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AADS- An Automated Active Site Identification, Docking, and Scoring Protocol for Protein Targets Based on Physicochemical Descriptors
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Outgoing claims: the papers this work cites, builds on, or argues with.
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Strength of hydrogen bonds in ? helices
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Assessing energy functions for flexible docking
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Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
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Prodock: Software package for protein modeling and docking
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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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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
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Molecular docking using surface complementarity
inferredcites →https://doi.org/10.1002/(sici)1097-0134(1997)1+<215::aid-prot29>3.0.co;2-qopenalex-snapshot
Flexible protein–ligand docking by global energy optimization in internal coordinates
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990101)34:1<17::aid-prot3>3.0.co;2-1openalex-snapshot
The particle concept: placing discrete water molecules during protein-ligand docking predictions
inferredcites →https://doi.org/10.1002/(sici)1097-0134(19991001)37:1<88::aid-prot9>3.0.co;2-oopenalex-snapshot
Exhaustive docking of molecular fragments with electrostatic solvation
inferredcites →https://doi.org/10.1002/1097-0134(20000901)40:4<623::aid-prot70>3.0.co;2-iopenalex-snapshot
Similarity-driven flexible ligand docking
inferredcites →https://doi.org/10.1002/1097-0134(20001101)41:2<173::aid-prot30>3.0.co;2-3openalex-snapshot
DARWIN: A program for docking flexible molecules
inferredcites →https://doi.org/10.1002/1097-0134(20010501)43:2<113::aid-prot1023>3.0.co;2-topenalex-snapshot
High throughput docking for library design and library prioritization
inferredcites →https://doi.org/10.1002/bip.10541openalex-snapshot
Calculation of ligand‐nucleic acid binding free energies with the generalized‐born model in DOCK
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Yucca: An Efficient Algorithm for Small-Molecule Docking
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Functional Classification of Protein Kinase Binding Sites Using Cavbase
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Free‐energy component analysis of 40 protein–DNA complexes: A consensus view on the thermodynamics of binding at the molecular level
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FDS: Flexible ligand and receptor docking with a continuum solvent model and soft‐core energy function
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Detailed analysis of grid‐based molecular docking: A case study of CDOCKER—A CHARMm‐based MD docking algorithm
inferredcites →https://doi.org/10.1002/jcc.1129openalex-snapshot
EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
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Development and testing of a general amber force field
inferredcites →https://doi.org/10.1002/jcc.20542openalex-snapshot
SODOCK: Swarm optimization for highly flexible protein–ligand docking
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A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid–vapor interface of water
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AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
inferredcites →https://doi.org/10.1002/jcc.540130714openalex-snapshot
Validation of the general purpose QUANTA ®3.2/CHARMm® force field
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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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Flexible ligand docking without parameter adjustment across four ligand–receptor complexes
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Metformin and glitazones: does similarity in biomolecular mechanism originate from tautomerism in these drugs?
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Protein clefts in molecular recognition and function.
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Automatic identification and representation of protein binding sites for molecular docking
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Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
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Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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Pharmacophore‐based molecular docking to account for ligand flexibility
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Improved protein–ligand docking using GOLD
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GEMDOCK: A generic evolutionary method for molecular docking
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A method for localizing ligand binding pockets in protein structures
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PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking
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On the nature of cavities on protein surfaces: Application to the identification of drug‐binding sites
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Effective handling of induced‐fit motion in flexible docking
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Protein–ligand docking: Current status and future challenges
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ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility
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PIPER: An FFT‐based protein docking program with pairwise potentials
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Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites
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Computational protocol for predicting the binding affinities of zinc containing metalloprotein–ligand complexes
inferredcites →https://doi.org/10.1002/prot.21367openalex-snapshot
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization
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FLIPDock: Docking flexible ligands into flexible receptors
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Prediction of interaction sites from apo 3D structures when the holo conformation is different
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Highly accurate method for ligand‐binding site prediction in unbound state (apo) protein structures
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CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three‐dimensional structure
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A multiple‐start Monte Carlo docking method
inferredcites →https://doi.org/10.1002/qsar.200510183openalex-snapshot
Dock around the Clock – Current Status of Small Molecule Docking and Scoring
inferredcites →https://doi.org/10.1006/jcph.1998.6173openalex-snapshot
Free Energy Analysis of Protein–DNA Binding: The EcoRI Endonuclease–DNA Complex
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Rational Automatic Search Method for Stable Docking Models of Protein and Ligand
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The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria
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A Fast Flexible Docking Method using an Incremental Construction Algorithm
inferredcites →https://doi.org/10.1006/jmbi.1996.0776openalex-snapshot
Molecular docking to ensembles of protein structures 1 1Edited by B. Honig
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.1997.1203openalex-snapshot
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
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An example of a protein ligand found by database mining: description of the docking method and its verification by a 2.3 Å X-ray structure of a Thrombin-Ligand complex
inferredcites →https://doi.org/10.1006/jmbi.1998.2248openalex-snapshot
Three-dimensional profiles: a new tool to identify protein surface similarities
inferredcites →https://doi.org/10.1006/jmbi.1998.2393openalex-snapshot
Recognition of spatial motifs in protein structures 1 1Edited by J. Thornton
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Knowledge-based scoring function to predict protein-ligand interactions
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Docking ligands onto binding site representations derived from proteins built by homology modelling
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ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
inferredcites →https://doi.org/10.1006/jmbi.2001.4551openalex-snapshot
FlexE: efficient molecular docking considering protein structure variations
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PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design
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Cavity search: An algorithm for the isolation and display of cavity-like binding regions
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FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure
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Flexible ligand docking using a genetic algorithm
inferredcites →https://doi.org/10.1007/s008940050096openalex-snapshot
SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex
inferredcites →https://doi.org/10.1007/s10822-004-5291-4openalex-snapshot
Unsupervised guided docking of covalently bound ligands
inferredcites →https://doi.org/10.1007/s10822-006-9041-7openalex-snapshot
Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures
inferredcites →https://doi.org/10.1007/s10822-006-9060-4openalex-snapshot
Development and validation of a modular, extensible docking program: DOCK 5
inferredcites →https://doi.org/10.1007/s10822-007-9114-2openalex-snapshot
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
inferredcites →https://doi.org/10.1007/s10969-011-9110-6openalex-snapshot
Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures
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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/10.1016/0022-2836(82)90153-xopenalex-snapshot
A geometric approach to macromolecule-ligand interactions
inferredcites →https://doi.org/10.1016/0263-7855(92)80052-fopenalex-snapshot
