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Investigation of MM-PBSA Rescoring of Docking Poses
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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<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)1096-987x(199905)20:7<720::aid-jcc7>3.0.co;2-xopenalex-snapshot
MMFF VI. MMFF94s option for energy minimization studies
inferredcites →https://doi.org/10.1002/0471224413openalex-snapshot
Reviews in Computational Chemistry
inferredcites →https://doi.org/10.1002/chin.200642205openalex-snapshot
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large‐Scale Survey on the Retrieval of Protein‐Bound Ligand Conformations.
inferredcites →https://doi.org/10.1002/jcc.540130311openalex-snapshot
Molecular docking using shape descriptors
inferredcites →https://doi.org/10.1002/jcc.540130412openalex-snapshot
Automated docking with grid‐based energy evaluation
inferredcites →https://doi.org/10.1002/prot.10232openalex-snapshot
A new test set for validating predictions of protein–ligand interaction
inferredcites →https://doi.org/10.1002/prot.10266openalex-snapshot
Pharmacophore‐based molecular docking to account for ligand flexibility
inferredcites →https://doi.org/10.1002/prot.10296openalex-snapshot
Automated generation of MCSS‐derived pharmacophoric DOCK site points for searching multiconformation databases
inferredcites →https://doi.org/10.1006/jmbi.1999.3371openalex-snapshot
Knowledge-based scoring function to predict protein-ligand interactions
inferredcites →https://doi.org/10.1007/bf00126743openalex-snapshot
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
inferredcites →https://doi.org/10.1007/s00894-005-0013-yopenalex-snapshot
Comparison between Generalized-Born and Poisson–Boltzmann methods in physics-based scoring functions for protein structure prediction
inferredcites →https://doi.org/10.1016/0010-4655(95)00041-dopenalex-snapshot
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
inferredcites →https://doi.org/10.1016/s1359-6446(02)02483-2openalex-snapshot
Structure-based virtual screening: an overview
inferredcites →https://doi.org/10.1016/s1574-1400(05)01012-1openalex-snapshot
Chapter 12 Structure-Based Lead Optimization
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/ci0502855openalex-snapshot
Physics-Based Scoring of Protein−Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening
inferredcites →https://doi.org/10.1021/ci060084gopenalex-snapshot
Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations
inferredcites →https://doi.org/10.1021/ct6003406openalex-snapshot
Improving Docking Accuracy through Molecular Mechanics Generalized Born Optimization and Scoring
inferredcites →https://doi.org/10.1021/ja00086a004openalex-snapshot
Structure-Based Design of Synthetic Azobenzene Ligands for Streptavidin
inferredcites →https://doi.org/10.1021/ja00124a002openalex-snapshot
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
inferredcites →https://doi.org/10.1021/ja003834qopenalex-snapshot
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
inferredcites →https://doi.org/10.1021/ja981844+openalex-snapshot
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate−DNA Helices
inferredcites →https://doi.org/10.1021/jm000241hopenalex-snapshot
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm0100279openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
inferredcites →https://doi.org/10.1021/jm0205043openalex-snapshot
A Computational Model of Binding Thermodynamics: The Design of Cyclin-dependent Kinase 2 Inhibitors
inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm049726mopenalex-snapshot
Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation
inferredcites →https://doi.org/10.1021/jm050306mopenalex-snapshot
Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
inferredcites →https://doi.org/10.1021/jm050436vopenalex-snapshot
DrugScore CSD Knowledge-Based Scoring Function Derived from Small Molecule Crystal Data with Superior Recognition Rate of Near-Native Ligand Poses and Better Affinity Prediction
inferredcites →https://doi.org/10.1021/jm060522aopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jp952986iopenalex-snapshot
Calculation of Alkane to Water Solvation Free Energies Using Continuum Solvent Models
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
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inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1039/b608269fopenalex-snapshot
Molecular mechanics methods for predicting protein–ligand binding
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.2011744openalex-snapshot
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inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
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inferredcites →https://doi.org/10.1177/1087057105281220openalex-snapshot
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inferredcites →https://doi.org/10.1201/9781420028775.ch10openalex-snapshot
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inferredcites →https://doi.org/10.1201/9781420028775.ch13openalex-snapshot
Pharmacophore-Based Molecular Docking
inferredcites →https://doi.org/10.2210/pdb1sre/pdbopenalex-snapshot
CRYSTALLOGRAPHIC AND THERMODYNAMIC COMPARISON OF NATURAL AND SYNTHETIC LIGANDS BOUND TO STREPTAVIDIN
