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Conformational Sampling by Self-Organization
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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<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/(sici)1097-0134(199710)29:2<240::aid-prot11>3.0.co;2-oopenalex-snapshot
Prediction of protein conformational freedom from distance constraints
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/bip.360291415openalex-snapshot
Conformational sampling using high‐temperature molecular dynamics
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.540110103openalex-snapshot
High temperature annealed molecular dynamics simulations as a tool for conformational sampling. Application to the bicyclic “222” cryptand
inferredcites →https://doi.org/10.1002/pro.5560070916openalex-snapshot
Distance geometry generates native‐like folds for small helical proteins using the consensus distances of predicted protein structures
inferredcites →https://doi.org/10.1002/prot.340170305openalex-snapshot
Orientational sampling and rigid‐body minimization in molecular docking
inferredcites →https://doi.org/10.1006/jmbi.1995.0631openalex-snapshot
Automated Assignment of Simulated and Experimental NOESY Spectra of Proteins by Feedback Filtering and Self-correcting Distance Geometry
inferredcites →https://doi.org/10.1007/bf00123666openalex-snapshot
Flexibases: A way to enhance the use of molecular docking methods
inferredcites →https://doi.org/10.1007/bf02192799openalex-snapshot
Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
inferredcites →https://doi.org/10.1016/0022-2836(85)90346-8openalex-snapshot
An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution
inferredcites →https://doi.org/10.1016/0022-2836(91)90603-4openalex-snapshot
A new method for building protein conformations from sequence alignments with homologues of known structure
inferredcites →https://doi.org/10.1016/s1093-3263(97)00014-4openalex-snapshot
Conformational analysis using distance geometry methods
inferredcites →https://doi.org/10.1021/ci000464gopenalex-snapshot
Comparison of Knowledge-Based and Distance Geometry Approaches for Generation of Molecular Conformations
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/ja00226a005openalex-snapshot
Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
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/jp960880xopenalex-snapshot
Monte Carlo vs Molecular Dynamics for Conformational Sampling
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/10.1073/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.
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Advanced Artificial Intelligence Methods Used in the Design of Pharmaceutical Agents
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Cluster distance geometry of polypeptide chains
inferred← citeshttps://doi.org/10.1002/jcc.20506openalex-snapshot
A distance geometry heuristic for expanding the range of geometries sampled during conformational search
inferred← citeshttps://doi.org/10.1002/jcc.20622openalex-snapshot
Self‐organizing superimposition algorithm for conformational sampling
inferred← citeshttps://doi.org/10.1002/jcc.20854openalex-snapshot
A self‐organizing algorithm for molecular alignment and pharmacophore development
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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/10.1007/978-1-4614-5128-0_15openalex-snapshot
Distance Geometry for Realistic Molecular Conformations
inferred← citeshttps://doi.org/10.1007/s10898-010-9584-yopenalex-snapshot
On the computation of protein backbones by using artificial backbones of hydrogens
inferred← citeshttps://doi.org/10.1007/s11042-018-6172-5openalex-snapshot
Visualizing the Hotspots and Emerging Trends of Multimedia Big Data through Scientometrics
inferred← citeshttps://doi.org/10.1016/j.bmc.2007.12.005openalex-snapshot
Synthesis and structure–activity relationships of thiadiazole-derivatives as potent and orally active peroxisome proliferator-activated receptors α/δ dual agonists
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‘Fuzziness’ in pharmacophore-based virtual screening and de novo design
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Indole-like Trk receptor antagonists
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Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities
inferred← citeshttps://doi.org/10.1021/ci034150fopenalex-snapshot
Nearest Neighbor Search in General Metric Spaces Using a Tree Data Structure with a Simple Heuristic
inferred← citeshttps://doi.org/10.1021/ci200420copenalex-snapshot
Stochastic Proximity Embedding on Graphics Processing Units: Taking Multidimensional Scaling to a New Scale
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/ci700395fopenalex-snapshot
Technique for Generating Three-Dimensional Alignments of Multiple Ligands from One-Dimensional Alignments
inferred← citeshttps://doi.org/10.1021/ci9001926openalex-snapshot
Conformational Sampling with Stochastic Proximity Embedding and Self-Organizing Superimposition: Establishing Reasonable Parameters for Their Practical Use
inferred← citeshttps://doi.org/10.1021/ci900238aopenalex-snapshot
Conformational Analysis of Macrocycles: Finding What Common Search Methods Miss
inferred← citeshttps://doi.org/10.1021/jm100677sopenalex-snapshot
Electron Density Guided Fragment-Based Lead Discovery of Ketohexokinase Inhibitors
inferred← citeshttps://doi.org/10.1023/b:jcam.0000017375.61558.adopenalex-snapshot
Comparison of correlation vector methods for ligand-based similarity searching
inferred← citeshttps://doi.org/10.1111/j.1475-3995.2009.00757.xopenalex-snapshot
Molecular distance geometry methods: from continuous to discrete
inferred← citeshttps://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
inferred← citeshttps://doi.org/10.1137/120875909openalex-snapshot
Euclidean Distance Geometry and Applications
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1000478openalex-snapshot
A Self-Organizing Algorithm for Modeling Protein Loops
inferred← citeshttps://doi.org/10.1517/17460441.2010.513711openalex-snapshot
Biasing conformational ensembles towards bioactive-like conformers for ligand-based drug design
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THE ROLE OF QUANTUM CHEMICAL CALCULATIONS IN CATALYSIS: A REVIEW
inferred← citeshttps://doi.org/10.3390/molecules23081847openalex-snapshot
Identification of Natural Compounds against Neurodegenerative Diseases Using In Silico Techniques
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