Reliability Of Alphafold Vs Experimental Structure

AI-Enhanced Adaptive Virtual Screening Platform Enabling Exploration of 69 Billion Molecules Discovers Structurally Vali

Fully flexible molecular alignment enables accurate ligand structure modelling

Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design

Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors

Therapeutic Potential of Natural Products in the Treatment of Schistosomiasis

The Prediction of LptA and LptC Protein–Protein Interactions and Virtual Screening for Potential Inhibitors

Riluzole, a Derivative of Benzothiazole as a Potential Anti-Amoebic Agent against Entamoeba histolytica

Computer simulation of molecular recognition in biomolecular system: from in silico screening to generalized ensembles

Navigating the landscape of enzyme design: from molecular simulations to machine learning

Molecular determinants of antagonist interactions with chemokine receptors CCR2 and CCR5

Fast and accurate modeling and design of antibody-antigen complex using tFold

Towards a Truly General Intermolecular Binding Affinity Calculator for Drug Discovery & Design

Protein Function Analysis through Machine Learning

Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools

Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer

Computer-Aided Drug Design towards New Psychotropic and Neurological Drugs

Opportunities and Challenges for In Silico Drug Discovery at Delta Opioid Receptors

Recent Progress of Protein Tertiary Structure Prediction

Quality Assessment of Selected Protein Structures Derived from Homology Modeling and AlphaFold

Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis

A Comprehensive Computational Insight into the PD-L1 Binding to PD-1 and Small Molecules

A Shortcut from Genome to Drug: The Employment of Bioinformatic Tools to Find New Targets for Gastric Cancer Treatment

ML-Driven Approach to Discovery of Peptide-Based BACE1 Inhibitors

The Recent Advances in the Approach of Artificial Intelligencetowards Medicine Discovery

FABind+: Enhancing Molecular Docking through Improved Pocket Prediction and Pose Generation

EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions

Enhancing Ligand Pose Sampling for Molecular Docking

Artificial Intelligence and Machine Learning Approaches for Target-Based Drug Discovery: A Focus on GPCR-Ligand Interact

EQUIBIND: A geometric deep learning-based protein-ligand binding prediction method

The Role of Artificial Intelligence in Drug Discovery

Machine Learning-Driven Anticancer Drug Discovery: From Virtual Screening to Preclinical Validation

Protein Structure Prediction Tools and Computational Approaches

FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction.

The Role of Artificial Intelligence in Drug Discovery

Structure-guided computational insecticide discovery targeting <i>β</i>-N-acetyl-D-hexosaminidase of <i>Ostrinia furnaca

Role of Chemoinformatics and Machine Learning in Drug Repurposing

Fundamentals of Molecular Docking and Comparative Analysis of Protein–Small-Molecule Docking Approaches

Structure-guided computational insecticide discovery targeting <i>β</i>-N-acetyl-D-hexosaminidase of <i>Ostrinia furnaca

RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field

Exploration and augmentation of pharmacological space via adversarial auto-encoder model for facilitating kinase-centric

Identification of Potential WSB1 Inhibitors by AlphaFold Modeling, Virtual Screening, and Molecular Dynamics Simulation

List of the compounds selected from propolis.

Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally

KIFC1 inhibition: Exploring the potential of propolis-derived small molecules for targeting cancer progression through i

Stepwise schematic workflow of the present study.

AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark protein

Modeling Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery

Exploration of Dark Chemical Genomics Space viaPortal Learning: Applied to Targeting theUndruggable Genome and COVID-19

Accurate Protein-Ligand Complex Structure Prediction using Geometric Deep Learning

One substrate many enzymes virtual screening uncovers missing genes of carnitine biosynthesis in human and mouse.

Lira: Rotational Invariant Shape and Electrostatic Descriptors for Small Molecules based on Real Spherical Harmonics

3DinforCPI: Enhancing Efficiency of Compound-Protein Interaction Prediction Through Novel Perspectives on Multi-level In

DynamicBind: predicting ligand-specific protein-ligand complex structure with a deep equivariant generative model

Inferring molecular inhibition potency with AlphaFold predicted structures

Structure prediction of protein-ligand complexes from sequence information with Umol

Sequence-based drug design using transformers

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

Revolutionizing Healthcare: AI-driven Innovations in Drug Development and Personalized Medicine

Computational Approaches to Molecular Docking and Protein Modeling in Drug Discovery

Conformational changes in the AdeB transmembrane efflux pump by amphiphilic peptide Mastoparan-B, down-regulates express

Evaluation of AlphaFold-derived Structures for Earlystage Virtual Screening: Utility and Limitations

Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

Poxviridae Protein kinases as targets for control of LSDV , Monkeypox like outbreaks

Automated benchmarking of combined protein structure and ligand conformation prediction

Cosolvent and Dynamic Effects in Binding Pocket Search by Docking Simulations

DeepPocket: Ligand Binding Site Detection and Segmentation using 3D Convolutional Neural Networks

zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15

Uni-Mol: A Universal 3D Molecular Representation Learning Framework

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Addressing sub-optimal poses in non-equilibrium alchemical calculations

How good are AlphaFold models for docking-based virtual screening?

