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Toward a more efficient handling of conformational flexibility in computer-assisted modelling of drug molecules
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Structure Correlation and Ligand/Receptor Interactions
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Dielectric effects in biopolymers: The theory of ionic saturation revisited
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Solvent effect on the conformation of the hydroxymethyl group established by molecular dynamics simulations of methyl‐β‐ D ‐glucoside in water
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Complex heterocyclic structures ‐ a challenge for computer‐assisted molecular modeling
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Generic shapes for the conformation analysis of macrocyclic structures
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CHARMM : A program for macromolecular energy, minimization, and dynamics calculations
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An all atom force field for simulations of proteins and nucleic acids
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A New Method for Molecular Mechanics
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Stochastic search for the conformations of bicyclic hydrocarbons
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Validation of the general purpose tripos 5.2 force field
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Different approaches to conformational analysis: A comparison of completeness, efficiency, and reliability based on the study of a nine‐membered lactam
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Searching for conformers of nine‐ to twelve‐ring hydrocarbons on the MM2 and MM3 energy surfaces: Stochastic search for interconversion pathways
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Efficient search for all low energy conformations of polypeptides by Monte Carlo methods
inferredcites →https://doi.org/10.1002/jcc.540120908openalex-snapshot
An unbounded systematic search of conformational space
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Conformational sampling and ensemble generation by molecular dynamics simulations: 18‐Crown‐6 as a test case
inferredcites →https://doi.org/10.1002/jcc.540130308openalex-snapshot
Exploring the conformation space of cycloalkanes by linearized embedding
inferredcites →https://doi.org/10.1002/jcc.540130505openalex-snapshot
Improvements to the distance geometry algorithm for conformational sampling of cyclic structures
inferredcites →https://doi.org/10.1002/jcc.540130604openalex-snapshot
DMC: A multifunctional hybrid dynamics/Monte Carlo simulation algorithm for the evaluation of conformational space
inferredcites →https://doi.org/10.1002/jcc.540140308openalex-snapshot
Stochastic searches for lactone and cycloalkene conformers
inferredcites →https://doi.org/10.1002/jcc.540140610openalex-snapshot
Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space
inferredcites →https://doi.org/10.1002/jcc.540140907openalex-snapshot
Conformational searching methods for small molecules. I. Study of the sybyl search method
inferredcites →https://doi.org/10.1002/jcc.540150606openalex-snapshot
Direct search methods for the molecular conformation problem
inferredcites →https://doi.org/10.1002/prot.340020408openalex-snapshot
Calibration of effective van der Waals atomic contact radii for proteins and peptides
inferredcites →https://doi.org/10.1002/prot.340040106openalex-snapshot
Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase‐trimethoprim, a drug‐receptor system
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The Use of Composite Crystal-field Environments in Molecular Recognition and the de Novo Design of Protein Ligands
inferredcites →https://doi.org/10.1007/978-1-4615-3700-7openalex-snapshot
The Application of Charge Density Research to Chemistry and Drug Design
inferredcites →https://doi.org/10.1007/978-1-4615-3700-7_12openalex-snapshot
Correlation of Crystal Data and Charge Density with the Reactivity and Activity of Molecules: Towards a Description of Elementary Steps in Enzyme Reactions
inferredcites →https://doi.org/10.1007/bf00123667openalex-snapshot
A fast and efficient method to generate biologically relevant conformations
inferredcites →https://doi.org/10.1007/bf00124019openalex-snapshot
Different approaches toward an automatic structural alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors
inferredcites →https://doi.org/10.1007/bf00124341openalex-snapshot
?-SCF-Molecular Mechanics PIMM: Formulation, parameters, applications
inferredcites →https://doi.org/10.1007/bf00124350openalex-snapshot
Novel algorithms for searching conformational space
inferredcites →https://doi.org/10.1007/bf00124456openalex-snapshot
MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry
inferredcites →https://doi.org/10.1007/bf00126669openalex-snapshot
Automatic search for maximum similarity between molecular electrostatic potential distributions
inferredcites →https://doi.org/10.1007/bf00130398openalex-snapshot
Automatic superposition of drug molecules based on their common receptor site
inferredcites →https://doi.org/10.1007/bf00135311openalex-snapshot
OVID and SUPER: Two overlap programs for drug design
inferredcites →https://doi.org/10.1007/bf00141577openalex-snapshot
A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
inferredcites →https://doi.org/10.1007/bf01680553openalex-snapshot