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/9783527633326.ch6openalex-snapshot
Docking Methods for Virtual Screening: Principles and Recent Advances
inferred← citeshttps://doi.org/10.1002/9783527633326.ch7openalex-snapshot
The Challenge of Affinity Prediction: Scoring Functions for Structure‐Based Virtual Screening
inferred← citeshttps://doi.org/10.1002/9783527645947.ch12openalex-snapshot
Scoring Functions for Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1002/9783527645947.ch9openalex-snapshot
Implicit Solvent Models and Electrostatics in Molecular Recognition
inferred← citeshttps://doi.org/10.1002/9783527673025.ch3openalex-snapshot
Computation of Drug‐Binding Thermodynamics
inferred← citeshttps://doi.org/10.1002/jcc.21666openalex-snapshot
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
inferred← citeshttps://doi.org/10.1002/jcc.21668openalex-snapshot
Electrostatic solvation free energy of amino acid side chain analogs: Implications for the validity of electrostatic linear response in water
inferred← citeshttps://doi.org/10.1002/jcc.22888openalex-snapshot
Assessment of free energy predictors for ligand binding to a methyllysine histone code reader
inferred← citeshttps://doi.org/10.1002/jcc.23728openalex-snapshot
A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model
inferred← citeshttps://doi.org/10.1002/jmr.2848openalex-snapshot
Understanding the disrupting mechanism of the Tau aggregation motif “ 306 VQIVYK 311 ” by phenylthiazolyl‐hydrazides inhibitors
inferred← citeshttps://doi.org/10.1002/minf.200900071openalex-snapshot
Predicting Cyclooxygenase Inhibition by Three‐Dimensional Pharmacophoric Profiling. Part I: Model Generation, Validation and Applicability in Ethnopharmacology
inferred← citeshttps://doi.org/10.1002/minf.201100135openalex-snapshot
Free Energy Calculations by the Molecular Mechanics Poisson−Boltzmann Surface Area Method
inferred← citeshttps://doi.org/10.1002/prot.25322openalex-snapshot
Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships
inferred← citeshttps://doi.org/10.1002/wcms.18openalex-snapshot
Outstanding challenges in protein–ligand docking and structure‐based virtual screening
inferred← citeshttps://doi.org/10.1007/978-1-0716-3311-3_4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-030-18375-2_11openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-3-319-76599-0_14openalex-snapshot
Molecular Dynamics and Related Computational Methods with Applications to Drug Discovery
inferred← citeshttps://doi.org/10.1007/s00894-011-1065-9openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-009-9281-4openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-010-9320-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-010-9356-2openalex-snapshot
Chemical space sampling by different scoring functions and crystal structures
inferred← citeshttps://doi.org/10.1007/s10822-011-9506-1openalex-snapshot
Molecular simulation methods in drug discovery: a prospective outlook
inferred← citeshttps://doi.org/10.1007/s10822-012-9565-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-012-9590-xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-013-9689-8openalex-snapshot
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
inferred← citeshttps://doi.org/10.1007/s10822-016-0005-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-018-0112-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-019-00249-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-020-00339-5openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-020-00340-yopenalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s10822-021-00389-3openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s11030-024-10932-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/s42250-022-00376-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-819132-3.00014-2openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/b978-0-12-822312-3.00001-1openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.abb.2024.110270openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbagen.2018.09.015openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbapap.2009.11.010openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bbapap.2025.141095openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2010.05.060openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmc.2015.12.046openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmcl.2012.08.047openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.bmcl.2022.128867openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2020.107292openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2020.107376openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2009.12.025openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2011.03.061openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2012.10.024openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.ejmech.2015.02.045openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.10.012openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2021.107937openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.virusres.2012.05.011openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/s1574-1400(10)06014-7openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.chemrev.9b00055openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.6c00356openