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Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules
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Molecular mechanics (MM4) calculations on conjugated hydrocarbons
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Parametrization of aliphatic CHn united atoms of GROMOS96 force field
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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BLEEP?potential of mean force describing protein-ligand interactions: I. Generating potential
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BLEEP?potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
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Influence of protein structure databases on the predictive power of statistical pair potentials
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Ligand solvation in molecular docking
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Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
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Knowledge-based interaction potentials for proteins
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Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
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How to generate improved potentials for protein tertiary structure prediction: A lattice model study
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Discrimination of near-native protein structures from misfolded models by empirical free energy functions
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Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
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A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force‐field parameter sets 53A5 and 53A6
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An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
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An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
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Validation of the general purpose tripos 5.2 force field
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Automated docking with grid‐based energy evaluation
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Statistical potentials for fold assessment
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Verification of protein structures: Patterns of nonbonded atomic interactions
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Flexible ligand docking using conformational ensembles
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A distance‐dependent atomic knowledge‐based potential for improved protein structure selection
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A consistent set of statistical potentials for quantifying local side‐chain and backbone interactions
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Atomically detailed potentials to recognize native and approximate protein structures
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SFCscore: Scoring functions for affinity prediction of protein–ligand complexes
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Knowledge Based Potentials: the Reverse Boltzmann Methodology, Virtual Screening and Molecular Weight Dependence
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Dock around the Clock – Current Status of Small Molecule Docking and Scoring
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Comparative Protein Modelling by Satisfaction of Spatial Restraints
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Factors Influencing the Ability of Knowledge-based Potentials to Identify Native Sequence-Structure Matches
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Recognizing Native Folds by the Arrangement of Hydrophobic and Polar Residues
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Residue – Residue Potentials with a Favorable Contact Pair Term and an Unfavorable High Packing Density Term, for Simulation and Threading
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Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
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Factors affecting the ability of energy functions to discriminate correct from incorrect folds
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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
inferredcites →https://doi.org/10.1006/jmbi.1997.1237openalex-snapshot
Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence
inferredcites →https://doi.org/10.1006/jmbi.1997.1479openalex-snapshot
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction 1 1Edited by F. Cohen
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GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences
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Knowledge-based scoring function to predict protein-ligand interactions
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Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
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Customizing scoring functions for docking
inferredcites →https://doi.org/10.1016/1074-5521(95)90050-0openalex-snapshot
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
inferredcites →https://doi.org/10.1016/j.bmc.2008.08.014openalex-snapshot
Evaluation of ligand-binding affinity using polynomial empirical scoring functions
