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Overview of Computational Methods Employed in Early-Stage Drug Discovery
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Structural stability of binding sites: Consequences for binding affinity and allosteric effects
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Empirical force fields for biological macromolecules: Overview and issues
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The Amber biomolecular simulation programs
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A multipole‐based water potential with implicit polarization for biomolecular simulations
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The cost of biopharmaceutical R&D: is biotech different?
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Combining docking and molecular dynamic simulations in drug design
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A new implicit solvent model for protein–ligand docking
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Convergence of molecular dynamics simulations of membrane proteins
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
inferredcites →https://doi.org/10.1007/s10822-006-9078-7openalex-snapshot
Efficient overlay of small organic molecules using 3D pharmacophores
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Structure and reaction based evaluation of synthetic accessibility
inferredcites →https://doi.org/10.1007/s10822-008-9238-zopenalex-snapshot
An improved method to predict the entropy term with the MM/PBSA approach
inferredcites →https://doi.org/10.1016/j.bpc.2005.05.002openalex-snapshot
Importance of polyunsaturated acyl chains in chlorpromazine interaction with phosphatidylserines: A 13C and 31P solid-state NMR study
inferredcites →https://doi.org/10.1016/j.bpc.2008.01.002openalex-snapshot
Olanzapine interaction with dipalmitoyl phosphatidylcholine (DPPC) and 1-palmitoyl-2-oleoyl phosphatidylserine (POPS) bilayer: A 13C and 31P solid-state NMR study
inferredcites →https://doi.org/10.1016/j.cbpa.2008.01.045openalex-snapshot
Structural genomics and drug discovery: all in the family
inferredcites →https://doi.org/10.1016/j.cbpa.2008.03.009openalex-snapshot
Peptidomimetics, a synthetic tool of drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2006.03.009openalex-snapshot
Consensus scoring for protein–ligand interactions
inferredcites →https://doi.org/10.1016/j.drudis.2006.04.008openalex-snapshot
I want a new drug: G-protein-coupled receptors in drug development
inferredcites →https://doi.org/10.1016/j.drudis.2006.12.011openalex-snapshot
Targeting structural flexibility in HIV-1 protease inhibitor binding
inferredcites →https://doi.org/10.1016/j.drudis.2007.08.004openalex-snapshot
Multi-dimensional QSAR in drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2007.12.007openalex-snapshot
Computational toxicology in drug development
inferredcites →https://doi.org/10.1016/j.pbiomolbio.2004.07.005openalex-snapshot
Adaptive inhibitors of the HIV-1 protease
inferredcites →https://doi.org/10.1016/j.sbi.2008.01.004openalex-snapshot
Flexible ligand docking to multiple receptor conformations: a practical alternative
inferredcites →https://doi.org/10.1016/s0006-3495(01)76044-4openalex-snapshot
Dynamical View of the Positions of Key Side Chains in Protein-Protein Recognition
inferredcites →https://doi.org/10.1016/s0006-3495(04)74084-9openalex-snapshot
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
inferredcites →https://doi.org/10.1016/s0169-409x(00)00129-0openalex-snapshot
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings 1PII of original article: S0169-409X(96)00423-1. The article was originally published in Advanced Drug Delivery Reviews 23 (1997) 3–25. 1
inferredcites →https://doi.org/10.1016/s0304-4157(96)00009-3openalex-snapshot
Lateral pressure in membranes
inferredcites →https://doi.org/10.1016/s1359-6446(02)02556-4openalex-snapshot
Chris Lipinski discusses life and chemistry after the Rule of Five
inferredcites →https://doi.org/10.1021/ar000033jopenalex-snapshot
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferredcites →https://doi.org/10.1021/ci0342728openalex-snapshot
Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors
inferredcites →https://doi.org/10.1021/ci050488topenalex-snapshot
High-Throughput Calculation of Protein−Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing
inferredcites →https://doi.org/10.1021/ci700345nopenalex-snapshot
Optimizing the Signal-to-Noise Ratio of Scoring Functions for Protein−Ligand Docking
inferredcites →https://doi.org/10.1021/ci700470copenalex-snapshot
Investigation of MM-PBSA Rescoring of Docking Poses
inferredcites →https://doi.org/10.1021/ci7004725openalex-snapshot
Active Site Pressurization: A New Tool for Structure-Guided Drug Design and Other Studies of Protein Flexibility
inferredcites →https://doi.org/10.1021/cr00023a004openalex-snapshot
Free energy calculations: Applications to chemical and biochemical phenomena
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/ja049281ropenalex-snapshot
Development of a Quantum Mechanics-Based Free-Energy Perturbation Method: Use in the Calculation of Relative Solvation Free Energies