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00412openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00095openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.jcim.9b01062openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.2c00219openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci100354xopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci100469nopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci2000727openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci200159gopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci300030uopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci300298dopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci3003599openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci300502hopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci400731wopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci4007326openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci500020mopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci5003735openalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci500742bopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci900022hopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ci900056copenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/ct500189sopenalex-snapshot
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inferred← citeshttps://doi.org/10.1021/jm100533popenalex-snapshot
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inferred← citeshttps://doi.org/10.1038/aps.2013.129openalex-snapshot
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inferred← citeshttps://doi.org/10.1039/9781849735377-00195openalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c0cp00151aopenalex-snapshot
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inferred← citeshttps://doi.org/10.1039/c5ra11896dopenalex-snapshot
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inferred← citeshttps://doi.org/10.1080/17460441.2019.1623202openalex-snapshot
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inferred← citeshttps://doi.org/10.1093/bioinformatics/btx638openalex-snapshot
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inferred← citeshttps://doi.org/10.1101/2023.05.12.540544openalex-snapshot
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inferred← citeshttps://doi.org/10.1111/cbdd.12763openalex-snapshot
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inferred← citeshttps://doi.org/10.1186/1472-6807-11-24openalex-snapshot
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inferred← citeshttps://doi.org/10.1371/journal.pone.0023215openalex-snapshot
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inferred← citeshttps://doi.org/10.2174/1568026618666180821145215openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fmolb.2016.00046openalex-snapshot
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inferred← citeshttps://doi.org/10.3389/fphar.2022.907437openalex-snapshot
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inferred← citeshttps://doi.org/10.3390/ijms11083016openalex-snapshot
Advances and Challenges in Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/ijms20102568openalex-snapshot
Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide
inferred← citeshttps://doi.org/10.3390/ijms21010005openalex-snapshot
Tetrahydroquinoline-Isoxazole/Isoxazoline Hybrid Compounds as Potential Cholinesterases Inhibitors: Synthesis, Enzyme Inhibition Assays, and Molecular Modeling Studies
inferred← citeshttps://doi.org/10.3390/ijms232314830openalex-snapshot
ES-Screen: A Novel Electrostatics-Driven Method for Drug Discovery Virtual Screening
inferred← citeshttps://doi.org/10.3390/molecules21111604openalex-snapshot
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking
inferred← citeshttps://doi.org/10.3390/molecules24020277openalex-snapshot
PeptoGrid—Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries
inferred← citeshttps://doi.org/10.3390/molecules25174016openalex-snapshot
Targeting the Initiator Protease of the Classical Pathway of Complement Using Fragment-Based Drug Discovery
inferred← citeshttps://doi.org/10.3410/f.1710958.1219056openalex-snapshot
Faculty Opinions recommendation of Blueprint for antimicrobial hit discovery targeting metabolic networks.
inferred← citeshttps://doi.org/10.4018/978-1-5225-1762-7.ch044openalex-snapshot
Rational Drug Design Rational Drug Design
inferred← citeshttps://doi.org/10.4155/9781909453012openalex-snapshot
In Silico Drug Discovery and Design
inferred← citeshttps://doi.org/10.4155/ebo.13.181openalex-snapshot
Molecular docking and structure-based virtual screening
inferred← citeshttps://doi.org/10.4155/fmc-2017-0156openalex-snapshot
A Multistep Docking and Scoring Protocol for Congeneric Series: Implementation on Kinase DFG-Out Type II Inhibitors
inferred← citeshttps://doi.org/10.4155/fmc.09.7openalex-snapshot
Overview of Computational Methods Employed in Early-Stage Drug Discovery
inferred← citeshttps://doi.org/10.4155/fmc.11.30openalex-snapshot
Physics-Based Scoring of Protein–Ligand Interactions: Explicit Polarizability, Quantum Mechanics and Free Energies
inferred← citeshttps://doi.org/10.7939/r3-hnsp-7c04openalex-snapshot
Computer-Aided Drug Design of DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease
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