☆ 4.5 Review

Advances in the discovery of new chemotypes through ultra-large library docking

EXPERT OPINION ON DRUG DISCOVERY (2023)

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Article Chemistry, Medicinal

Relative Binding Free Energy Calculations for Ligands with Diverse Scaffolds with the Alchemical Transfer Method

Solmaz Azimi et al.

Summary: We propose an extension of the alchemical transfer method (ATM) called ATM-RBFE for estimating relative binding free energies of molecular complexes. The method is implemented in the OpenMM molecular simulation package and aims to provide a simpler and more generally applicable route to the calculation of relative binding free energies. The method is validated against benchmark sets and yields consistent and converged estimates in agreement with reference values and experimental measurements.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Article Chemistry, Multidisciplinary

Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Andreas Luttens et al.

Summary: Developing drug inhibitors targeting SARS-CoV-2 is crucial for saving lives and preparing for future outbreaks. Two virtual screening strategies were explored, resulting in the identification of compounds with inhibitory effects, including one compound with promising antiviral activity.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

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Article Chemistry, Medicinal

Structure-Based Pharmacophore Modeling, Virtual Screening, Molecular Docking, ADMET, and Molecular Dynamics (MD) Simulation of Potential Inhibitors of PD-L1 from the Library of Marine Natural Products

Lianxiang Luo et al.

Summary: In this study, marine natural compound 51320 was identified as a small molecule inhibitor of PD-L1 through various screening methods.

MARINE DRUGS (2022)

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Article Multidisciplinary Sciences

Synthon-based ligand discovery in virtual libraries of over 11 billion compounds

Arman A. Sadybekov et al.

Summary: Structure-based virtual ligand screening using V-SYNTHES method is effective in rapidly identifying high-scoring compounds from a large chemical space, with experimental results demonstrating successful hit rates and potencies. This approach shows promise for lead discovery and is easily scalable for use with diverse docking algorithms.

NATURE (2022)

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Article Chemistry, Multidisciplinary

An Enhanced Hybrid Screening Approach to Identify Potent Inhibitors for the SARS-CoV-2 Main Protease From the NCI Compound Library

Shuhua G. Li et al.

Summary: This study developed a refined virtual screening strategy to search for antiviral drugs for COVID-19. The strategy successfully identified several potent inhibitors through screening a compound library. This strategy improves hit rates in virtual screening and accelerates drug discovery.

FRONTIERS IN CHEMISTRY (2022)

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Review Pharmacology & Pharmacy

Guided structure-based ligand identification and design via artificial intelligence modeling

Juan Di Filippo et al.

Summary: The implementation of AI methodologies in drug discovery is increasing, particularly in structure-based virtual screening. AI methods provide alternative frameworks for ligand identification and de novo ligand design. Future trends include more structure-based generative models and standard guidelines for validating generated structures.

EXPERT OPINION ON DRUG DISCOVERY (2022)

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Article Chemistry, Medicinal

Design of SARS-CoV-2 Mpro, PLpro dual-target inhibitors based on deep reinforcement learning and virtual screening

Li-chuan Zhang et al.

Summary: In this study, three compounds were identified that have the potential to inhibit the main protease and papain-like protease of SARS-CoV-2. These compounds can be further investigated as potential lead compounds for SARS-CoV-2 inhibitors.

FUTURE MEDICINAL CHEMISTRY (2022)

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Article Chemistry, Multidisciplinary

Mechanisms, challenges, and opportunities of dual Ni/photoredox-catalyzed C(sp2)-C(sp3) cross-couplings

Mingbin Yuan et al.

Summary: The merging of photoredox and nickel catalysis has revolutionized C-C cross-coupling, but detailed mechanistic investigations are lacking. Computational tools are powerful in elucidating factors controlling reactivity and selectivity. The mechanistic understanding of catalytic systems depends on specific choices of substrates, ligands, and photocatalysts, necessitating more accurate computational methods and user-friendly simulation tools.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2022)

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Review Chemistry, Medicinal

Drug Design by Pharmacophore and Virtual Screening Approach

Deborah Giordano et al.

Summary: Computer-aided drug discovery techniques have reduced the time and costs involved in developing new drugs. Pharmacophore approaches, which define the molecular features required for the binding of a molecule to a specific receptor, have proven to be one of the most interesting tools in this field. The use of computational tools for pharmacophore modeling and virtual screening has resulted in successful studies and applications.

PHARMACEUTICALS (2022)

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Article Chemistry, Medicinal

Organic Compound Synthetic Accessibility Prediction Based on the Graph Attention Mechanism

Jiahui Yu et al.