A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies
inferredcites →https://doi.org/10.1007/bf02171858openalex-snapshot
Crystal structures of thrombin and thrombin complexes as a framework for antithrombotic drug design
inferredcites →https://doi.org/10.1007/bf02171859openalex-snapshot
Small-molecule inhibitors of thrombin
inferredcites →https://doi.org/10.1016/0022-2836(92)91054-sopenalex-snapshot
Refined 2·3ÅX-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA
inferredcites →https://doi.org/10.1016/0032-3861(86)90342-3openalex-snapshot
Macromolecule self-diffusion in poly(ethylene glycol) melts
inferredcites →https://doi.org/10.1016/0097-8485(93)80028-copenalex-snapshot
Multiconformational investigations of polypeptidic structures, using clustering methods and principal components analysis
inferredcites →https://doi.org/10.1016/0165-6147(89)90173-9openalex-snapshot
Distance geometry and molecular conformation
inferredcites →https://doi.org/10.1016/0166-1280(92)87183-zopenalex-snapshot
DAISY, a computational method: a novel tool for the study of the conformational behavior of flexible molecules
inferredcites →https://doi.org/10.1016/0166-1280(92)87184-2openalex-snapshot
ROSE, a computer program for automatic generation of probable conformations
inferredcites →https://doi.org/10.1016/0166-1280(93)87031-8openalex-snapshot
Viewpoint 11 — approaches to the global minimum problem
inferredcites →https://doi.org/10.1016/0166-1280(94)80091-xopenalex-snapshot
Computer program CICADA — travelling along conformational potential energy hypersurface
inferredcites →https://doi.org/10.1016/0166-1280(94)80094-4openalex-snapshot
Mapping common molecular fragments in crystal structures to explore conformation and configuration space under the conditions of a molecular environment
inferredcites →https://doi.org/10.1016/0196-9781(86)90215-9openalex-snapshot
Central injections of arginine vasopressin prolong extinction of active avoidance
inferredcites →https://doi.org/10.1016/0263-7855(87)80064-4openalex-snapshot
Molecular recognition: optimized searching through rotational 3-space for pattern matches on molecular surfaces
inferredcites →https://doi.org/10.1016/0263-7855(88)80055-9openalex-snapshot
Molecular recognition: blindsearching for regions of strong structural match on the surfaces of two dissimilar molecules
inferredcites →https://doi.org/10.1016/0898-5529(88)90010-3openalex-snapshot
SHADEMOL: An algorithm for presentation of three-dimensional structures on a laser printer using depth-shading
inferredcites →https://doi.org/10.1016/0898-5529(90)90156-3openalex-snapshot
Automatic generation of 3D-atomic coordinates for organic molecules
inferredcites →https://doi.org/10.1016/0898-5529(90)90162-2openalex-snapshot
An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
inferredcites →https://doi.org/10.1016/s0021-9258(18)54894-8openalex-snapshot
Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors.
inferredcites →https://doi.org/10.1016/s0021-9258(19)47326-2openalex-snapshot
The region of the thrombin receptor resembling hirudin binds to thrombin and alters enzyme specificity.
inferredcites →https://doi.org/10.1016/s0022-2836(77)80200-3openalex-snapshot
The protein data bank: A computer-based archival file for macromolecular structures
inferredcites →https://doi.org/10.1016/s0040-4020(01)80308-2openalex-snapshot
How many conformers are there for small n-alkanes? Consequences of asymmetric deformation in GG′ segment
inferredcites →https://doi.org/10.1016/s0040-4020(01)80439-7openalex-snapshot
Simulated annealing of rings using an exact ring closure algorithm
inferredcites →https://doi.org/10.1016/s0040-4020(01)87698-5openalex-snapshot
A novel method for superimposing molecules and receptor mapping
inferredcites →https://doi.org/10.1016/s0040-4020(01)91874-5openalex-snapshot
A distance geometry study of ring systems
inferredcites →https://doi.org/10.1016/s0040-4039(00)91618-6openalex-snapshot
Further developments in the algorithm for generating cyclic conformers. Test with cycloheptadecane
inferredcites →https://doi.org/10.1021/ar00089a001openalex-snapshot
Systematic analysis of structural data as a research technique in organic chemistry
inferredcites →https://doi.org/10.1021/ci00007a002openalex-snapshot
Utilization of Gaussian functions for the rapid evaluation of molecular similarity
inferredcites →https://doi.org/10.1021/ci00016a013openalex-snapshot
Comparison of conformations of small molecule structures from the Protein Data Bank with those generated by Concord, Cobra, ChemDBS-3D, and Converter and those extracted from the Cambridge Structural Database
inferredcites →https://doi.org/10.1021/ci00017a026openalex-snapshot
Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching
inferredcites →https://doi.org/10.1021/ci00063a006openalex-snapshot
Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics
inferredcites →https://doi.org/10.1021/j100060a019openalex-snapshot
Distribution of Conformational Energy Minima in Molecules with Multiple Torsional Degrees of Freedom
inferredcites →https://doi.org/10.1021/ja00050a049openalex-snapshot
Conformations of Arg-Gly-Asp containing heterodetic cyclic peptides: solution and crystal studies
inferredcites →https://doi.org/10.1021/ja00050a082openalex-snapshot
The first design and synthesis of a steroidal peptidomimetic. The potential value of peptidomimetics in elucidating the bioactive conformation of peptide ligands