inferredcites →https://doi.org/10.1016/j.drudis.2006.05.012openalex-snapshot
Virtual ligand screening: strategies, perspectives and limitations
inferredcites →https://doi.org/10.1016/j.jmb.2004.06.091openalex-snapshot
Local Propensities and Statistical Potentials of Backbone Dihedral Angles in Proteins
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An Atomic Environment Potential for use in Protein Structure Prediction
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OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing
inferredcites →https://doi.org/10.1016/j.jmgm.2003.11.002openalex-snapshot
A practical approach to docking of zinc metalloproteinase inhibitors
inferredcites →https://doi.org/10.1016/j.jmgm.2004.11.007openalex-snapshot
LigScore: a novel scoring function for predicting binding affinities
inferredcites →https://doi.org/10.1016/j.sbi.2004.03.002openalex-snapshot
Development of novel statistical potentials for protein fold recognition
inferredcites →https://doi.org/10.1016/s0022-2836(03)00323-1openalex-snapshot
A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics
inferredcites →https://doi.org/10.1016/s0022-2836(05)80068-3openalex-snapshot
Identification of native protein folds amongst a large number of incorrect models
inferredcites →https://doi.org/10.1016/s0022-2836(05)80269-4openalex-snapshot
Calculation of conformational ensembles from potentials of mena force
inferredcites →https://doi.org/10.1016/s0959-440x(00)00063-4openalex-snapshot
Effective energy functions for protein structure prediction
inferredcites →https://doi.org/10.1016/s0959-440x(96)80075-3openalex-snapshot
Structure-derived potentials and protein simulations
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Potential energy functions for threading
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Comparison of database potentials and molecular mechanics force fields
inferredcites →https://doi.org/10.1016/s0959-440x(97)80029-2openalex-snapshot
Empirical potentials and functions for protein folding and binding
inferredcites →https://doi.org/10.1016/s1357-4310(95)91170-7openalex-snapshot
Comparative protein modeling by satisfaction of spatial restraints
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Lead discovery using molecular docking
inferredcites →https://doi.org/10.1021/bi00147a009openalex-snapshot
Crystal structure of chicken liver dihydrofolate reductase complexed with NADP+ and biopterin
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Evidence for transition-state stabilization by serine-148 in the catalytic mechanism of chloramphenicol acetyltransferase
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Highly Selective Mechanism-Based Thrombin Inhibitors: Structures of Thrombin and Trypsin Inhibited with Rigid Peptidyl Aldehydes
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Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein−Ligand Interactions
inferredcites →https://doi.org/10.1021/ci9003706openalex-snapshot
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Enzymatic Deamination of the Epigenetic Base N-6-Methyladenine
inferredcites →https://doi.org/10.1021/ja9621760openalex-snapshot
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
inferredcites →https://doi.org/10.1021/ja984102popenalex-snapshot
Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
inferredcites →https://doi.org/10.1021/jm0003992openalex-snapshot
Detailed Analysis of Scoring Functions for Virtual Screening
inferredcites →https://doi.org/10.1021/jm0105833openalex-snapshot
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein−Ligand Interactions
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Structure-Based Approach for Binding Site Identification on AmpC β-Lactamase
inferredcites →https://doi.org/10.1021/jm0203783openalex-snapshot
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inferredcites →https://doi.org/10.1021/jm030489hopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
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PostDOCK: A Structural, Empirical Approach to Scoring Protein Ligand Complexes
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Parameter Estimation for Scoring Protein−Ligand Interactions Using Negative Training Data
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/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm0608356openalex-snapshot
Benchmarking Sets for Molecular Docking
inferredcites →https://doi.org/10.1021/jm060999mopenalex-snapshot
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inferredcites →https://doi.org/10.1021/jm061277yopenalex-snapshot
Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
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Automated Docking Screens: A Feasibility Study
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Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
inferredcites →https://doi.org/10.1023/a:1008158231558openalex-snapshot
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inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1023/b:jcam.0000046819.20241.16openalex-snapshot
PLASS: Protein-ligand affinity statistical score – a knowledge-based force-field model of interaction derived from the PDB
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Ligand discovery from a dopamine D3 receptor homology model and crystal structure
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Structure of chloramphenicol acetyltransferase at 1.75-A resolution.
