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Conformational Sampling of Bioactive Molecules: A Comparative Study
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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(199604)17:5/6<490::aid-jcc1>3.0.co;2-popenalex-snapshot
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<520::aid-jcc2>3.0.co;2-wopenalex-snapshot
Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<553::aid-jcc3>3.0.co;2-topenalex-snapshot
Merck molecular force field. III. Molecular geometries and vibrational frequencies for MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<587::aid-jcc4>3.0.co;2-qopenalex-snapshot
Merck molecular force field. IV. conformational energies and geometries for MMFF94
inferredcites →https://doi.org/10.1002/(sici)1096-987x(199604)17:5/6<616::aid-jcc5>3.0.co;2-xopenalex-snapshot
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
inferredcites →https://doi.org/10.1002/9780470125793.ch1openalex-snapshot
A Survey of Methods for Searching the Conformational Space of Small and Medium‐Sized Molecules
inferredcites →https://doi.org/10.1002/bip.360260114openalex-snapshot
Prediction of the folding of short polypeptide segments by uniform conformational sampling
inferredcites →https://doi.org/10.1002/jcc.20506openalex-snapshot
A distance geometry heuristic for expanding the range of geometries sampled during conformational search
inferredcites →https://doi.org/10.1002/jcc.540080710openalex-snapshot
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inferredcites →https://doi.org/10.1002/jcc.540090409openalex-snapshot
The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space
inferredcites →https://doi.org/10.1002/jcc.540160205openalex-snapshot
Poling: Promoting conformational variation
inferredcites →https://doi.org/10.1016/0021-9991(78)90081-5openalex-snapshot
Note rapid calculation of coordinates from distance matrices
inferredcites →https://doi.org/10.1016/s1093-3263(00)00064-4openalex-snapshot
Oriented substituent pharmacophore PRopErtY space (OSPPREYS): a substituent-based calculation that describes combinatorial library products better than the corresponding product-based calculation
inferredcites →https://doi.org/10.1016/s1093-3263(02)00204-8openalex-snapshot
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
inferredcites →https://doi.org/10.1016/s1093-3263(97)00014-4openalex-snapshot
Conformational analysis using distance geometry methods
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Chemical Function Queries for 3D Database Search
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Comparison of Knowledge-Based and Distance Geometry Approaches for Generation of Molecular Conformations
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Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms
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A new approach to probing conformational space with molecular mechanics: random incremental pulse search
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An internal-coordinate Monte Carlo method for searching conformational space
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/ja952478mopenalex-snapshot
Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides
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Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
inferredcites →https://doi.org/10.1021/ma00154a069openalex-snapshot
Chain closure with bond angle variations
inferredcites →https://doi.org/10.1021/ma60014a012openalex-snapshot
Ring Closure and Local Conformational Deformations of Chain Molecules
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Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
inferredcites →https://doi.org/10.1023/a:1016320106741openalex-snapshot
Can we separate active from inactive conformations?
inferredcites →https://doi.org/10.1038/80734openalex-snapshot
The Protein Data Bank and the challenge of structural genomics.
inferredcites →https://doi.org/10.1073/pnas.242424399openalex-snapshot
A self-organizing principle for learning nonlinear manifolds
inferredcites →https://doi.org/10.1107/s0567739478000522openalex-snapshot
Stable calculation of coordinates from distance information
What points at this work
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inferred← citeshttps://doi.org/10.1002/9781394167258.ch1openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527633326.ch2openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527636402.ch7openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/9783527677016.ch1openalex-snapshot
De NovoDesign: From Models to Molecules
inferred← citeshttps://doi.org/10.1002/9783527677016.ch9openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/chem.201100854openalex-snapshot
Dynamics of the Glycosidic Bond: Conformational Space of Lactose
inferred← citeshttps://doi.org/10.1002/chin.200734201openalex-snapshot
Conformational Sampling of Bioactive Molecules: A Comparative Study.