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes

Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

DSDPFlex: An Improved Flexible-Receptor Docking Method with GPU Acceleration

A Protein-Ligand Interaction-focused 3D Molecular Generative Framework for Generalizable Structure-based Drug Design

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes

A Computational Workflow for Refining AF2 Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A

Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes

Augmentation of Structure Information to the Sequence-Based Machine Learning-Assisted Directed Protein Evolution

Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study

ACFIS 2.0: an improved web-server for fragment-based drug discovery via a dynamic screening strategy

SH2db, an information system for the SH2 domain

BioLiP2: an updated structure database for biologically relevant ligand–protein interactions

SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets

Proteins Plus : a comprehensive collection of web-based molecular modeling tools

Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition

Generative AI in drug discovery and development: the next revolution of drug discovery and development would be directed

Transferability of Geometric Patterns from Protein Self-Interactions to Protein-Ligand Interactions

AlphaDrug: protein target specific de novo molecular generation

Assessing Protein Homology Models with Docking Reproducibility

Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionar

AlphaFold Models Illuminate Half of Dark Human Proteins

Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks

Computational model of the full-length TSH receptor

AI-Assisted chemical probe discovery for the understudied Calcium-Calmodulin Dependent Kinase, PNCK

TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction

PrePCI: A structure- and chemical similarity-informed database of predicted protein compound interactions

Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interac

Widely Used and Fast De Novo Drug Design by a Protein Sequence-Based Reinforcement Learning Model

Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands

BindingSiteAugmentedDTA: Enabling A Next-Generation Pipeline for Interpretable Prediction Models in Drug-Repurposing

PIsToN: Evaluating Protein Binding Interfaces with Transformer Networks

The structure, catalytic mechanism, and inhibitor identification of phosphatidylinositol remodeling MBOAT7

Challenges in antibody structure prediction

Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures

End-to-end protein–ligand complex structure generation with diffusion-based generative models

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency o

Structural insights into the heterotrimeric alternatively spliced P2X7 receptors

Assessment of AlphaFold structures and optimization methods for virtual screening

Flexible protein–protein docking with a multitrack iterative transformer

Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally

Exploring the Druggable Conformational Space of Protein Kinases Using AI-Generated Structures

Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

PSICHIC: physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data

EquiScore: A generic protein-ligand interaction scoring method integrating physical prior knowledge with data augmentati

Interpreting Molecular Dynamics Forces as Deep Learning Gradients Improves Quality Of Predicted Protein Structures

Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom

Graph Attention Site Prediction (GrASP): Identifying Druggable Binding Sites Using Graph Neural Networks with Attention

GTExome: Modeling commonly expressed missense mutations in the human genome

Structure prediction of protein-ligand complexes from sequence information with Umol

AlphaFold2 structures template ligand discovery

Towards the accurate modelling of antibody-antigen complexes from sequence using machine learning and information-driven

Sequence-based drug design using transformers

A new paradigm for applying deep learning to protein–ligand interaction prediction

Benchmarking Reverse Docking through AlphaFold2 Human Proteome

Molecular dynamics of outer membrane-embedded polysaccharide secretion porins reveals closed resting-state surface gates

SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction

PackDock: a Diffusion Based Side Chain Packing Model for Flexible Protein-Ligand Docking

SAXS DATA BASED GLYCOSYLATED MODELS OF HUMAN ALPHA-1-ACID GLYCORPROTEIN, A KEY PLAYER IN HEALTH, DISEASE AND DRUG CIRCUL

Applying multi-state modeling using AlphaFold2 for kinases and its application for ensemble screening

PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold

Comprehensive detection and characterization of human druggable pockets through novel binding site descriptors

Protein language models are performant in structure-free virtual screening

AlphaFold 3-enabled in silico exploration of PGAM1 interactions in cancer

Recent Developments in Ultralarge and Structure-Based Virtual Screening Approaches

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale

BioMolFormer: A Novel Approach to Molecular Generation with SELFIES and Monte Carlo Tree Search

Evaluation of AlphaFold2 structures as docking targets

The role of cholesterol binding in the control of cholesterol by the Scap–Insig system

zPoseScore model for accurate and robust protein–ligand docking pose scoring in CASP15

Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching

Toward physics‐based precision medicine: Exploiting protein dynamics to design new therapeutics and interpret variants

Keeping pace with the explosive growth of chemical libraries with structure‐based virtual screening

The effects of nature‐inspired amino acid substitutions on structural and biochemical properties of the <i>E. coli</i> L

AlphaFold Kinase Optimizer: Enhancing Virtual Screening Performance Through Automated Refinement of AlphaFold-Based Kina

Drug repurposing for SARS-CoV-2: a high-throughput molecular docking, molecular dynamics, machine learning, and DFT stud

Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction.

