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High quality binding modes in docking ligands to proteins

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What this work says

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

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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function

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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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Protein-protein recognition: exploring the energy funnels near the binding sites

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A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays

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NMR Spectroscopy Techniques for Screening and Identifying Ligand Binding to Protein Receptors

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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function

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ICM—A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation

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A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

inferredcites →https://doi.org/10.1002/prot.20497openalex-snapshot

Comparing protein–ligand docking programs is difficult

inferredcites →https://doi.org/10.1002/prot.21082openalex-snapshot

Protein–ligand docking: Current status and future challenges

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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility

inferredcites →https://doi.org/10.1002/prot.21437openalex-snapshot

Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein–protein interfaces

inferredcites →https://doi.org/10.1002/prot.340080302openalex-snapshot

Automated docking of substrates to proteins by simulated annealing

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A Fast Flexible Docking Method using an Incremental Construction Algorithm

inferredcites →https://doi.org/10.1006/jmbi.1996.0897openalex-snapshot

Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

inferredcites →https://doi.org/10.1006/jmbi.2001.4870openalex-snapshot

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking

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The computer program LUDI: A new method for the de novo design of enzyme inhibitors

inferredcites →https://doi.org/10.1007/bf00124499openalex-snapshot

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

inferredcites →https://doi.org/10.1007/pl00000791openalex-snapshot

Transthyretin: a review from a structural perspective

inferredcites →https://doi.org/10.1016/0223-5234(92)90126-lopenalex-snapshot

The design of drugs to macromolecular targets

inferredcites →https://doi.org/10.1016/j.bbrc.2003.09.120openalex-snapshot

Analysis of the full-length integrase–DNA complex by a modified approach for DNA docking

inferredcites →https://doi.org/10.1016/j.bbrc.2006.09.089openalex-snapshot

Adrenomedullin in adipocyte differentiation of human mesenchymal stem cells

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/j.jmgm.2003.12.012openalex-snapshot

Exploring the conformational space of cyclic peptides by a stochastic search method

inferredcites →https://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot

Flexible protein–protein docking

inferredcites →https://doi.org/10.1016/s0006-3495(02)75671-3openalex-snapshot

Computational Simulation of the Docking of Prochlorothrix hollandica Plastocyanin to Photosystem I: Modeling the Electron Transfer Complex

inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot

Prediction of protein–protein interactions by docking methods

inferredcites →https://doi.org/10.1016/s1093-3263(03)00153-0openalex-snapshot

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction

inferredcites →https://doi.org/10.1016/s1367-5931(02)00341-1openalex-snapshot

Protein flexibility and drug design: how to hit a moving target

inferredcites →https://doi.org/10.1021/bi036149fopenalex-snapshot

Mapping the Topology and Determination of a Low-Resolution Three-Dimensional Structure of the Calmodulin−Melittin Complex by Chemical Cross-Linking and High-Resolution FTICRMS: Direct Demonstration of Multiple Binding Modes

inferredcites →https://doi.org/10.1021/bi051689topenalex-snapshot

Cooperative Binding of Midazolam with Testosterone and α-Naphthoflavone within the CYP3A4 Active Site: A NMR T1 Paramagnetic Relaxation Study

inferredcites →https://doi.org/10.1021/ci600186bopenalex-snapshot

Prediction of Multiple Binding Modes of the CDK2 Inhibitors, Anilinopyrazoles, Using the Automated Docking Programs GOLD, FlexX, and LigandFit: An Evaluation of Performance

inferredcites →https://doi.org/10.1021/jm000040dopenalex-snapshot

Calculation and Prediction of Binding Free Energies for the Matrix Metalloproteinases

inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot

Comparative Evaluation of 11 Scoring Functions for Molecular Docking

inferredcites →https://doi.org/10.1021/jm020406hopenalex-snapshot

Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine

inferredcites →https://doi.org/10.1021/jm0302997openalex-snapshot

Evaluation of Docking Performance: Comparative Data on Docking Algorithms

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/jm0498147openalex-snapshot

Assessment of Multiple Binding Modes in Ligand−Protein Docking

inferredcites →https://doi.org/10.1021/jm0498497openalex-snapshot

On the Function of the 14 Å Long Internal Cavity of Histone Deacetylase-Like Protein: Implications for the Design of Histone Deacetylase Inhibitors

