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Binding Energy Landscape Analysis Helps to Discriminate True Hits from High-Scoring Decoys in Virtual Screening
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes
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Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions
inferredcites →https://doi.org/10.1002/jcc.20246openalex-snapshot
New and fast statistical‐thermodynamic method for computation of protein‐ligand binding entropy substantially improves docking accuracy
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Role of binding entropy in the refinement of protein–ligand docking predictions: Analysis based on the use of 11 scoring functions
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Combining docking and molecular dynamic simulations in drug design
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Funnels, pathways, and the energy landscape of protein folding: A synthesis
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Post Docking Filtering Using Cartesian Genetic Programming
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Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment
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SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex
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Scoring Functions – the First 100 Years
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Calculations of protein-ligand binding entropy of relative and overall molecular motions
inferredcites →https://doi.org/10.1007/s10822-007-9163-6openalex-snapshot
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection—What can we learn from earlier mistakes?
inferredcites →https://doi.org/10.1007/s10822-008-9182-yopenalex-snapshot
Improving database enrichment through ensemble docking
inferredcites →https://doi.org/10.1007/s10822-008-9189-4openalex-snapshot
Community benchmarks for virtual screening
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Virtual ligand screening: strategies, perspectives and limitations
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Cooperativity Principles in Protein Folding
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Complexity and simplicity of ligand–macromolecule interactions: the energy landscape perspective
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Analysis and optimization of structure-based virtual screening protocols
inferredcites →https://doi.org/10.1021/bi00107a010openalex-snapshot
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
inferredcites →https://doi.org/10.1021/ci049641uopenalex-snapshot
Virtual Screening of Molecular Databases Using a Support Vector Machine
inferredcites →https://doi.org/10.1021/ci049885eopenalex-snapshot
LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
inferredcites →https://doi.org/10.1021/cr040425uopenalex-snapshot
Protein Folding Thermodynamics and Dynamics: Where Physics, Chemistry, and Biology Meet
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A New Concept for Multidimensional Selection of Ligand Conformations (MultiSelect) and Multidimensional Scoring (MultiScore) of Protein−Ligand Binding Affinities
inferredcites →https://doi.org/10.1021/jm0493360openalex-snapshot
PostDOCK: A Structural, Empirical Approach to Scoring Protein Ligand Complexes
inferredcites →https://doi.org/10.1021/jm0498147openalex-snapshot
Assessment of Multiple Binding Modes in Ligand−Protein Docking
inferredcites →https://doi.org/10.1021/jm050040jopenalex-snapshot
Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data
inferredcites →https://doi.org/10.1021/jm0501026openalex-snapshot
Statistical Tools for Virtual Screening
inferredcites →https://doi.org/10.1021/jm0505720openalex-snapshot
A Multistep Approach to Structure-Based Drug Design: Studying Ligand Binding at the Human Neutrophil Elastase
inferredcites →https://doi.org/10.1021/jm0603365openalex-snapshot
Comparison of Shape-Matching and Docking as Virtual Screening Tools
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
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Exploiting Protein Fluctuations at the Active-Site Gorge of Human Cholinesterases: Further Optimization of the Design Strategy to Develop Extremely Potent Inhibitors
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Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1023/a:1008158231558openalex-snapshot
Deciphering common failures in molecular docking of ligand-protein complexes
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Protein ligand docking based on empirical method for binding affinity estimation
inferredcites →https://doi.org/10.1023/a:1023866311551openalex-snapshot
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
inferredcites →https://doi.org/10.1038/35011000openalex-snapshot
A surprising simplicity to protein folding
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1073/pnas.0406234101openalex-snapshot
Hidden complexity of free energy surfaces for peptide (protein) folding
inferredcites →https://doi.org/10.1073/pnas.0509768103openalex-snapshot
P versus Q : Structural reaction coordinates capture protein folding on smooth landscapes
inferredcites →https://doi.org/10.1073/pnas.90.15.7195openalex-snapshot
Engineering of stable and fast-folding sequences of model proteins.
inferredcites →https://doi.org/10.1073/pnas.92.19.8798openalex-snapshot
On constructing folding heteropolymers.
inferredcites →https://doi.org/10.1073/pnas.93.1.60openalex-snapshot
A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding.
inferredcites →https://doi.org/10.1073/pnas.93.17.8945openalex-snapshot
Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.
inferredcites →https://doi.org/10.1103/physrevlett.67.1665openalex-snapshot
Protein folding bottlenecks: A lattice Monte Carlo simulation
inferredcites →https://doi.org/10.1103/physrevlett.72.3907openalex-snapshot
Proteins with selected sequences fold into unique native conformation
inferredcites →https://doi.org/10.1103/physrevlett.90.188101openalex-snapshot
Energy Landscape Theory, Funnels, Specificity, and Optimal Criterion of Biomolecular Binding
inferredcites →https://doi.org/10.1103/physrevlett.99.198101openalex-snapshot
Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening
inferredcites →https://doi.org/10.1110/ps.0207102openalex-snapshot
Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Free Energy Calculations in Drug Lead Optimization
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Latest developments in molecular docking: 2010–2011 in review
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Discovery of binding proteins for a protein target using protein-protein docking-based virtual screening
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Assessing the mechanical energy costs of various tissue reshaping mechanisms
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Systems Biology Brings New Dimensions for Structure-Based Drug Design
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Specificity quantification of biomolecular recognition and its implication for drug discovery
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Drug repositioning by structure-based virtual screening
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Discovery of novel chemoeffectors and rational design of Escherichia coli chemoreceptor specificity
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Identification of novel CDK2 inhibitors by a multistage virtual screening method based on SVM, pharmacophore and docking model
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Accurate Scoring of Drug Conformations at the Extreme Scale
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Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review
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Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins
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Prediction of Ligand Binding Using an Approach Designed to Accommodate Diversity in Protein-Ligand Interactions
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Can the Energy Gap in the Protein-Ligand Binding Energy Landscape Be Used as a Descriptor in Virtual Ligand Screening?
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A Dynamic Study of Protein Secretion and Aggregation in the Secretory Pathway
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Logistic Regression of Ligands of Chemotaxis Receptors Offers Clues about Their Recognition by Bacteria
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Empirical Scoring Functions for Structure-Based Virtual Screening: Applications, Critical Aspects, and Challenges
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Identification of Novel PI3Kδ Selective Inhibitors by SVM-Based Multistage Virtual Screening and Molecular Dynamics Simulations
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In silico docking and pharmacophoric analysis of 3-indolyl pyridine derivatives toward cyclooxygenase-2
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