inferred← citeshttps://doi.org/10.1002/ddr.20405openalex-snapshot
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inferred← citeshttps://doi.org/10.1002/jcc.20854openalex-snapshot
A self‐organizing algorithm for molecular alignment and pharmacophore development
inferred← citeshttps://doi.org/10.1002/minf.201000134openalex-snapshot
Stochastic Proximity Embedding: Methods and Applications
inferred← citeshttps://doi.org/10.1002/minf.201501028openalex-snapshot
Use of Integrated Computational Approaches in the Search for New Therapeutic Agents
inferred← citeshttps://doi.org/10.1007/7355_2021_130openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-0716-0282-9_14openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4614-5128-0_14openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-7899-1_12openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-030-18375-2_11openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-981-99-9871-5_7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s00894-024-05962-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-010-9365-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-010-9367-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-011-9442-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-017-0089-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-018-0132-zopenalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-08-100098-4.00002-8openalex-snapshot
Structure-Based Ligand Design I
inferred← citeshttps://doi.org/10.1016/b978-0-08-100098-4.00003-xopenalex-snapshot
Structure-Based Ligand Design II
inferred← citeshttps://doi.org/10.1016/b978-0-12-374194-3.00028-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-409547-2.12346-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-417205-0.00021-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2013.10.003openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2016.03.022openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.comptc.2021.113550openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.tet.2012.06.077openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00025openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00243openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.5b00654openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00221openalex-snapshot
Conformation Generation: The State of the Art
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00697openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.8b00151openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00565openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00716openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acsomega.0c01370openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acsomega.5c00562openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci100015jopenalex-snapshot
ConfGen: A Conformational Search Method for Efficient Generation of Bioactive Conformers
inferred← citeshttps://doi.org/10.1021/ci100026xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci100031xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci100209aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci200420copenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci2004658openalex-snapshot
Freely Available Conformer Generation Methods: How Good Are They?
inferred← citeshttps://doi.org/10.1021/ci2005274openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci200528dopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci300314kopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci5001696openalex-snapshot
Macrocycle Conformational Sampling with MacroModel
inferred← citeshttps://doi.org/10.1021/ci7000583openalex-snapshot
Recursive Distance Partitioning Algorithm for Common Pharmacophore Identification
inferred← citeshttps://doi.org/10.1021/ci700059gopenalex-snapshot
Recent Advances in Chemoinformatics
inferred← citeshttps://doi.org/10.1021/ci700359jopenalex-snapshot
Flexophore, a New Versatile 3D Pharmacophore Descriptor That Considers Molecular Flexibility
inferred← citeshttps://doi.org/10.1021/ci800081sopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci800130kopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci8001793openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci800393wopenalex-snapshot
Novel Method for the Evaluation of 3D Conformation Generators
inferred← citeshttps://doi.org/10.1021/ci8004463openalex-snapshot
Flexible Alignment of Small Molecules Using the Penalty Method
inferred← citeshttps://doi.org/10.1021/ci900163topenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci9001926openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci900238aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ct300097sopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jacs.6c11246openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jm900817uopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jp506779yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c1md00044fopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c9cp03557eopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/d0ra01895copenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/d1cp02507dopenalex-snapshot
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inferred← citeshttps://doi.org/10.1063/5.0018314openalex-snapshot
Unsupervised search of low-lying conformers with spectroscopic accuracy: A two-step algorithm rooted into the island model evolutionary algorithm
inferred← citeshttps://doi.org/10.1111/j.1747-0285.2007.00538.xopenalex-snapshot
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inferred← citeshttps://doi.org/10.11606/d.60.2011.tde-21032011-102116openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/1471-2105-10-101openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/1758-2946-4-13openalex-snapshot
Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2
inferred← citeshttps://doi.org/10.1186/s13321-017-0208-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/s13321-021-00524-0openalex-snapshot
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inferred← citeshttps://doi.org/10.1201/b11196-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1201/b19853-6openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000478openalex-snapshot
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inferred← citeshttps://doi.org/10.1517/17460441.2010.513711openalex-snapshot
Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
inferred← citeshttps://doi.org/10.18632/oncotarget.21545openalex-snapshot
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inferred← citeshttps://doi.org/10.2174/1573409915666181221114107openalex-snapshot
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inferred← citeshttps://doi.org/10.2174/9789815196986123010011openalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-s0tcvopenalex-snapshot
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inferred← citeshttps://doi.org/10.26434/chemrxiv-2024-s0tcv-v3openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fbioe.2019.00485openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms10051978openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms25126453openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/molecules200713384openalex-snapshot
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inferred← citeshttps://doi.org/10.4155/fmc-2018-0400openalex-snapshot
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inferred← citeshttps://doi.org/10.4310/cis.241021221101openalex-snapshot
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inferred← citeshttps://doi.org/10.5821/dissertation-2117-93788openalex-snapshot
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inferred← citeshttps://doi.org/10.6084/m9.figshare.15080215openalex-snapshot
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inferred← citeshttps://doi.org/10.70675/ff1b1b1bz4ecfz4beaz84cdzd1749249403dopenalex-snapshot
Generative topographic mapping : a powerful tool for big chemical data visualization, analysis and modeling
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