inferredcites →https://doi.org/10.1021/ja00072a058openalex-snapshot
Direct design of a potent non-peptide fibrinogen receptor antagonist based on the structure and conformation of a highly constrained cyclic RGD peptide
inferredcites →https://doi.org/10.1021/ja00091a008openalex-snapshot
From Peptide to Non-Peptide. 2. The de Novo Design of Potent, Non-peptidal Inhibitors of Platelet Aggregation Based on a Benzodiazepinedione Scaffold
inferredcites →https://doi.org/10.1021/ja00160a020openalex-snapshot
Conformations of cycloheptadecane. A comparison of methods for conformational searching
inferredcites →https://doi.org/10.1021/ja00194a034openalex-snapshot
A new approach to probing conformational space with molecular mechanics: random incremental pulse search
inferredcites →https://doi.org/10.1021/ja00225a045openalex-snapshot
Conformational mimicry. 1. 1,5-Disubstituted tetrazole ring as a surrogate for the cis amide bond
inferredcites →https://doi.org/10.1021/ja00233a016openalex-snapshot
A new technique to calculate low-energy conformations of cyclic molecules utilizing the ellipsoid algorithm and molecular dynamics: application to 18-crown-6
inferredcites →https://doi.org/10.1021/ja00244a051openalex-snapshot
Stochastic exploration of molecular mechanics energy surfaces. Hunting for the global minimum
inferredcites →https://doi.org/10.1021/ja00299a024openalex-snapshot
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
inferredcites →https://doi.org/10.1021/ja00467a001openalex-snapshot
Conformational analysis. 130. MM2. A hydrocarbon force field utilizing V1 and V2 torsional terms
inferredcites →https://doi.org/10.1021/jm00049a008openalex-snapshot
Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors
inferredcites →https://doi.org/10.1021/jm00117a001openalex-snapshot
An analysis of current methodologies for conformational searching of complex molecules
inferredcites →https://doi.org/10.1039/p29930000187openalex-snapshot
An efficient algorithm for searching low-energy conformers of cyclic and acyclic molecules
inferredcites →https://doi.org/10.1063/1.467236openalex-snapshot
A deterministic global optimization approach for molecular structure determination
inferredcites →https://doi.org/10.1107/s0108768190011600openalex-snapshot
Rotation barriers in crystals from diffraction studies: 2,2',4,4',6,6'-hexa-tert-butylazobenzene
inferredcites →https://doi.org/10.5860/choice.27-0916openalex-snapshot
Distance geometry and molecular conformation
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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MIMIC: A molecular-field matching program. Exploiting applicability of molecular similarity approaches
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Molecular Dynamics-Based Models Explain the Unexpected Diastereoselectivity of the Sharpless Asymmetric Dihydroxylation of Allyl D-Xylosides
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Current Issues in De Novo Molecular Design
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Was läßt sich aus der molekularen Erkennung in Protein‐Ligand‐Komplexen für das Design neuer Wirkstoffe lernen?
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What Can We Learn from Molecular Recognition in Protein–Ligand Complexes for the Design of New Drugs?
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QM/MM refinement and analysis of protein bound retinoic acid
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Neue Leitstrukturen aus dem Computer
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Comparative Molecular Similarity Indices Analysis: CoMSIA
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Structural and Energetic Aspects of Protein-Ligand Binding in Drug Design
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New Tools for Drug Design Based on Protein Ligand Recognition Principles
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Structure-Based Design of Novel Heparin-Like Anticoagulants
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3D Molecular Similarity Methods
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3D Molecular Similarity Methods
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Computer Aided Drug Design
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Drug design for ever, from hype to hope
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Drug Discovery, Design, and Development
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Lead Discovery and Lead Modification
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Time-efficient flexible superposition of medium-sized molecules
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Methodological developments and strategies for a fast flexible superposition of drug-size molecules
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A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching
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Comparative molecular similarity indices analysis: CoMSIA
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Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity
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The binding conformation of Taxol in β-tubulin: A model based on electron crystallographic density
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Quantum mechanics implementation in drug-design workflows: does it really help?
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