inferredcites →https://doi.org/10.1021/jm050114ropenalex-snapshot

Improving Binding Mode Predictions by Docking into Protein-Specifically Adapted Potential Fields

inferredcites →https://doi.org/10.1021/jm050362nopenalex-snapshot

A Critical Assessment of Docking Programs and Scoring Functions

inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot

Prediction of Protein−Ligand Interactions. Docking and Scoring: Successes and Gaps

inferredcites →https://doi.org/10.1023/a:1025313705564openalex-snapshot

On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data

inferredcites →https://doi.org/10.1038/358774a0openalex-snapshot

Prediction of the structure of a receptor–protein complex using a binary docking method

inferredcites →https://doi.org/10.1038/nrd1129openalex-snapshot

Implications of protein flexibility for drug discovery

inferredcites →https://doi.org/10.1038/nsb770openalex-snapshot

Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site

inferredcites →https://doi.org/10.1042/bj20042035openalex-snapshot

Human transthyretin in complex with iododiflunisal: structural features associated with a potent amyloid inhibitor

inferredcites →https://doi.org/10.1073/pnas.022418199openalex-snapshot

A stochastic algorithm for global optimization and for best populations: A test case of side chains in proteins

inferredcites →https://doi.org/10.1073/pnas.0603236103openalex-snapshot

Structural basis for ligand promiscuity in cytochrome P450 3A4

inferredcites →https://doi.org/10.1080/07391102.2000.10506582openalex-snapshot

Structural Differences of Matrix Metalloproteinases. Homology Modeling and Energy Minimization of Enzyme-Substrate Complexes

inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot

The Protein Data Bank

inferredcites →https://doi.org/10.1093/nar/gkl412openalex-snapshot

Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

inferredcites →https://doi.org/10.1093/protein/12.9.713openalex-snapshot

Folding funnels and binding mechanisms

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/10.1110/ps.8.6.1181openalex-snapshot

Folding funnels, binding funnels, and protein function

inferredcites →https://doi.org/10.1110/ps.8701openalex-snapshot

How common is the funnel‐like energy landscape in protein‐protein interactions?

inferredcites →https://doi.org/10.1186/1742-4682-3-1openalex-snapshot

Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b

inferredcites →https://doi.org/10.2174/0929867043455701openalex-snapshot

Stochastic Algorithm for Kinase Homology Model Construction

inferredcites →https://doi.org/10.2307/2988136openalex-snapshot

Clustering Algorithms.

What points at this work

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

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In s ilicoDrug Design

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Docking Methods for Virtual Screening: Principles and Recent Advances

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Iterative Stochastic Elimination for Solving Complex Combinatorial Problems in Drug Discovery

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Computational and experimental investigation of DNA repair protein photolyase interactions with low molecular weight drugs

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Automated site preparation in physics‐based rescoring of receptor ligand complexes

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Molecular Docking for Virtual Screening of Potential Active Ingredients in Chinese Medicines

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Probe staurosporine drug binding site on protein kinase by PFSC

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Identification of novel imidazole flavonoids as potent and selective inhibitors of protein tyrosine phosphatase

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inferred← citeshttps://doi.org/10.1016/j.bpc.2010.01.011openalex-snapshot

Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase

inferred← citeshttps://doi.org/10.1016/j.chembiol.2010.12.020openalex-snapshot

Novel Ligands for a Purine Riboswitch Discovered by RNA-Ligand Docking

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Baicalein protects cardiomyocytes from oxidative stress induced programmed necrosis by stabilizing carboxyl terminus of Hsc70-interacting protein

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“Homology modeling of Rab11 protein of retina involved in Choroideremia (Homo sapiens)”

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Beware of docking!

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Unraveling the Stability of Plasma Proteins upon Interaction of Synthesized Androstenedione and Its Derivatives─A Biophysical and Computational Approach

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Multiple Fragment Docking and Linking in Primary and Secondary Pockets of Dopamine Receptors

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Binding and Molecular Dynamics Studies of 7-Hydroxycoumarin Derivatives with Human Serum Albumin and Its Pharmacological Importance

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Decorated 6,6′,7,7′-tetrahydro-1H,1′H-2,3′-biindole scaffold as promising candidate for recognition of the CDK2 allosteric site

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