Finding and filling protein cavities using cellular logic operations
inferredcites →https://doi.org/10.1016/0263-7855(92)80074-nopenalex-snapshot
POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids
inferredcites →https://doi.org/10.1016/0263-7855(93)85003-9openalex-snapshot
A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I) Search for pocket regions
inferredcites →https://doi.org/10.1016/0263-7855(95)00071-2openalex-snapshot
Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations
inferredcites →https://doi.org/10.1016/j.abb.2004.05.019openalex-snapshot
A molecular thermodynamic view of DNA–drug interactions: a case study of 25 minor-groove binders
inferredcites →https://doi.org/10.1016/j.bmcl.2004.06.091openalex-snapshot
GAsDock: a new approach for rapid flexible docking based on an improved multi-population genetic algorithm
inferredcites →https://doi.org/10.1016/j.febslet.2005.10.031openalex-snapshot
An all atom energy based computational protocol for predicting binding affinities of protein–ligand complexes
inferredcites →https://doi.org/10.1016/j.jmb.2006.04.024openalex-snapshot
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
inferredcites →https://doi.org/10.1016/j.jmb.2006.07.022openalex-snapshot
Travel Depth, a New Shape Descriptor for Macromolecules: Application to Ligand Binding
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.jmgm.2007.10.002openalex-snapshot
Pocket extraction on proteins via the Voronoi diagram of spheres
inferredcites →https://doi.org/10.1016/j.jsb.2007.09.005openalex-snapshot
PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins
inferredcites →https://doi.org/10.1016/j.str.2004.09.005openalex-snapshot
Accurate Detection of Protein:Ligand Binding Sites Using Molecular Dynamics Simulations
inferredcites →https://doi.org/10.1016/s0006-3495(04)74256-3openalex-snapshot
First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin
inferredcites →https://doi.org/10.1016/s0006-3495(97)78756-3openalex-snapshot
The statistical-thermodynamic basis for computation of binding affinities: a critical review
inferredcites →https://doi.org/10.1016/s0022-2836(03)00515-1openalex-snapshot
Using A Neural Network and Spatial Clustering to Predict the Location of Active Sites in Enzymes
inferredcites →https://doi.org/10.1016/s0969-2126(03)00060-1openalex-snapshot
Discovery of a Novel Family of CDK Inhibitors with the Program LIDAEUS
inferredcites →https://doi.org/10.1016/s1074-5521(96)90093-9openalex-snapshot
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites
inferredcites →https://doi.org/10.1016/s1093-3263(02)00164-xopenalex-snapshot
LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites
inferredcites →https://doi.org/10.1016/s1093-3263(02)00203-6openalex-snapshot
A new method for mapping macromolecular topography
inferredcites →https://doi.org/10.1016/s1093-3263(98)00002-3openalex-snapshot
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
inferredcites →https://doi.org/10.1021/ci0496393openalex-snapshot
ProPose: Steered Virtual Screening by Simultaneous Protein−Ligand Docking and Ligand−Ligand Alignment
inferredcites →https://doi.org/10.1021/ci050268fopenalex-snapshot
Grand Canonical Monte Carlo Simulation of Ligand−Protein Binding
inferredcites →https://doi.org/10.1021/ci600229zopenalex-snapshot
Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model
inferredcites →https://doi.org/10.1021/ci6002637openalex-snapshot
Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
inferredcites →https://doi.org/10.1021/ci7001236openalex-snapshot
GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein−Ligand Complexes
inferredcites →https://doi.org/10.1021/ci700149kopenalex-snapshot
Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces
inferredcites →https://doi.org/10.1021/j100159a074openalex-snapshot
Grand canonical Monte Carlo simulations on aqueous solutions of sodium chloride and sodium DNA: excess chemical potentials and sources of nonideality in electrolyte and polyelectrolyte solutions
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/ja0103288openalex-snapshot
Calculation of Relative Binding Free Energy Differences for Fructose 1,6-Bisphosphatase Inhibitors Using the Thermodynamic Cycle Perturbation Approach
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/ja202726yopenalex-snapshot
How Does a Drug Molecule Find Its Target Binding Site?
inferredcites →https://doi.org/10.1021/ja9539002openalex-snapshot
VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands
inferredcites →https://doi.org/10.1021/ja960751uopenalex-snapshot
SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
inferredcites →https://doi.org/10.1021/ja961482aopenalex-snapshot
Simulated Annealing of Chemical Potential: A General Procedure for Locating Bound Waters. Application to the Study of the Differential Hydration Propensities of the Major and Minor Grooves of DNA
inferredcites →https://doi.org/10.1021/jm000467kopenalex-snapshot
Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
inferredcites →https://doi.org/10.1021/jm00053a018openalex-snapshot
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
inferredcites →https://doi.org/10.1021/jm00053a019openalex-snapshot
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