Fungal Foe Unveiled: AlphaFold-based 3D structure prediction of Rhizopus delemar 1,3-β-Glucan synthase and virtual scree

Beyond sequence: Structure-based machine learning

Identification of novel compounds against Trypanosoma cruzi using AlphaFold structures.

AI protein structure prediction-based modeling and mutagenesis of a protostome receptor and peptide ligands reveal key r

Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein

Identification of probable inhibitors for the DNA polymerase of the Monkeypox virus through the virtual screening approa

Binding affinity between coronavirus spike protein and human ACE2 receptor

AlphaFold illuminates half of the dark human proteins.

A Structure-Based Approach for Predicting Odor Similarity of Molecules via Docking Simulations with Human Olfactory Rece

RAPID-Net: Accurate Pocket Identification for Binding-Site-Agnostic Docking.

Structure-Based Drug Design with a Deep Hierarchical Generative Model.

‘Druggability’ of the Per–Arnt–Sim (PAS) domains of human PAS domain kinase, a therapeutic target for metabolic and live

Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development

Natural Product-Inspired Bis(trifluoromethyl) Phenyl Hydroxycinnamate Derivatives as Promising Nonsteroidal Inhibitors o

RAPID-Net: Accurate Pocket Identification for Binding-Site-AgnosticDocking

Discovery of Chemical Scaffolds as Lysophosphatidic Acid Receptor 1 Antagonists: Virtual Screening, In Vitro Validation,

Computational approaches streamlining drug discovery

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiati

AI is a viable alternative to high throughput screening: a 318-target study

A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein–protein and protein–ligand bin

Computational biology assisted exploration of phytochemicals derived natural inhibitors to block BZLF1 gene activation o

Inferring molecular inhibition potency with AlphaFold predicted structures

Augmented BindingNet dataset for enhanced ligand binding pose predictions using deep learning

Accelerating drug discovery for Disease X <i>via</i> an AlphaFold2 driven drug repositioning strategy

A chronotherapeutics-applicable multi-target therapeutics based on AI: Example of therapeutic hypothermia

Deep learning guided high-throughput virtual screening for in vitro antibody maturation

AI in drug design: evolution or revolution?

Computational methods directed towards drug repurposing for COVID-19: advantages and limitations

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies

Artificial Intelligence-based database for prediction of protein structure and their alterations in ocular diseases

Pocket to concavity: a tool for the refinement of protein–ligand binding site shape from alpha spheres

PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions wit

Structure-guided computational insecticide discovery targeting β-N-acetyl-D-hexosaminidase of Ostrinia furnacalis.

MulinforCPI: enhancing precision of compound–protein interaction prediction through novel perspectives on multi-level in

A new paradigm for applying deep learning to protein–ligand interaction prediction

Guided docking as a data generation approach facilitates structure-based machine learning on kinases

Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti

AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative mode

Docking-informed machine learning for kinome wide affinity prediction

Deep Learning Strategies for Enhanced Molecular Docking and Virtual Screening

AlphaFold meets de novo drug design: leveraging structural protein information in multi-target molecular generative mode

İLAÇ TASARIMINDA YAPAY ZEKÂ UYGULAMALARI

Application of vision transformers to protein-ligand affinity prediction.

The use of machine learning-based sequential virtual screening in the search of new ligands of 5-HT6 receptor

Structure-Guided Computational Approaches to Unravel Druggable Proteomic Landscape of Mycobacterium leprae

The Use of AlphaFold for In Silico Exploration of Drug Targets in the Parasite Trypanosoma cruzi

NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules

Essential Dynamics Ensemble Docking for Structure-Based GPCR Drug Discovery

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency o

Structural modeling of antibody variable regions using deep learning—progress and perspectives on drug discovery

Recent Progress in Antibody Epitope Prediction

Predicting the Assembly of the Transmembrane Domains of Viral Channel Forming Proteins and Peptide Drug Screening Using

Multitasking Na+/Taurocholate Cotransporting Polypeptide (NTCP) as a Drug Target for HBV Infection: From Protein Enginee

Conjecturing about Small-Molecule Agonists and Antagonists of α4β1 Integrin: From Mechanistic Insight to Potential Thera

Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from Taeni

Evaluation of Myocilin Variant Protein Structures Modeled by AlphaFold2

Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein

Using AlphaFold Predictions in Viral Research

Artificial Intelligence in Aptamer–Target Binding Prediction

Machine Learning Assisted Approach for Finding Novel High Activity Agonists of Human Ectopic Olfactory Receptors

A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining P

Structure Prediction, Evaluation, and Validation of GPR18 Lipid Receptor Using Free Programs

Estimating the Similarity between Protein Pockets

Structural Modifications Introduced by NS2B Cofactor Binding to the NS3 Protease of the Kyasanur Forest Disease Virus.

Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter

Identification of Potential Druggable Targets and Structure-Based Virtual Screening for Drug-like Molecules against the

Pharmacoinformatic Investigation of Silymarin as a Potential Inhibitor against Nemopilema nomurai Jellyfish Metalloprote

Pharmacological Chaperones and Protein Conformational Diseases: Approaches of Computational Structural Biology

Identification of Catechins’ Binding Sites in Monomeric Aβ42 through Ensemble Docking and MD Simulations

Inhibitor Trapping in N-Myristoyltransferases as a Mechanism for Drug Potency

Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor.

Target Prediction by Multiple Virtual Screenings: Analyzing the SARS-CoV-2 Phenotypic Screening by the Docking Simulatio

Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold

Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols

Anopheles gambiae Trehalase Inhibitors for Malaria Vector Control: A Molecular Docking and Molecular Dynamics Study

Identifying Residues for Substrate Recognition in Human GPAT4 by Molecular Dynamics Simulations

P-Loop Channels: Experimental Structures, and Physics-Based and Neural Networks-Based Models

Bioactive Phytoconstituents as Potent Inhibitors of Tyrosine-Protein Kinase Yes (YES1): Implications in Anticancer Thera

Drug Design: Where We Are and Future Prospects

Protein–Ligand Docking in the Machine-Learning Era

Neuropeptides, New Ligands of SARS-CoV-2 Nucleoprotein, a Potential Link between Replication, Inflammation and Neurotran

Identification of Disalicyloyl Curcumin as a Potential DNA Polymerase Inhibitor for Marek’s Disease Herpesvirus: A Compu

Solubilization, purification, and characterization of the hexameric form of phosphatidylserine synthase from Candida alb

Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1

Drug design and repurposing with a sequence-to-drug paradigm

Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations

Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy

Deep contrastive learning enables genome-wide virtual screening.

In silico studies of the open form of human tissue transglutaminase

Prediction of protein–ligand binding affinity via deep learning models

In silico discovery of potent inhibitors against monkeypox’s major structural proteins

FlowDock: Geometric Flow Matching for Generative Protein-Ligand Docking and Affinity Prediction

TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.

Neural Networks to Calculate CDK2 Inhibition.

SAnDReS 2.0: Development of machine-learning models to explore the scoring function space.

Critical assessment of methods of protein structure prediction ( CASP )—Round XV

In silico screening of IMPPAT-derived phytochemicals targeting ERG6 and drug resistance–associated proteins in drug-resi

Quantum chemical optimization and residue-specific stabilization of CDK20 inhibitors in hepatocellular carcinoma.

Binding mode of brazzein to the taste receptor based on crystal structure and docking simulation.

An Integrated Computational and Biophysical Approach for Investigating the Structure-Function Impact of blaOXA-58 Mutati

Structure of epoxide hydrolase 2 from Mangifera indica throws light on the substrate specificity determinants of plant e

Structure-based identification of small molecule inhibitors targeting trigger factor and peptidyl prolyl cis/trans isome

An automated pipeline integrating AlphaFold 2 and MODELLER for protein structure prediction

Computational modeling and prediction of deletion mutants.

In-Silico targeting of SARS-CoV-2 NSP6 for drug and natural products repurposing.

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Combining AlphaFold with Focused Virtual Library Design in the Development of Novel CCR2 and CCR5 Antagonists.

Assessing AlphaFold 3 for Per- and Polyfluoroalkyl Substances Docking in Protein Structures

Integrating Machine Learning into Free Energy Perturbation Workflows

AlphaFold2 versus experimental structures: evaluation on G protein-coupled receptors

In-silico design of Multi-Epitope Vaccine Against Glioblastoma Using Tumor-Associated Antigens and TLR Agonist Adjuvants

New computational methods to study the relationship between protein structure and function

In-silico analysis of papain fibrinolytic mechanism from Carica papaya

Modeling study of the HlyBD-TolC hemolysin secretion system using the AI-based structural prediction and molecular dynam

Applications of reinforcement learning, machine learning, and virtual screening in SARS-CoV-2-related proteins

Atomistic simulations identify the Tetrandrine as potent anti-malarial drug candidate against Plasmodium falciparum targ

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.