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Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints
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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/(sici)1096-987x(19970430)18:6<723::aid-jcc1>3.0.co;2-uopenalex-snapshot
Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP?substrate complex
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19980115)19:1<21::aid-jcc2>3.0.co;2-0openalex-snapshot
Docking small ligands in flexible binding sites
inferredcites →https://doi.org/10.1002/(sici)1096-987x(19981115)19:14<1623::aid-jcc8>3.0.co;2-lopenalex-snapshot
Assessing search strategies for flexible docking
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199912)20:16<1740::aid-jcc6>3.0.co;2-aopenalex-snapshot
A critical evaluation of several global optimization algorithms for the purpose of molecular docking
inferredcites →https://doi.org/10.1002/(sici)1097-0134(1999)37:3+<2::aid-prot2>3.3.co;2-uopenalex-snapshot
Critical assessment of methods of protein structure prediction (CASP): Round III
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<29::aid-prot4>3.0.co;2-uopenalex-snapshot
New general approach for determining the solution structure of a ligand bound weakly to a receptor: structure of a fibrinogen A?-like peptide bound to thrombin(S195A) obtained using NOE distance constraints and an ECEPP/3 flexible docking program
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<4::aid-prot2>3.0.co;2-6openalex-snapshot
Ligand solvation in molecular docking
inferredcites →https://doi.org/10.1002/(sici)1097-0134(20000101)38:1<79::aid-prot9>3.0.co;2-uopenalex-snapshot
QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock)
inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot
CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
inferredcites →https://doi.org/10.1002/jcc.540150503openalex-snapshot
ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
inferredcites →https://doi.org/10.1002/jcc.540160409openalex-snapshot
A molecular mechanics/grid method for evaluation of ligand–receptor interactions
inferredcites →https://doi.org/10.1002/prot.340110407openalex-snapshot
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
inferredcites →https://doi.org/10.1002/prot.340130305openalex-snapshot
Monte Carlo docking of oligopeptides to proteins
inferredcites →https://doi.org/10.1002/prot.340140111openalex-snapshot
Monte carlo minimization with thermalization for global optimization of polypeptide conformations in cartesian coordinate space
inferredcites →https://doi.org/10.1006/jmbi.1995.0493openalex-snapshot
Molecular Surface Complementarity at Protein-Protein Interfaces: The Critical Role Played by Surface Normals at Well Placed, Sparse, Points in Docking
inferredcites →https://doi.org/10.1006/jmrb.1993.1042openalex-snapshot
Protein Indirect Relaxation Effects in Exchange-Transferred NOESY by a Rate-Matrix Analysis
inferredcites →https://doi.org/10.1007/bf00213558openalex-snapshot
A refined three-dimensional solution structure of a carboxy terminal fragment of apolipoprotein CII
inferredcites →https://doi.org/10.1007/bf00228148openalex-snapshot
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
inferredcites →https://doi.org/10.1016/0014-5793(90)80211-zopenalex-snapshot
The crystal structure of human muscle aldolase at 3.0 Å resolution
inferredcites →https://doi.org/10.1016/0020-711x(91)90124-6openalex-snapshot
Erythrocyte band 3 protein
inferredcites →https://doi.org/10.1016/0022-2364(92)90014-xopenalex-snapshot
Problems with, and alternatives to, the NMR R factor
inferredcites →https://doi.org/10.1016/0022-2836(91)90650-uopenalex-snapshot
Activity and specificity of human aldolases
inferredcites →https://doi.org/10.1016/0166-1280(88)80133-7openalex-snapshot
Structure and free energy of complex thermodynamic systems
inferredcites →https://doi.org/10.1016/0167-4838(90)90242-8openalex-snapshot
Interactions of glycolytic enzymes with erythrocyte membranes
inferredcites →https://doi.org/10.1016/0263-7855(96)00030-6openalex-snapshot
Molecular recognition via face center representation of a molecular surface
inferredcites →https://doi.org/10.1016/0304-4157(86)90009-2openalex-snapshot
Structure and function of the cytoplasmic domain of band 3: center of erythrocyte membrane—peripheral protein interactions
inferredcites →https://doi.org/10.1016/s0021-9258(17)42710-4openalex-snapshot
Association of phosphofructokinase and aldolase with the membrane of the intact erythrocyte.