inferredcites →https://doi.org/10.1021/jm00125a025openalex-snapshot
New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
inferredcites →https://doi.org/10.1021/jm00145a002openalex-snapshot
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
inferredcites →https://doi.org/10.1021/jm010175zopenalex-snapshot
Free Energy Component Analysis for Drug Design: A Case Study of HIV-1 Protease−Inhibitor Binding
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/jm0300330openalex-snapshot
Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
inferredcites →https://doi.org/10.1021/jm030271vopenalex-snapshot
HierVLS Hierarchical Docking Protocol for Virtual Ligand Screening of Large-Molecule Databases
inferredcites →https://doi.org/10.1021/jm0306430openalex-snapshot
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
inferredcites →https://doi.org/10.1021/jm040015yopenalex-snapshot
SDOCKER: A Method Utilizing Existing X-ray Structures To Improve Docking Accuracy
inferredcites →https://doi.org/10.1021/jm049314dopenalex-snapshot
A Knowledge-Based Energy Function for Protein−Ligand, Protein−Protein, and Protein−DNA Complexes
inferredcites →https://doi.org/10.1021/jm0493818openalex-snapshot
Ph4Dock: Pharmacophore-Based Protein−Ligand Docking
inferredcites →https://doi.org/10.1021/jm050196jopenalex-snapshot
Receptor Flexibility in de Novo Ligand Design and Docking
inferredcites →https://doi.org/10.1021/jm050540copenalex-snapshot
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
inferredcites →https://doi.org/10.1021/jm050543popenalex-snapshot
Modeling Water Molecules in Protein−Ligand Docking Using GOLD
inferredcites →https://doi.org/10.1021/jm051197eopenalex-snapshot
MolDock: A New Technique for High-Accuracy Molecular Docking
inferredcites →https://doi.org/10.1021/jm060542copenalex-snapshot
A Swift All-Atom Energy-Based Computational Protocol to Predict DNA−Ligand Binding Affinity and ΔTm
inferredcites →https://doi.org/10.1021/jm060838iopenalex-snapshot
Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking
inferredcites →https://doi.org/10.1021/jm061134bopenalex-snapshot
Identification of Hot Spots within Druggable Binding Regions by Computational Solvent Mapping of Proteins
inferredcites →https://doi.org/10.1021/jm9006966openalex-snapshot
Automated Docking Screens: A Feasibility Study
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1021/jm990609eopenalex-snapshot
DoMCoSAR: A Novel Approach for Establishing the Docking Mode That Is Consistent with the Structure−Activity Relationship. Application to HIV-1 Protease Inhibitors and VEGF Receptor Tyrosine Kinase Inhibitors
inferredcites →https://doi.org/10.1021/jp9813692openalex-snapshot
Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments
inferredcites →https://doi.org/10.1023/a:1007907728892openalex-snapshot
QXP: Powerful, rapid computer algorithms for structure-based drug design
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1007999920146openalex-snapshot
Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
inferredcites →https://doi.org/10.1023/a:1008005918983openalex-snapshot
MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
inferredcites →https://doi.org/10.1023/a:1008015827877openalex-snapshot
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
inferredcites →https://doi.org/10.1023/a:1008124202956openalex-snapshot
Fast prediction and visualization of protein binding pockets with PASS
inferredcites →https://doi.org/10.1023/a:1008737207775openalex-snapshot
Virtual screening with solvation and ligand-induced complementarity
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/10.1023/a:1016307520660openalex-snapshot
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
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.0000035199.48747.1eopenalex-snapshot
Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®
inferredcites →https://doi.org/10.1023/b:jcam.0000046820.08222.83openalex-snapshot
Molecular modelling prediction of ligand binding site flexibility
inferredcites →https://doi.org/10.1038/nrd1549openalex-snapshot
Docking and scoring in virtual screening for drug discovery: methods and applications
inferredcites →https://doi.org/10.1038/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/10.1039/b502226fopenalex-snapshot
A computational pathway for bracketing native-like structures for small alpha helical globular proteins
inferredcites →https://doi.org/10.1073/pnas.0707684105openalex-snapshot
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
inferredcites →https://doi.org/10.1073/pnas.211436698openalex-snapshot
THEMATICS: A simple computational predictor of enzyme function from structure
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Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease.
inferredcites →https://doi.org/10.1074/mcp.m400159-mcp200openalex-snapshot
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes
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MetaPocket: A Meta Approach to Improve Protein Ligand Binding Site Prediction
inferredcites →https://doi.org/10.1093/bioinformatics/18.suppl_1.s71openalex-snapshot
Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
