A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity
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Summary
The preliminary docking results implies that H-DOCK can be potentially used for large scale virtual screening as a pre-filter for a more accurate but less efficient docking algorithm.
- Type
- article
- Published
- 2010-05-01
- Cited by
- 32
- References
- 31
- OpenAlex
- https://openalex.org/W19823881
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:2255129
Keywords
Business, Computer science
References
- MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
- QXP: Powerful, rapid computer algorithms for structure-based drug design
- LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
- DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
- Protein ligand docking based on empirical method for binding affinity estimation
- Hydrogen bonding in globular proteins.
- Rational automatic search method for stable docking models of protein and ligand.
- Comparative evaluation of 11 scoring functions for molecular docking.
- Prodock: Software package for protein modeling and docking
- LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites.
- Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.
- ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
- DARWIN: A program for docking flexible molecules
- Flexible docking using tabu search and an empirical estimate of binding affinity
- Development and validation of a genetic algorithm for flexible docking.
- Improved protein–ligand docking using GOLD
- FLOG: A system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure
- Empirical energy functions for energy minimization and dynamics of nucleic acids
- High throughput docking for library design and library prioritization
- Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking.
Cited by
- ProSelection: A Novel Algorithm to Select Proper Protein Structure Subsets for in Silico Target Identification and Drug Discovery Research
- Modeliranje 3D struktur interakcijmed proteini in RNA
- PRL‐dock: Protein‐ligand docking based on hydrogen bond matching and probabilistic relaxation labeling
- A solvated ligand rotamer approach and its application in computational protein design
- Analysis of surface structures of hydrogen bonding in protein–ligand interactions using the alpha shape model
- Performance of the MM/GBSA scoring using a binding site hydrogen bond network-based frame selection: the protein kinase case.
- Predicting HLA Class I Non-Permissive Amino Acid Residues Substitutions
- The relationship between geometric patterns of hydrogen bonds and periodic dinucleotides in nucleosome structures.
- Collective variable driven molecular dynamics to improve protein-protein docking scoring
- A python-based docking program utilizing a receptor bound ligand shape: PythDock
- The Human Proteome Organization Chromosome 6 Consortium: Integrating chromosome-centric and biology/disease driven strategies
- A matching algorithm for catalytic residue site selection in computational enzyme design
- Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking
- Latest developments in molecular docking: 2010–2011 in review
- Binding mode study of β-glucosidase b from p.Polymyxca with cellobiose and laminaribiose
- Docking study of b-glucosidase b (bglb) from p. polymyxca with cellobiose and cellotetrose
- An efficient searching algorithm based on local shape complementarity of hydrogen bonds and relaxation labeling for protein-ligand docking
- GPU‐accelerated atom and dynamic bond visualization using hyperballs: A unified algorithm for balls, sticks, and hyperboloids
- Systematic optimization model and algorithm for binding sequence selection in computational enzyme design
- Looking for agonists of β2 adrenergic receptor from Fuzi and Chuanwu by virtual screening and dual-luciferase reporter assay
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