Mondal et al., 2019 - Google Patents
Exploring the effectiveness of binding free energy calculationsMondal et al., 2019
View HTML- Document ID
- 4569258101173209277
- Author
- Mondal D
- Florian J
- Warshel A
- Publication year
- Publication venue
- The Journal of Physical Chemistry B
External Links
Snippet
Increasing the accuracy of the evaluation of ligand-binding energies is one of the most important tasks of current computational biology. Here we explore the accuracy of free energy perturbation (FEP) approaches by comparing the performance of a “regular” FEP …
- 230000027455 binding 0 title abstract description 239
Classifications
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/16—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for molecular structure, e.g. structure alignment, structural or functional relations, protein folding, domain topologies, drug targeting using structure data, involving two-dimensional or three-dimensional structures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
- G06F19/706—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for drug design with the emphasis on a therapeutic agent, e.g. ligand-biological target interactions, pharmacophore generation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
- G06F19/701—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for molecular modelling, e.g. calculation and theoretical details of quantum mechanics, molecular mechanics, molecular dynamics, Monte Carlo methods, conformational analysis or the like
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
- G06F19/704—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for prediction of properties of compounds, e.g. calculating and selecting molecular descriptors, details related to the development of SAR/QSAR/QSPR models, ADME/Tox models or PK/PD models
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
- G06F19/12—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for modelling or simulation in systems biology, e.g. probabilistic or dynamic models, gene-regulatory networks, protein interaction networks or metabolic networks
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/70—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds
- G06F19/708—Chemoinformatics, i.e. data processing methods or systems for the retrieval, analysis, visualisation, or storage of physicochemical or structural data of chemical compounds for data visualisation, e.g. molecular structure representations, graphics generation, display of maps or networks or other visual representations
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/50—Computer-aided design
- G06F17/5009—Computer-aided design using simulation
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
- G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
- G06F19/30—Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by the preceding groups
- G01N33/48—Investigating or analysing materials by specific methods not covered by the preceding groups biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
-
- G—PHYSICS
- G06—COMPUTING; CALCULATING; COUNTING
- G06F—ELECTRICAL DIGITAL DATA PROCESSING
- G06F11/00—Error detection; Error correction; Monitoring
Similar Documents
Publication | Publication Date | Title |
---|---|---|
Wang et al. | Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field | |
Gill et al. | Binding modes of ligands using enhanced sampling (BLUES): rapid decorrelation of ligand binding modes via nonequilibrium candidate Monte Carlo | |
Lakkaraju et al. | Sampling of organic solutes in aqueous and heterogeneous environments using oscillating excess chemical potentials in grand canonical-like Monte Carlo-molecular dynamics simulations | |
Raman et al. | Automated, accurate, and scalable relative protein–ligand binding free-energy calculations using lambda dynamics | |
Chen et al. | Parameters of monovalent ions in the AMBER-99 forcefield: Assessment of inaccuracies and proposed improvements | |
Ross et al. | Water sites, networks, and free energies with grand canonical Monte Carlo | |
Khalak et al. | Chemical space exploration with active learning and alchemical free energies | |
Paliwal et al. | A benchmark test set for alchemical free energy transformations and its use to quantify error in common free energy methods | |
Singh et al. | AADS-An automated active site identification, docking, and scoring protocol for protein targets based on physicochemical descriptors | |
Mobley et al. | Small molecule hydration free energies in explicit solvent: an extensive test of fixed-charge atomistic simulations | |
Dunbar Jr et al. | CSAR benchmark exercise of 2010: selection of the protein–ligand complexes | |
Sindhikara et al. | Analysis of biomolecular solvation sites by 3D-RISM theory | |
Giese et al. | A GPU-accelerated parameter interpolation thermodynamic integration free energy method | |
Baumann et al. | Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations | |
Bursulaya et al. | Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models | |
Ratkova et al. | An accurate prediction of hydration free energies by combination of molecular integral equations theory with structural descriptors | |
Samways et al. | grand: a Python module for grand canonical water sampling in OpenMM | |
Bodnarchuk et al. | Strategies to calculate water binding free energies in protein–ligand complexes | |
Liu et al. | Is ring breaking feasible in relative binding free energy calculations? | |
Bottaro et al. | Variational optimization of an all-atom implicit solvent force field to match explicit solvent simulation data | |
Mondal et al. | Exploring the effectiveness of binding free energy calculations | |
Wahl et al. | Assessing the predictive power of relative binding free energy calculations for test cases involving displacement of binding site water molecules | |
Chys et al. | Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure | |
Calabrò et al. | Elucidation of nonadditive effects in protein–ligand binding energies: Thrombin as a case study | |
Cui et al. | The role of interfacial water in protein–ligand binding: Insights from the indirect solvent mediated potential of mean force |