical characterization of novel inhibitors of NQO1
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Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
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Computational tools for structure-based ligand design
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Genetic algorithms in molecular recognition and design
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viwish: A visualisation server for protein modelling and docking
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Current computational tools for de novo ligand design
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Virtual screening—an overview
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Expanded Interaction Fingerprint Method for Analyzing Ligand Binding Modes in Docking and Structure-Based Drug Design
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Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New Scale
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Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin-Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency of the inhibitors by Docking and ONIOM Calculations
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Combinatorial Library Design: Maximizing Model-Fitting Compounds within Matrix Synthesis Constraints
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A Simple Method for Improving Torsion Optimization of Ligand Molecules in Receptor Binding Sites
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Calculation of the Relative Binding Affinity of Enzyme Inhibitors Using the Generalized Linear Response Method
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Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention
inferred← citeshttps://doi.org/10.1023/a:1007934310264openalex-snapshot
A comparison of heuristic search algorithms for molecular docking
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Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
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The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
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Methodological developments and strategies for a fast flexible superposition of drug-size molecules
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Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
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PRO_SELECT: Combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology
inferred← citeshttps://doi.org/10.1023/a:1008716720979openalex-snapshot
A recursive algorithm for efficient combinatorial library docking
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Similarity versus docking in 3D virtual screening
inferred← citeshttps://doi.org/10.1023/a:1015756220637openalex-snapshot
A Study of the Binding of Estradiol and 8-Isoestradiol to the Estrogen α-Receptor by Molecular Modeling
inferred← citeshttps://doi.org/10.1023/a:1017037831628openalex-snapshot
3D QSAR: current state, scope, and limitations
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A review of protein-small molecule docking methods
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Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case
inferred← citeshttps://doi.org/10.1063/1.1287147openalex-snapshot
Free energy screening of small ligands binding to an artificial protein cavity
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Molecular Mechanics Calculations of Proteins. Comparison of Different Energy Minimization Strategies
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Computational Chemistry in Lead Identification, Library Design and Lead Optimisation
inferred← citeshttps://doi.org/10.1080/08927022.2021.1935926openalex-snapshot
Theoretical studies of Thiazolyl-Pyrazoline derivatives as promising drugs against malaria by QSAR modelling combined with molecular docking and molecular dynamics simulation
inferred← citeshttps://doi.org/10.1080/10629369808039144openalex-snapshot
Automated Docking and the Search for HIV Protease Inhibitors
inferred← citeshttps://doi.org/10.1080/1062936x.2021.1960601openalex-snapshot
Molecular modelling on SARS-CoV-2 papain-like protease: an integrated study with homology modelling, molecular docking, and molecular dynamics simulations
inferred← citeshttps://doi.org/10.1080/17460441.2022.2079632openalex-snapshot
The emerging potential of interactive virtual reality in drug discovery
inferred← citeshttps://doi.org/10.1093/bioinformatics/15.3.243openalex-snapshot
Docking of hydrophobic ligands with interaction-based matching algorithms.
inferred← citeshttps://doi.org/10.1093/bioinformatics/18.7.939openalex-snapshot
Ligand-induced changes in the binding sites of proteins
inferred← citeshttps://doi.org/10.1109/icip.1995.537694openalex-snapshot
Segmentation of molecular surfaces based on their convex hull
inferred← citeshttps://doi.org/10.1109/iis.1997.645168openalex-snapshot
Search techniques for rational drug design
inferred← citeshttps://doi.org/10.1109/tcbb.2015.2401020openalex-snapshot
A Novel Scoring Based Distributed Protein Docking Application to Improve Enrichment
inferred← citeshttps://doi.org/10.1111/cbdd.13415openalex-snapshot
Inhibition of key enzymes in the inflammatory pathway by hybrid molecules of terpenes and synthetic drugs: In vitro and in silico studies
inferred← citeshttps://doi.org/10.11131/2016/101202openalex-snapshot
Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors
inferred← citeshttps://doi.org/10.1147/sj.402.0265openalex-snapshot
Computational challenges in structural and functional genomics
inferred← citeshttps://doi.org/10.11606/d.9.2014.tde-26052015-160701openalex-snapshot
Antichagásicos potenciais: planejamento e síntese de bioisósteros 1,2,4-triazólicos do hidroximetilnitrofural e análogos
inferred← citeshttps://doi.org/10.1385/1-59259-329-1:425openalex-snapshot
Discovering Novel Anticancer Drugs Practical Aspects and Recent Advances
inferred← citeshttps://doi.org/10.1517/13543776.7.9.937openalex-snapshot
Recent advances in computer-aided drug design methods
inferred← citeshttps://doi.org/10.2174/1570163819666220117161308openalex-snapshot
Computational Approach to Combat COVID-19 Infection: Emerging Tools for Accelerating Drug Research
inferred← citeshttps://doi.org/10.2174/1570180820666221111151104openalex-snapshot
Role of Docking in Anticancer Drug Discovery
inferred← citeshttps://doi.org/10.2174/1573409916666200213124929openalex-snapshot
Investigation of New Inhibitors of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) by Virtual Screening with Antibacterial Assessment
inferred← citeshttps://doi.org/10.2174/2210315506666160218224112openalex-snapshot
Screening of Potential Anticancer Compounds from Sargassum wightii to Target Breast Cancer Specific HER2 Receptor using in-silico Analysis
inferred← citeshttps://doi.org/10.25004/ijpsdr.2021.130108openalex-snapshot
In silico prediction and molecular docking study on the interaction of bioactive compounds of Adenanthera pavonina exploring the potential antifungal activity against Candida glabrata cell wall proteins
inferred← citeshttps://doi.org/10.31031/madd.2018.01.000518openalex-snapshot
Molecular Docking an Important Tool for Drug Designing
inferred← citeshttps://doi.org/10.3109/14756366.2011.582467openalex-snapshot
Exploring QSARs for inhibitory effect of a set of heterocyclic thrombin inhibitors by multilinear regression refined by artificial neural network and molecular docking simulations
inferred← citeshttps://doi.org/10.3797/scipharm.0803-03openalex-snapshot
Virtual Screening: A Fast Tool for Drug Design
inferred← citeshttps://doi.org/10.3897/pharmacia.69.e77740openalex-snapshot
Inhibitory effects of Moringa oleifera leaves extract on xanthine oxidase activity from bovine milk
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch010openalex-snapshot
Molecular Docking Technique to Understand Enzyme-Ligand Interactions
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch028openalex-snapshot
Molecular Docking Technique to Understand Enzyme-Ligand Interactions
inferred← citeshttps://doi.org/10.5772/intechopen.70554openalex-snapshot
Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts
inferred← citeshttps://doi.org/10.7897/2230-8407.1207151openalex-snapshot
PHARMACOINFORMATICS APPROACH OF IDENTIFIED BIOLOGICAL COMPOUNDS FROM SELECTED PLECTRANTHUS (L.) SPECIES IN TAMIL NADU, INDIA: AN IN-SILICO APPROACH
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.