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Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use

https://doi.org/10.1021/ci9001926

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/9780470125809openalex-snapshot

Reviews in Computational Chemistry

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Prediction of the folding of short polypeptide segments by uniform conformational sampling

inferredcites →https://doi.org/10.1002/jcc.10234openalex-snapshot

Stochastic proximity embedding

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.20622openalex-snapshot

Self‐organizing superimposition algorithm for conformational sampling

inferredcites →https://doi.org/10.1002/jcc.21439openalex-snapshot

Fast determination of the optimal rotational matrix for macromolecular superpositions

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/10.1016/0021-9991(78)90081-5openalex-snapshot

Note rapid calculation of coordinates from distance matrices

inferredcites →https://doi.org/10.1016/0968-0896(95)00031-bopenalex-snapshot

Conformational changes of small molecules binding to proteins

inferredcites →https://doi.org/10.1016/j.jmb.2005.12.012openalex-snapshot

Conformational Diversity of Ligands Bound to Proteins

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(03)00155-4openalex-snapshot

A modified update rule for stochastic proximity embedding

inferredcites →https://doi.org/10.1016/s1093-3263(97)00014-4openalex-snapshot

Conformational analysis using distance geometry methods

inferredcites →https://doi.org/10.1021/ci0340557openalex-snapshot

Conformational Sampling by Self-Organization

inferredcites →https://doi.org/10.1021/ci049753lopenalex-snapshot

Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms

inferredcites →https://doi.org/10.1021/ci6005454openalex-snapshot

Conformational Sampling of Bioactive Molecules: A Comparative Study

inferredcites →https://doi.org/10.1021/ci800084xopenalex-snapshot

An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD

inferredcites →https://doi.org/10.1021/ci800130kopenalex-snapshot

Conformational Sampling of Druglike Molecules with MOE and Catalyst: Implications for Pharmacophore Modeling and Virtual Screening

inferredcites →https://doi.org/10.1021/ci900238aopenalex-snapshot

Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss

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/ja00194a035openalex-snapshot

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/jm030563wopenalex-snapshot

Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding

inferredcites →https://doi.org/10.1021/jm060763iopenalex-snapshot

Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein−Ligand Binding

inferredcites →https://doi.org/10.1021/jm700967eopenalex-snapshot

Physicochemical Properties of Antibacterial Compounds: Implications for Drug Discovery

inferredcites →https://doi.org/10.1021/jp960880xopenalex-snapshot

Monte Carlo vs Molecular Dynamics for Conformational Sampling

inferredcites →https://doi.org/10.1021/jp994072sopenalex-snapshot

Modification of the Generalized Born Model Suitable for Macromolecules

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

inferredcites →https://doi.org/10.1023/a:1008055202136openalex-snapshot

Do active site conformations of small ligands correspond to low free-energy solution structures?

inferredcites →https://doi.org/10.1023/a:1015930826903openalex-snapshot

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/nrd2201openalex-snapshot

Drugs for bad bugs: confronting the challenges of antibacterial discovery

inferredcites →https://doi.org/10.1071/ch06217openalex-snapshot

Conformational Boosting

inferredcites →https://doi.org/10.1073/pnas.242424399openalex-snapshot

A self-organizing principle for learning nonlinear manifolds

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/10.1111/j.1747-0285.2007.00538.xopenalex-snapshot

On the Effects of Permuted Input on Conformational Sampling of Drug‐like Molecules: an Evaluation of Stochastic Proximity Embedding

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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GC–MS Analysis, Biological Characterization, Quorum Sensing Inhibition, and Molecular Docking of Cinnamomum camphora L.

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LC–MS/MS Profiling and Evaluation of Antibacterial, Antivirulence, Antioxidant, and Anti‐Inflammatory Activities of Pinus halepensis Mill. Bark Extracts: In Vitro and In Silico Analysis

inferred← citeshttps://doi.org/10.1002/minf.201000134openalex-snapshot

Stochastic Proximity Embedding: Methods and Applications

inferred← citeshttps://doi.org/10.1007/978-1-4614-5128-0_14openalex-snapshot

Stochastic Proximity Embedding: A Simple, Fast and Scalable Algorithm for Solving the Distance Geometry Problem

inferred← citeshttps://doi.org/10.1007/s10822-011-9442-0openalex-snapshot

Application of shape-based and pharmacophore-based in silico screens for identification of Type II protein kinase inhibitors

inferred← citeshttps://doi.org/10.1007/s11696-026-05026-7openalex-snapshot

Discovery of potent VEGFR2 inhibitors as anticancer target, using pharmacophore based virtual screening, molecular docking and molecular dynamics simulation

inferred← citeshttps://doi.org/10.1016/j.ddtec.2010.10.003openalex-snapshot

Conformations and 3D pharmacophore searching

inferred← citeshttps://doi.org/10.1016/j.jmgm.2014.07.006openalex-snapshot

QSAR design of triazolopyridine mGlu2 receptor positive allosteric modulators

inferred← citeshttps://doi.org/10.1021/ci100026xopenalex-snapshot

Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst

inferred← citeshttps://doi.org/10.1021/ci200528dopenalex-snapshot

Recognizing Pitfalls in Virtual Screening: A Critical Review

inferred← citeshttps://doi.org/10.1186/1471-2105-11-545openalex-snapshot

Bioactive conformational generation of small molecules: A comparative analysis between force-field and multiple empirical criteria based methods

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/10.2174/1573409916666200213124929openalex-snapshot

Investigation of New Inhibitors of UDP-N-Acetylglucosamine Enolpyruvyl Transferase (MurA) by Virtual Screening with Antibacterial Assessment

inferred← citeshttps://doi.org/10.4155/fmc-2018-0400openalex-snapshot

Energy Windows for Computed Compound Conformers: Covering Artefacts Or Truly Large Reorganization Energies?

inferred← citeshttps://doi.org/10.4155/fmc.10.244openalex-snapshot

Modeling Approaches for Ligand-Based 3D Similarity

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