[go: up one dir, main page]
More Web Proxy on the site http://driver.im/

Chen, 2015 - Google Patents

Hybrid steered molecular dynamics approach to computing absolute binding free energy of Ligand–Protein Complexes: A brute force approach that is fast and …

Chen, 2015

View PDF
Document ID
6792981411752535781
Author
Chen L
Publication year
Publication venue
Journal of chemical theory and computation

External Links

Snippet

Computing the free energy of binding a ligand to a protein is a difficult task of essential importance for which purpose various theoretical/computational approaches have been pursued. In this paper, we develop a hybrid steered molecular dynamics (hSMD) method …
Continue reading at pubs.acs.org (PDF) (other versions)

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
    • 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
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F3/00—Input arrangements for transferring data to be processed into a form capable of being handled by the computer; Output arrangements for transferring data from processing unit to output unit, e.g. interface arrangements
    • G06F3/01—Input arrangements or combined input and output arrangements for interaction between user and computer
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity

Similar Documents

Publication Publication Date Title
Nawrocki et al. Slow-down in diffusion in crowded protein solutions correlates with transient cluster formation
Chen Hybrid steered molecular dynamics approach to computing absolute binding free energy of Ligand–Protein Complexes: A brute force approach that is fast and accurate
Albaugh et al. Advanced potential energy surfaces for molecular simulation
Harada et al. Reduced native state stability in crowded cellular environment due to protein–protein interactions
Ufimtsev et al. Quantum chemistry on graphical processing units. 3. Analytical energy gradients, geometry optimization, and first principles molecular dynamics
Costa et al. Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes
Wolf et al. Targeted molecular dynamics calculations of free energy profiles using a nonequilibrium friction correction
Gilman-Politi et al. Unraveling the molecular mechanism of enthalpy driven peptide folding by polyol osmolytes
Comer et al. Calculation of lipid-bilayer permeabilities using an average force
Huggins et al. Thermodynamic properties of water molecules at a protein–protein interaction surface
Stafford et al. Vibrational Stark Effect Spectroscopy at the Interface of Ras and Rap1A Bound to the Ras Binding Domain of RalGDS Reveals an Electrostatic Mechanism for Protein− Protein Interaction
Domanski et al. Balancing force field protein–lipid interactions to capture transmembrane helix–helix association
Tanizaki et al. Molecular dynamics simulations of large integral membrane proteins with an implicit membrane model
Rodriguez et al. Computing protein–protein association affinity with hybrid steered molecular dynamics
White et al. Free energy of solvated salt bridges: A simulation and experimental study
Johnson et al. Mapping allostery through computational glycine scanning and correlation analysis of Residue–Residue contacts
Batista et al. Free energy profiles along consensus normal modes provide insight into HIV-1 protease flap opening
Levine et al. Trp-cage folding on organic surfaces
Ramezanghorbani et al. Optimizing protein–polymer interactions in a poly (ethylene glycol) coarse-grained model
Kondo et al. Free-energy landscapes of protein domain movements upon ligand binding
Kubiak-Ossowska et al. Fibronectin module FNIII9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics
Geist et al. Replica-based protein structure sampling methods II: advanced hybrid solvent TIGER2hs
van Adrichem et al. AIM: a mapping program for infrared spectroscopy of proteins
Chen et al. Conserved functional surface of antimammalian scorpion β-toxins
Moreira et al. Hot spot occlusion from bulk water: a comprehensive study of the complex between the lysozyme HEL and the antibody FVD1. 3