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A statistical mechanical method to optimize energy functions for protein folding
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Residue-residue mean-force potentials for protein structure recognition
inferredcites →https://doi.org/10.1093/protein/10.9.999openalex-snapshot
Hydrogen bonds and salt bridges across protein-protein interfaces
inferredcites →https://doi.org/10.1093/protein/8.9.849openalex-snapshot
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inferredcites →https://doi.org/10.1107/s0108768102003890openalex-snapshot
The Cambridge Structural Database: a quarter of a million crystal structures and rising
inferredcites →https://doi.org/10.1110/ps.0217002openalex-snapshot
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
inferredcites →https://doi.org/10.1110/ps.03488704openalex-snapshot
Orientational potentials extracted from protein structures improve native fold recognition
inferredcites →https://doi.org/10.1110/ps.051440705openalex-snapshot
Lessons from the design of a novel atomic potential for protein folding
inferredcites →https://doi.org/10.1110/ps.062095806openalex-snapshot
A composite score for predicting errors in protein structure models
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Statistical potential for assessment and prediction of protein structures
inferredcites →https://doi.org/10.1110/ps.072796107openalex-snapshot
OPUS‐Ca: A knowledge‐based potential function requiring only Cα positions
inferredcites →https://doi.org/10.1110/ps.8.2.361openalex-snapshot
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
inferredcites →https://doi.org/10.1110/ps.9.9.1753openalex-snapshot
Modeling of loops in protein structures
inferredcites →https://doi.org/10.1146/annurev.biophys.32.110601.142532openalex-snapshot
Molecular Recognition and Docking Algorithms
inferredcites →https://doi.org/10.1146/annurev.biophys.36.040306.132550openalex-snapshot
Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1186/1471-2105-11-128openalex-snapshot
New statistical potential for quality assessment of protein models and a survey of energy functions
inferredcites →https://doi.org/10.1186/1472-6807-4-8openalex-snapshot
Improved protein structure selection using decoy-dependent discriminatory functions
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Mathematical Methods of Statistics (PMS-9)
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The Dependence of All-Atom Statistical Potentials on Structural Training Database
inferredcites →https://doi.org/10.1529/biophysj.105.079434openalex-snapshot
A New Generation of Statistical Potentials for Proteins
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Docking and Scoring - Theoretically Easy, Practically Impossible?
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Molecular Recognition and Binding Free Energy Calculations in Drug Development
inferredcites →https://doi.org/10.2174/138920306778559395openalex-snapshot
Scoring Functions for Protein-Ligand Docking
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Hierarchical Docking of Databases of Multiple Ligand Conformations
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An Atomistic Statistically Effective Energy Function for Computational Protein Design
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Generation of Pairwise Potentials Using Multidimensional Data Mining
inferred← citeshttps://doi.org/10.1021/acs.jpca.0c11347openalex-snapshot
Extension of an Atom–Atom Dispersion Function to Halogen Bonds and Its Use for Rational Design of Drugs and Biocatalysts
inferred← citeshttps://doi.org/10.1021/acsomega.0c04672openalex-snapshot
How Far Are We from the Rapid Prediction of Drug Resistance Arising Due to Kinase Mutations?
inferred← citeshttps://doi.org/10.1021/ci200627vopenalex-snapshot
Using Novel Descriptor Accounting for Ligand–Receptor Interactions To Define and Visually Explore Biologically Relevant Chemical Space
inferred← citeshttps://doi.org/10.1021/ci300194aopenalex-snapshot
CRDOCK: An Ultrafast Multipurpose Protein–Ligand Docking Tool
inferred← citeshttps://doi.org/10.1021/ci300619xopenalex-snapshot
Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein–Ligand Interactions
inferred← citeshttps://doi.org/10.1021/ci500091ropenalex-snapshot
Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
inferred← citeshttps://doi.org/10.1021/ci5001554openalex-snapshot
Prediction of Substrates for Glutathione Transferases by Covalent Docking
inferred← citeshttps://doi.org/10.1021/ct4005992openalex-snapshot
The Movable Type Method Applied to Protein–Ligand Binding
inferred← citeshttps://doi.org/10.1038/s41401-025-01659-8openalex-snapshot
Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions
inferred← citeshttps://doi.org/10.1038/s42256-021-00409-9openalex-snapshot
A geometric deep learning approach to predict binding conformations of bioactive molecules
inferred← citeshttps://doi.org/10.1039/d5cs00415bopenalex-snapshot
Modeling protein–ligand interactions for drug discovery in the era of deep learning
inferred← citeshttps://doi.org/10.1063/1.4981207openalex-snapshot
Coarse-graining strategy for molecular pair interactions: A reaction coordinate study for two- and three-dimensional systems
inferred← citeshttps://doi.org/10.1080/07391102.2022.2051742openalex-snapshot
Discovery of a novel inhibitor against urokinase-type plasminogen activator, a potential enzyme with a role in atherosclerotic plaque instability
inferred← citeshttps://doi.org/10.1080/07391102.2022.2072951openalex-snapshot
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study
inferred← citeshttps://doi.org/10.1088/1742-6596/1228/1/012019openalex-snapshot
Systematic approach for enrichment of docking outcome using consensus scoring functions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt560openalex-snapshot
Optimized atomic statistical potentials: assessment of protein interfaces and loops
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty879openalex-snapshot
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods
inferred← citeshttps://doi.org/10.1093/jpp/rgae051openalex-snapshot
In silico evidence of bitopertin’s broad interactions within the SLC6 transporter family
inferred← citeshttps://doi.org/10.1093/nar/gkt1144openalex-snapshot
ModBase, a database of annotated comparative protein structure models and associated resources
inferred← citeshttps://doi.org/10.1111/cbdd.13084openalex-snapshot
Aromatic interactions at the ligand–protein interface: Implications for the development of docking scoring functions
inferred← citeshttps://doi.org/10.1111/jam.12843openalex-snapshot
Metagenomics reveals the high polycyclic aromatic hydrocarbon-degradation potential of abundant uncultured bacteria from chronically polluted subantarctic and temperate coastal marine environments
inferred← citeshttps://doi.org/10.1142/s0219720021500037openalex-snapshot
An evaluation of combined strategies for improving the performance of molecular docking
inferred← citeshttps://doi.org/10.1155/2014/162150openalex-snapshot
Evaluation of 11 Scoring Functions Performance on Matrix Metalloproteinases
inferred← citeshttps://doi.org/10.1186/1756-0500-5-526openalex-snapshot
Role of Serine140 in the mode of action of Mycobacterium tuberculosis β-ketoacyl-ACP Reductase (MabA)
inferred← citeshttps://doi.org/10.2174/1381612811319120005openalex-snapshot
Scoring Functions for Prediction of Protein-Ligand Interactions
inferred← citeshttps://doi.org/10.2174/1389450119666181022153016openalex-snapshot
Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective
inferred← citeshttps://doi.org/10.2174/1568026611313070007openalex-snapshot
Molecular Modeling and Ligand Docking for Solute Carrier (SLC) Transporters
inferred← citeshttps://doi.org/10.2174/1568026616666160530181328openalex-snapshot
Drug Repositioning Through Network Pharmacology
inferred← citeshttps://doi.org/10.3390/molecules200713384openalex-snapshot
Molecular Docking and Structure-Based Drug Design Strategies
inferred← citeshttps://doi.org/10.3390/v14020338openalex-snapshot
Detailed Analyses of Molecular Interactions between Favipiravir and RNA Viruses In Silico
inferred← citeshttps://doi.org/10.3390/v17020258openalex-snapshot
In Vitro Evaluation of the Antiviral Activity of Polyphenol (-)-Epigallocatechin-3-Gallate (EGCG) Against Mayaro Virus
inferred← citeshttps://doi.org/10.35652/igjps.2022.12006openalex-snapshot
A Review on Computational Software Tools for Drug Design and Discovery
inferred← citeshttps://doi.org/10.4018/978-1-5225-0115-2.ch001openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-5225-0549-5.ch030openalex-snapshot
Molecular Docking at a Glance
inferred← citeshttps://doi.org/10.4018/978-1-6684-7337-5.ch013openalex-snapshot
Computer-Aided Drug Design of Plant-Based Compounds
inferred← citeshttps://doi.org/10.4018/978-1-7998-6530-8.ch003openalex-snapshot
Advancements in Cancer Therapeutics
inferred← citeshttps://doi.org/10.70675/85b94100z51fbz416ez8640zfd51c7cdf743openalex-snapshot
Development of molecularly imprinted polymers for chemical sensors
inferred← citeshttps://doi.org/10.7555/jbr.35.20210111openalex-snapshot
Target specificity of selective bioactive compounds in blocking α-dystroglycan receptor to suppress Lassa virus infection: an in silico approach
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