inferredcites →https://doi.org/10.1021/jm0497646openalex-snapshot
Tetrahydrobiopterin Binding to Aromatic Amino Acid Hydroxylases. Ligand Recognition and Specificity
inferredcites →https://doi.org/10.1021/jm7012198openalex-snapshot
Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-nucleoside Inhibitors to HIV-1 Reverse Transcriptase
inferredcites →https://doi.org/10.1021/jm8000373openalex-snapshot
Recent Developments in Fragment-Based Drug Discovery
inferredcites →https://doi.org/10.1021/jp7110988openalex-snapshot
Continuum Polarizable Force Field within the Poisson−Boltzmann Framework
inferredcites →https://doi.org/10.1023/a:1008737207775openalex-snapshot
Virtual screening with solvation and ligand-induced complementarity
inferredcites →https://doi.org/10.1038/nchembio.97openalex-snapshot
Insights into signaling from the β2-adrenergic receptor structure
inferredcites →https://doi.org/10.1038/nrd1799openalex-snapshot
Computer-based de novo design of drug-like molecules
inferredcites →https://doi.org/10.1038/nrd2220openalex-snapshot
A decade of fragment-based drug design: strategic advances and lessons learned
inferredcites →https://doi.org/10.1038/nrd2593openalex-snapshot
Pharmacogenetics in drug discovery and development: a translational perspective
inferredcites →https://doi.org/10.1038/nrd2615openalex-snapshot
Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening
inferredcites →https://doi.org/10.1038/sj.bjp.0707373openalex-snapshot
Origin and evolution of high throughput screening
inferredcites →https://doi.org/10.1038/sj.bjp.0707515openalex-snapshot
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go
inferredcites →https://doi.org/10.1063/1.1740409openalex-snapshot
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
inferredcites →https://doi.org/10.1080/07391102.1998.10508279openalex-snapshot
Continuum Solvent Studies of the Stability of RNA Hairpin Loops and Helices
inferredcites →https://doi.org/10.1093/nar/gkl999openalex-snapshot
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
inferredcites →https://doi.org/10.1111/j.1582-4934.2007.00028.xopenalex-snapshot
Structural genomics and drug discovery
inferredcites →https://doi.org/10.1126/science.1164772openalex-snapshot
The 2.6 Angstrom Crystal Structure of a Human A 2A Adenosine Receptor Bound to an Antagonist
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1172/jci34355openalex-snapshot
Identification of pharmacological chaperones as potential therapeutic agents to treat phenylketonuria
inferredcites →https://doi.org/10.1186/1471-2105-9-438openalex-snapshot
AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening
inferredcites →https://doi.org/10.1186/1472-6807-7-43openalex-snapshot
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field
inferredcites →https://doi.org/10.1309/xyqafanapync6x59openalex-snapshot
Pharmacogenomics and Clinical Biomarkers in Drug Discovery and Development
inferredcites →https://doi.org/10.1517/14656560802515553openalex-snapshot
Pharmacogenomics of multiple sclerosis: in search for a personalized therapy
inferredcites →https://doi.org/10.1517/17425225.3.5.635openalex-snapshot
In silicoprediction of ADMET properties: how far have we come?
inferredcites →https://doi.org/10.1517/17425255.4.6.759openalex-snapshot
Structure – ADME relationship: still a long way to go?
inferredcites →https://doi.org/10.1529/biophysj.107.104208openalex-snapshot
Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer
inferredcites →https://doi.org/10.2174/092986706779026165openalex-snapshot
Towards Predictive Ligand Design With Free-Energy Based Computational Methods?
inferredcites →https://doi.org/10.2174/092986707782360105openalex-snapshot
Computer Simulation of Antimicrobial Peptides
inferredcites →https://doi.org/10.2174/092986708784049630openalex-snapshot
Pharmacophore-Based Virtual Screening
inferredcites →https://doi.org/10.2174/092986708785132843openalex-snapshot
Enhancing Drug Discovery Through In Silico Screening: Strategies to Increase True Positives Retrieval Rates
inferredcites →https://doi.org/10.2174/1386207013330661openalex-snapshot
The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies
inferredcites →https://doi.org/10.2174/138920307781369427openalex-snapshot
Virtual Screening in Drug Discovery - A Computational Perspective
inferredcites →https://doi.org/10.2174/1389557043403765openalex-snapshot
Predicting Synthetic Accessibility: Application in Drug Discovery and Development
inferredcites →https://doi.org/10.2174/138955708785132792openalex-snapshot
Synergies of Virtual Screening Approaches
inferredcites →https://doi.org/10.2174/156802607780906753openalex-snapshot
Ligand Docking and Structure-based Virtual Screening in Drug Discovery
inferredcites →https://doi.org/10.2174/157016306778108884openalex-snapshot
The Nuclear Overhauser Effect in the Lead Identification Process Pharmacophore Models
inferredcites →https://doi.org/10.2174/1573409052952314openalex-snapshot
Recent Advances in Docking and Scoring
inferredcites →https://doi.org/10.2174/157340908785747474openalex-snapshot
Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Stratagems for effective function evaluation in computational chemistry
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