inferredcites →https://doi.org/10.1093/bioinformatics/19.1.163openalex-snapshot
ConSurf: Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information
inferredcites →https://doi.org/10.1093/bioinformatics/btg243openalex-snapshot
Protein Ligand Database (PLD): additional understanding of the nature and specificity of protein–ligand complexes
inferredcites →https://doi.org/10.1093/bioinformatics/bti242openalex-snapshot
Improved prediction of protein-protein binding sites using a support vector machines approach
inferredcites →https://doi.org/10.1093/bioinformatics/bti315openalex-snapshot
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btn263openalex-snapshot
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
inferredcites →https://doi.org/10.1093/bioinformatics/btp562openalex-snapshot
E asy MIF s and S ite H ound : a toolkit for the identification of ligand-binding sites in protein structures
inferredcites →https://doi.org/10.1093/bioinformatics/btq100openalex-snapshot
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment
inferredcites →https://doi.org/10.1093/nar/gki481openalex-snapshot
PatchDock and SymmDock: servers for rigid and symmetric docking
inferredcites →https://doi.org/10.1093/nar/gkl282openalex-snapshot
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
inferredcites →https://doi.org/10.1093/nar/gkq479openalex-snapshot
ProBiS: a web server for detection of structurally similar protein binding sites
inferredcites →https://doi.org/10.1093/protein/13.2.83openalex-snapshot
Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network
inferredcites →https://doi.org/10.1093/protein/13.2.89openalex-snapshot
Analysis and prediction of carbohydrate binding sites
inferredcites →https://doi.org/10.1107/s0021889883010985openalex-snapshot
Analytical molecular surface calculation
inferredcites →https://doi.org/10.1107/s0907444993011333openalex-snapshot
Detection, delineation, measurement and display of cavities in macromolecular structures
inferredcites →https://doi.org/10.1110/ps.041153605openalex-snapshot
Side‐chain flexibility in protein–ligand binding: The minimal rotation hypothesis
inferredcites →https://doi.org/10.1128/jvi.02395-06openalex-snapshot
Inhibition of Hepatitis B Virus Polymerase by Entecavir
inferredcites →https://doi.org/10.1142/9781860948732_0028openalex-snapshot
EFFECTIVE LABELING OF MOLECULAR SURFACE POINTS FOR CAVITY DETECTION AND LOCATION OF PUTATIVE BINDING SITES
inferredcites →https://doi.org/10.1146/annurev.biophys.33.110502.140414openalex-snapshot
The Role of Water in Protein-DNA Recognition
inferredcites →https://doi.org/10.1186/1471-2105-10-168openalex-snapshot
Fpocket: An open source platform for ligand pocket detection
inferredcites →https://doi.org/10.1186/1471-2105-11-286openalex-snapshot
Conserved residue clusters at protein-protein interfaces and their use in binding site identification
inferredcites →https://doi.org/10.1186/1471-2105-8-4openalex-snapshot
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines
inferredcites →https://doi.org/10.1186/1471-2105-8-s4-s9openalex-snapshot
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
inferredcites →https://doi.org/10.1186/1471-2105-9-184openalex-snapshot
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
inferredcites →https://doi.org/10.1186/1472-6807-6-19openalex-snapshot
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.
inferredcites →https://doi.org/10.1186/1752-153x-1-1openalex-snapshot
Natural products chemistry in the third millennium
inferredcites →https://doi.org/10.1186/1752-153x-1-7openalex-snapshot
PocketPicker: analysis of ligand binding-sites with shape descriptors
inferredcites →https://doi.org/10.1248/cpb.41.1200openalex-snapshot
Development of an efficient automated docking method.
inferredcites →https://doi.org/10.1371/journal.pcbi.0030094openalex-snapshot
Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
inferredcites →https://doi.org/10.1515/bc.2001.168openalex-snapshot
Fragment-Based Flexible Ligand Docking by Evolutionary Optimization
inferredcites →https://doi.org/10.2174/092986607780989877openalex-snapshot
Mapping Selectivity and Specificity of Active Site of Plasmepsins from Plasmodium falciparum Using Molecular Interaction Field Approach
inferredcites →https://doi.org/10.2174/092986607781483831openalex-snapshot
ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes
inferredcites →https://doi.org/10.2174/092986706778521797openalex-snapshot
Docking and Scoring - Theoretically Easy, Practically Impossible?
inferredcites →https://doi.org/10.2174/138161207782794220openalex-snapshot
From Drug Target to Leads-Sketching A Physicochemical Pathway for Lead Molecule Design In Silico
inferredcites →https://doi.org/10.2174/138920306778559412openalex-snapshot
eHiTS: An Innovative Approach to the Docking and Scoring Function Problems
inferredcites →https://doi.org/10.2174/138920307781369382openalex-snapshot
Structure-Based Drug Design: Docking and Scoring
inferredcites →https://doi.org/10.2174/138920310794109094openalex-snapshot
Proteins: Sequence to Structure and Function – Current Status
inferredcites →https://doi.org/10.2174/978160805201110703010081openalex-snapshot
Virtual Docking: How Are We Doing And How Can We Improve?