inferredcites →https://doi.org/10.1016/s0021-9258(18)82379-1openalex-snapshot
Regulation of glycolysis via reversible enzyme binding to the membrane protein, band 3
inferredcites →https://doi.org/10.1016/s0021-9258(18)83368-3openalex-snapshot
Association of Glyceraldehyde-3-phosphate Dehydrogenase with the Plasma Membrane of the Intact Human Red Blood Cell
inferredcites →https://doi.org/10.1016/s0021-9258(19)68212-8openalex-snapshot
Effect of red cell membrane binding on the catalytic activity of glyceraldehyde-3-phosphate dehydrogenase.
inferredcites →https://doi.org/10.1016/s0021-9258(19)68578-9openalex-snapshot
The aldolase-binding site of the human erythrocyte membrane is at the NH2 terminus of band 3.
inferredcites →https://doi.org/10.1016/s0021-9258(19)83549-4openalex-snapshot
The interaction of phosphofructokinase with erythrocyte membranes.
inferredcites →https://doi.org/10.1016/s0097-8485(96)00011-3openalex-snapshot
Hierarchic inertial projection: A fast distance matrix embedding algorithm
inferredcites →https://doi.org/10.1016/s0969-2126(99)80087-2openalex-snapshot
Soft docking an L and a D peptide to an anticholera toxin antibody using internal coordinate mechanics
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/bi00041a004openalex-snapshot
Solution Structure of the DNA-Binding Protein Sac7d from the Hyperthermophile Sulfolobus acidocaldarius
inferredcites →https://doi.org/10.1021/bi00051a005openalex-snapshot
Solution Structure of a Band 3 Peptide Inhibitor Bound to Aldolase: A Proposed Mechanism for Regulating Binding by Tyrosine Phosphorylation
inferredcites →https://doi.org/10.1021/bi00652a011openalex-snapshot
Binding of rabbit muscle aldolase to band 3, the predominant polypeptide of the human erythrocyte membrane
inferredcites →https://doi.org/10.1021/bi971445bopenalex-snapshot
Insights into Tyrosine Phosphorylation Control of Protein−Protein Association from the NMR Structure of a Band 3 Peptide Inhibitor Bound to Glyceraldehyde-3-phosphate Dehydrogenase,
inferredcites →https://doi.org/10.1021/ci960002wopenalex-snapshot
Similarity Searching in Files of Three-Dimensional Chemical Structures: Flexible Field-Based Searching of Molecular Electrostatic Potentials
inferredcites →https://doi.org/10.1021/ja993810nopenalex-snapshot
Quantitative Symmetry in Structure−Activity Correlations: The Near C2 Symmetry of Inhibitor/HIV Protease Complexes
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1021/jp993073hopenalex-snapshot
Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems
inferredcites →https://doi.org/10.1023/a:1008066310669openalex-snapshot
DREAM++: Flexible docking program for virtual combinatorial libraries
inferredcites →https://doi.org/10.1023/a:1008311703619openalex-snapshot
Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: A simulation study
inferredcites →https://doi.org/10.1023/a:1008360715569openalex-snapshot
RFAC, a program for automated NMR R-factor estimation
inferredcites →https://doi.org/10.1063/1.1699114openalex-snapshot
Equation of State Calculations by Fast Computing Machines
inferredcites →https://doi.org/10.1073/pnas.84.19.6611openalex-snapshot
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
inferredcites →https://doi.org/10.1089/cmb.1998.5.631openalex-snapshot
A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility
inferredcites →https://doi.org/10.1110/ps.8.2.291openalex-snapshot
Crystal structure of human muscle aldolase complexed with fructose 1,6‐bisphosphate: Mechanistic implications
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/cmdc.201000090openalex-snapshot
NMR‐Guided Molecular Docking of a Protein–Peptide Complex Based on Ant Colony Optimization
