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BALLDock/SLICK: A New Method for Protein-Carbohydrate Docking

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

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Flexible docking using tabu search and an empirical estimate of binding affinity
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Total Synthesis of Antigen Bacillus Anthracis Tetrasaccharide—Creation of an Anthrax Vaccine Candidate
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Specific empirical free energy function for automated docking of carbohydrates to proteins
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Molecular docking using shape descriptors
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ConsDock: A new program for the consensus analysis of protein–ligand interactions
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HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
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Automated docking of substrates to proteins by simulated annealing
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A Continuum Model for Protein–Protein Interactions: Application to the Docking Problem
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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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Evolutionary algorithms in computer-aided molecular design
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W3-SWEET: Carbohydrate Modeling By Internet
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BALLView: An object-oriented molecular visualization and modeling framework
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A geometric approach to macromolecule-ligand interactions
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Computational modeling of the sugar–lectin interaction
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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
inferredcites →https://doi.org/10.1021/ci050422yopenalex-snapshot
SLICK − Scoring and Energy Functions for Protein−Carbohydrate Interactions
inferredcites →https://doi.org/10.1021/ci0600758openalex-snapshot
GFscore: A General Nonlinear Consensus Scoring Function for High-Throughput Docking
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A scaled particle theory of aqueous and nonaqueous solutions
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Molecular Mechanical and Molecular Dynamic Simulations of Glycoproteins and Oligosaccharides. 1. GLYCAM_93 Parameter Development
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Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
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Involvement of Water in Carbohydrate−Protein Binding
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/ja051020+openalex-snapshot
Molecular Recognition of Saccharides by Proteins. Insights on the Origin of the Carbohydrate−Aromatic Interactions
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Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm001044lopenalex-snapshot
Protein-Based Virtual Screening of Chemical Databases. 1. Evaluation of Different Docking/Scoring Combinations
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1021/jm990408aopenalex-snapshot
Successful Virtual Screening of a Chemical Database for Farnesyltransferase Inhibitor Leads
inferredcites →https://doi.org/10.1023/a:1007934310264openalex-snapshot
A comparison of heuristic search algorithms for molecular docking
inferredcites →https://doi.org/10.1023/a:1008005918983openalex-snapshot
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
inferredcites →https://doi.org/10.1023/a:1008137707965openalex-snapshot
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
inferredcites →https://doi.org/10.1023/a:1011926026653openalex-snapshot
Lectin-Mediated Drug Targeting: Preparation, Binding Characteristics, and Antiproliferative Activity of Wheat Germ Agglutinin Conjugated Doxorubicin on Caco-2 Cells
inferredcites →https://doi.org/10.1023/a:1020155510718openalex-snapshot
A review of protein-small molecule docking methods
inferredcites →https://doi.org/10.1023/b:jcam.0000017496.76572.6fopenalex-snapshot
Comparative study of several algorithms for flexible ligand docking
inferredcites →https://doi.org/10.1038/news050418-6openalex-snapshot
Sugar coating improves anticancer treatment
inferredcites →https://doi.org/10.1093/bioinformatics/16.9.815openalex-snapshot
BALL—rapid software prototyping in computational molecular biology
inferredcites →https://doi.org/10.1093/bioinformatics/bti818openalex-snapshot
BALLView: a tool for research and education in molecular modeling
inferredcites →https://doi.org/10.1093/glycob/cwl062openalex-snapshot
Activity–structure correlations in divergent lectin evolution: fine specificity of chicken galectin CG-14 and computational analysis of flexible ligand docking for CG-14 and the closely related CG-16
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/protein/13.2.89openalex-snapshot
Analysis and prediction of carbohydrate binding sites
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Effective sampling and distance metrics for 3D rigid body path planning
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Hydrogen‐bonding pattern of methyl β‐lactoside binding to the Ricinus communis lectins
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.3109/10611869808997885openalex-snapshot
Lectin-Mediated Drug Targeting: Quantification of Binding and Internalization ofWheat germAgglutinin andSolatium tuberosumLectin Using Caco-2 and HT-29 Cells
inferredcites →https://doi.org/10.4049/jimmunol.173.2.797openalex-snapshot
Mechanism by Which Orally Administered β-1,3-Glucans Enhance the Tumoricidal Activity of Antitumor Monoclonal Antibodies in Murine Tumor Models

What points at this work

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

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ChemInform Abstract: BALLDock/SLICK: A New Method for Protein‐Carbohydrate Docking.
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Computational Prediction of Carbohydrate‐Binding Proteins and Binding Sites
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