What points at this work
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Investigating the Potential of 2‐Ethylbutyl‐(Phenoxy)phosphoryl‐D‐Alaninate Against RNA‐Dependent RNA Polymerase (RdRp) of SARS‐CoV‐2
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Latest developments in molecular docking: 2010–2011 in review
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Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites
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Suppressor of Cytokine Signalling‐3 as a Drug Target for Type 2 Diabetes Mellitus: A Structure‐Guided Approach
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Computational Approaches to Matrix Metalloprotease Drug Design
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Protein-Ligand Binding with Applications in Molecular Docking
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Safe-in-Man Broad Spectrum Antiviral Agents
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Identification of HPr kinase/phosphorylase inhibitors: novel antimicrobials against resistant Enterococcus faecalis
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Sulphated Fucooligosaccharide from Sargassum Horneri: Structural Analysis and Anti-Alzheimer Activity
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Homology modeling and virtual screening studies of FGF-7 protein—a structure-based approach to design new molecules against tumor angiogenesis
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Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery–a structure-based approach
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An Improved Protein Surface Extraction Method Using Rotating Cylinder Probe
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Peptide modelling and screening against human ACE2 and spike glycoprotein RBD of SARS-CoV-2
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The structure–function correlation of Cicer arietinum catalase 4 (Ca catalase 4): the key scavenger enzyme during chickpea–Fusarium interplay
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Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research
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Molecular Docking: A Structure-Based Approach for Drug Repurposing
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In silico bioremediation strategies for removal of environmental pollutants released from paper mills using bacterial ligninolytic enzymes
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Molecular dynamics in predicting the stability of drug-receptor interactions
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Comparative genomic analysis of Rickettsia rickettsii for identification of drug and vaccine targets: tolC as a proposed candidate for case study
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Multi-stage transcriptome profiling of the neglected food-borne echinostome Artyfechinostomum sufrartyfex reveal potential diagnostic and drug targets
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ProTSAV: A protein tertiary structure analysis and validation server
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Development of cyanopyridine–triazine hybrids as lead multitarget anti-Alzheimer agents
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Naphthalene-triazolopyrimidine hybrid compounds as potential multifunctional anti-Alzheimer’s agents
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Molecular basis for the affinity and specificity in the binding of five-membered iminocyclitols with glycosidases: an experimental and theoretical synergy
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A comprehensive automated computer-aided discovery pipeline from genomes to hit molecules
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In silico drug re-purposing against African sleeping sickness using GlcNAc-PI de- N -acetylase as an experimental target
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Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study
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Synthesis and screening of triazolopyrimidine scaffold as multi-functional agents for Alzheimer's disease therapies
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Rational design, synthesis and biological screening of triazine-triazolopyrimidine hybrids as multitarget anti-Alzheimer agents
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A multifunctional therapeutic approach: Synthesis, biological evaluation, crystal structure and molecular docking of diversified 1H-pyrazolo[3,4-b]pyridine derivatives against Alzheimer's disease
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In silico identification of strong binders of the SARS-CoV-2 receptor-binding domain
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Shotgun proteomics and molecular simulations on multifunctional bioactive peptides derived from the whey of unexplored “Gaddi” goat of Himalayas
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Novel insight into mutational impacts and binding mechanism of human glutaminase and glutaminase-interacting protein: A bio-molecular modeling and docking analysis
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In silico characterization of hypothetical proteins from Orientia tsutsugamushi str. Karp uncovers virulence genes
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Computational approach to study the synthesis of noscapine and potential of stereoisomers against nsP3 protease of CHIKV
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Computational investigation of turmeric phytochemicals targeting PTR1 enzyme of Leishmania species
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Deciphering the structural basis of the broad substrate specificity of myo-inositol monophosphatase (IMP) from Cicer arietinum