inferred← citeshttps://doi.org/10.1002/prot.21146openalex-snapshot
Pump‐probe molecular dynamics as a tool for studying protein motion and long range coupling
inferred← citeshttps://doi.org/10.1007/0-306-48533-8_4openalex-snapshot
Application of Angle-Selected Electron Nuclear Double Resonance to Characterize Structured Solvent in Small Molecules and Macromolecules
inferred← citeshttps://doi.org/10.1007/128_2007_144openalex-snapshot
Quantitative Analysis of STD-NMR Spectra of Reversibly Forming Ligand–Receptor Complexes
inferred← citeshttps://doi.org/10.1007/978-1-59745-483-4_15openalex-snapshot
Use of Residual Dipolar Couplings in Structural Analysis of Protein-Ligand Complexes by Solution NMR Spectroscopy
inferred← citeshttps://doi.org/10.1016/j.bcp.2005.12.010openalex-snapshot
Drug–protein recognition processes investigated by NMR relaxation data
inferred← citeshttps://doi.org/10.1016/j.bmc.2008.12.063openalex-snapshot
Interaction study of bioactive molecules with fibrinogen and human platelets determined by 1H NMR relaxation experiments
inferred← citeshttps://doi.org/10.1016/j.bpc.2007.05.020openalex-snapshot
Interactions of Lycopodium alkaloids with acetylcholinesterase investigated by 1H NMR relaxation rate
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Determination of the modified ‘affinity index’ of small ligands and macromolecular receptors from NMR spin-lattice relaxation data
inferred← citeshttps://doi.org/10.1016/j.jmr.2004.01.017openalex-snapshot
CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities
inferred← citeshttps://doi.org/10.1016/j.molstruc.2011.02.042openalex-snapshot
Topology and dynamics of the interaction between 5-nitroimidazole radiosensitizers and duplex DNA studied by a combination of docking, molecular dynamic simulations and NMR spectroscopy
inferred← citeshttps://doi.org/10.1016/j.molstruc.2014.05.073openalex-snapshot
Supramolecular complex formed by DNA oligonucleotide and thiacalix[4]arene. NMR-spectroscopy and molecular docking
inferred← citeshttps://doi.org/10.1016/j.pnmrs.2006.03.002openalex-snapshot
Complete relaxation and conformational exchange matrix analysis of STD-NMR spectra of ligand–receptor complexes
inferred← citeshttps://doi.org/10.1016/j.sbi.2003.09.012openalex-snapshot
Exchange-transferred NOE spectroscopy and bound ligand structure determination
inferred← citeshttps://doi.org/10.1016/s0066-4103(08)00203-2openalex-snapshot
Chapter 3 Applications of the NOE in Molecular Biology
inferred← citeshttps://doi.org/10.1016/s0959-440x(03)00075-7openalex-snapshot
Ligand binding: functional site location, similarity and docking
inferred← citeshttps://doi.org/10.1016/s0968-0896(03)00339-0openalex-snapshot
C2-Symmetric inhibitors of Plasmodium falciparum plasmepsin II: synthesis and theoretical predictions
inferred← citeshttps://doi.org/10.1021/ja0709728openalex-snapshot
Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
inferred← citeshttps://doi.org/10.1021/jm030447topenalex-snapshot
Validation of Molecular Docking Calculations Involving FGF-1 and FGF-2
inferred← citeshttps://doi.org/10.1021/jm049217kopenalex-snapshot
Structure of a Synthetic Fragment of the LALF Protein When Bound to Lipopolysaccharide
inferred← citeshttps://doi.org/10.1021/jm050762aopenalex-snapshot
Structure of a Synthetic Fragment of the Lipopolysaccharide (LPS) Binding Protein When Bound to LPS and Design of a Peptidic LPS Inhibitor
inferred← citeshttps://doi.org/10.1039/9781849735377-00319openalex-snapshot
Computational Strategies and Challenges for Targeting Protein–Protein Interactions with Small Molecules
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