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Discovery of novel CDK4/6 inhibitors from fungal secondary metabolites
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Novel quinoline-ferrocene-tetrahydropyrimidine hybrids integrated with triazole: Synthesis, in vitro and in silico antimalarial studies
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Evaluating the structural and immune mechanism of Interleukin-6 for the investigation of goat milk peptides as potential treatments for COVID-19
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Identification of potential therapeutic targets in Neisseria gonorrhoeae by an in-silico approach
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Trends in predictive biodegradation for sustainable mitigation of environmental pollutants: Recent progress and future outlook
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Evaluation of novobiocin and telmisartan for anti-CHIKV activity
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3-Oxo-hexahydro-1H-isoindole-4-carboxylic Acid as a Drug Chiral Bicyclic Scaffold: Structure-Based Design and Preparation of Conformationally Constrained Covalent and Noncovalent Prolyl Oligopeptidase Inhibitors
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Computational Screening of Potential Inhibitors of Desulfobacter postgatei for Pyrite Scale Prevention in Oil and Gas Wells
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Rational Engineering of Escherichia coli Nissle 1917 as Live Biotherapeutic to Degrade Uremic Toxin Precursors
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Selective Interception of Gelsolin Amyloidogenic Stretch Results in Conformationally Distinct Aggregates with Reduced Toxicity
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A novel piperazine derivative that targets hepatitis B surface antigen effectively inhibits tenofovir resistant hepatitis B virus
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Prediction of Functional Loss of Human Angiogenin Mutants Associated with ALS by Molecular Dynamics Simulations
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A plausible mechanism for the antimalarial activity of artemisinin: A computational approach
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A rapid identification of hit molecules for target proteins via physico-chemical descriptors
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Understanding the binding of inhibitors of matrix metalloproteinases by molecular docking, quantum mechanical calculations, molecular dynamics simulations, and a MMGBSA/MMBappl study
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Predicting the binding modes and sites of metabolism of xenobiotics
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Design, synthesis and glycosidase inhibition studies of novel triazole fused iminocyclitol-δ-lactams
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Quinoline-triazole hybrids inhibit falcipain-2 and arrest the development of Plasmodium falciparum at the trophozoite stage
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Curcumin specifically binds to the human calcium–calmodulin-dependent protein kinase IV: fluorescence and molecular dynamics simulation studies
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Toward a better understanding of the interaction between somatostatin receptor 2 and its ligands: a structural characterization study using molecular dynamics and conceptual density functional theory
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Atomistic simulation on flavonoids derivatives as potential inhibitors of bacterial gyrase of Staphylococcus aureus
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A review targeting the infection by CHIKV using computational and experimental approaches
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Bioavailability and Neuroprotectivity of 3-(3, 4-dimethoxy phenyl)-1-4 (methoxy phenyl) prop-2-en-1-one against Schizophrenia: an in silico approach
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Modulations in the ATPases during ketamine-induced schizophrenia and regulatory effect of “3-(3, 4-dimethoxy phenyl) -1- (4-methoxyphenyl) prop-2-en-1-one”: anin vivoandin silicostudies
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Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies
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Toward development of generic inhibitors against the 3C proteases of picornaviruses
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Structure-Guided Approach to Identify Potential Inhibitors of Large Envelope Protein to Prevent Hepatitis B Virus Infection
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Sequence Analysis and Structure Prediction of SARS‐CoV‐2 Accessory Proteins 9b and ORF14: Evolutionary Analysis Indicates Close Relatedness to Bat Coronavirus
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Molecular Characteristic and Insilico Analysis of KatG Gene in Isoniazid Resistance Mycobacterium Tuberculosis Isolate from Sudan
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Mechanisms of Loss of Functions of Human Angiogenin Variants Implicated in Amyotrophic Lateral Sclerosis
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Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds
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Identification of novel cyclin-dependent kinase 4/6 inhibitors from marine natural products
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Comparative modeling, structure and active site prediction of Sclerotinia disease-resistant gene BnaMPK3 in Oilseed rape (Brassica napus)
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Understanding the Exacerbating Role of the Metalloproteinase Meprin during AKI, an In Silico Approach
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In Search of Novel SGLT2 Inhibitors by High-throughput Virtual Screening
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Identification of Novel CDK 4/6 Inhibitors by High-throughput Virtual Screening
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Protein-Ligand Docking in the New Millennium – A Retrospective of 10 Years in the Field
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Genomes to Hits In Silico - A Country Path Today, A Highway Tomorrow: A Case Study of Chikungunya
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Computational Studies of Allylpyrocatechol from Piper betle L. as Inhibitor Against Superoxide Dismutase, Catalase, and Glutathione peroxidase as Antioxidant Enzyme
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Role of Docking in Anticancer Drug Discovery
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In silico Identification of HDAC Inhibitors for Multiple Myeloma: A Structure-based Virtual Screening, Drug Likeness, ADMET Profiling, Molecular Docking, and Molecular Dynamics Simulation Study
inferred← citeshttps://doi.org/10.29130/dubited.1652693openalex-snapshot
Computational Identification of Potential Antiviral Agents Against Monkeypox Virus
inferred← citeshttps://doi.org/10.3109/10799893.2014.969375openalex-snapshot
Homology modeling and virtual screening of ubiquitin conjugation enzyme E2A for designing a novel selective antagonist against cancer
inferred← citeshttps://doi.org/10.32657/10356/69603openalex-snapshot
Exploiting receptor flexibility to improve the accuracy of structure-based virtual screening
inferred← citeshttps://doi.org/10.33263/briac123.32593304openalex-snapshot
Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins
inferred← citeshttps://doi.org/10.3389/fbinf.2026.1821527openalex-snapshot
Molecular docking and dynamics simulation studies uncover the host–pathogen protein–protein interactions in soybean (Glycine max (L.) Merr.) and Groundnut bud necrosis virus: first report
inferred← citeshttps://doi.org/10.3389/fbinf.2026.1839606openalex-snapshot
In silico drug discovery pipelines targeting antibiotic resistance: from genomes to leads
inferred← citeshttps://doi.org/10.3389/fchem.2024.1389846openalex-snapshot
Peptidomics-based identification of antihypertensive and antidiabetic peptides from sheep milk fermented using Limosilactobacillus fermentum KGL4 MTCC 25515 with anti-inflammatory activity: in silico, in vitro, and molecular docking studies
inferred← citeshttps://doi.org/10.3389/fphar.2022.805344openalex-snapshot
Plant Source Derived Compound Exhibited In Silico Inhibition of Membrane Glycoprotein In SARS-CoV-2: Paving the Way to Discover a New Class of Compound For Treatment of COVID-19
inferred← citeshttps://doi.org/10.3390/computation13020034openalex-snapshot
Combining Subtractive Genomics with Computer-Aided Drug Discovery Techniques to Effectively Target S. sputigena in Periodontitis
inferred← citeshttps://doi.org/10.3390/molecules22101673openalex-snapshot
Systematic Identification of Machine-Learning Models Aimed to Classify Critical Residues for Protein Function from Protein Structure
inferred← citeshttps://doi.org/10.3390/molecules29225349openalex-snapshot
Recent Applications of In Silico Approaches for Studying Receptor Mutations Associated with Human Pathologies
inferred← citeshttps://doi.org/10.34626/0hnm-hn65openalex-snapshot
New Computational Methods to Calculate Drug-Receptor Binding Free Energies
inferred← citeshttps://doi.org/10.35118/apjmbb.2020.028.4.05openalex-snapshot
In silico molecular modelling and docking of allicin, epigallocatechin-3-gallate and gingerol against colon cancer cell proteins
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/10.4018/979-8-3693-5598-5.ch016openalex-snapshot
The Technological Leap in Drug Discovery With Cutting-Edge Solutions
inferred← citeshttps://doi.org/10.4172/2090-4924.1000112openalex-snapshot
In silico Study of Bacillus brevis Xylanase - Structure Prediction and Comparative Analysis with Other Bacterial and Fungal Xylanase
inferred← citeshttps://doi.org/10.53730/ijhs.v6ns6.10822openalex-snapshot
In-silico and in-vivo evaluation of comparative enhanced neurogenic performance by energy drinks
inferred← citeshttps://doi.org/10.5772/intechopen.98319openalex-snapshot
Utilization from Computational Methods and Omics Data for Antiviral Drug Discovery to Control of SARS-CoV-2
inferred← citeshttps://doi.org/10.6026/97320630009755openalex-snapshot
Comparative insights using the molecular homology model of BDNF (Brain derived neurotrophic factor) of Varanus komodoensis and the known NGF (Nerve growth factor) structure of Naja atra
inferred← citeshttps://doi.org/10.6026/97320630011296openalex-snapshot
Implication from the predicted docked interaction of sigma H and exploration of its interaction with RNA polymerase in Mycobacterium tuberculosis
inferred← citeshttps://doi.org/10.6026/97320630013122openalex-snapshot
Linear epitope prediction in HPV type 16 E7 antigen and their docked interaction with human TMEM 50A structural model
inferred← citeshttps://doi.org/10.6026/97320630081105openalex-snapshot
Modeling and structural analysis of cellulases using Clostridium thermocellum as template
inferred← citeshttps://doi.org/10.6026/97320630081271openalex-snapshot
Genetic relationship of Sardinella lemuru from lombok strait with fish rich in omega-3 fatty acid
inferred← citeshttps://doi.org/10.70675/2b288725z2446z48c5z833ezf53915cd324bopenalex-snapshot
Développement d’outils statistiques d’évaluation de méthodes de criblage virtuel : courbes de prédictivité & Screening Explorer
inferred← citeshttps://doi.org/10.70675/f0567b86z4fdfz4cc8zb716z49ec4d7b8548openalex-snapshot
Développements HPC pour une nouvelle méthode de docking inverse : applications aux protéines matricielles.
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