Summary: In this study, a data-driven interpretable prediction framework called GASA was proposed to evaluate the synthetic accessibility of small molecules. GASA, using a graph neural network architecture, achieved remarkable performance by automatically capturing important structural features to distinguish easy-to-synthesize and hard-to-synthesize compounds. GASA also learned the important features affecting molecular synthetic accessibility by assigning attention weights.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Editorial Material Pharmacology & Pharmacy

Library size in virtual screening: is it truly a number's game?

Maria Kontoyianni

EXPERT OPINION ON DRUG DISCOVERY (2022)

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Article Chemistry, Medicinal

Fundamental Redesign of the TIGER2hs Kernel to Address Severe Parameter Sensitivity

Lukas Schulig et al.

Summary: Replica exchange molecular dynamics simulations are a popular method for enhancing conformational sampling. The improved TIGER2hs algorithm eliminates sampling imbalance and parameter sensitivity issues, allowing for accurate calculations with less computational resources compared to REMD.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2022)

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Article Multidisciplinary Sciences

Structure-based discovery of nonopioid analgesics acting through the alpha(2A)-adrenergic receptor

Elissa A. Fink et al.

Summary: A new class of α(2A)AR agonists has been discovered through computational docking and experimental validation, which exhibit on-target analgesic activity in multiple pain models without inducing sedation.

SCIENCE (2022)

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Article Chemistry, Multidisciplinary

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

Karan Kapoor et al.

Summary: Proteins can sample a broad landscape as they undergo conformational transition between different functional states. Considering the different conformational states of a protein is central for a successful drug-design strategy. In this study, a novel docking protocol, termed extended-ensemble docking, is introduced for proteins that undergo large-scale conformational changes. The results show the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.

CHEMICAL SCIENCE (2022)

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Article Biochemistry & Molecular Biology

Drug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes

Ammar D. Elmezayen et al.

Summary: This study attempted to identify commercially available drugs for repurposing against coronavirus through structure-based virtual screening, successfully finding multiple potential inhibitors. The 3D structure of TMPRSS2 was generated using homology modeling, and promising inhibitors were identified through docking studies. ADMET profiles showed that the compounds discovered in the study are safe and drug-like.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2021)

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Article Biology

De novo design of novel protease inhibitor candidates in the treatment of SARS-CoV-2 using deep learning, docking, and molecular dynamic simulations

Amir Hossein Arshia et al.

Summary: The study focused on identifying potential inhibitors against the main protease of SARS-CoV-2 using computational approaches, such as molecular docking and molecular dynamics simulations. The selected candidates showed strong interaction with key residues, validated through extensive computational and statistical analyses. Further in vitro, in vivo, and clinical trials are needed to confirm their efficacy.

COMPUTERS IN BIOLOGY AND MEDICINE (2021)

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Article Chemistry, Medicinal

Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning

Joel Ricci-Lopez et al.

Summary: The study demonstrates that using machine learning methods to process ensemble docking results can significantly improve the predictive power of structure-based virtual screening.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Review Chemistry, Medicinal

Generative Deep Learning for Targeted Compound Design

Tiago Sousa et al.

Summary: De novo molecular design is increasingly using generative models from Deep Learning to propose novel compounds with desired properties. Different optimization strategies can guide the generation process towards specific aims, such as biological activities, synthesis processes, or chemical features.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Chemistry, Medicinal

Bioisosteres of the Phenyl Ring: Recent Strategic Applications in Lead Optimization and Drug Design

Murugaiah A. M. Subbaiah et al.

Summary: The benzene moiety is commonly found in drugs, but its indiscriminate use can lead to poor physicochemical properties. Bioisosteric replacements for benzene rings can improve potency, solubility, and metabolic stability while reducing lipophilicity and other negative effects.

JOURNAL OF MEDICINAL CHEMISTRY (2021)

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Article Chemistry, Medicinal

Discovery of spirohydantoins as selective, orally bioavailable inhibitors of p300/CBP histone acetyltransferases

Zhiqin Ji et al.

Summary: p300 and CBP play essential roles in cellular processes and dysregulation of their histone acetyltransferase activity is linked to various human diseases. The novel drug-like compound 21 is a selective orally bioavailable inhibitor of p300/CBP histone acetyltransferase, more potent than A-485 and lacking off-target inhibition of dopamine and serotonin transporters.

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS (2021)

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Article Biochemical Research Methods

A practical guide to large-scale docking

Brian J. Bender et al.

Summary: Structure-based docking screens of compound libraries are common in early drug and probe discovery. Best practices and control calculations are outlined to evaluate docking parameters prior to undertaking a large-scale prospective screen.

NATURE PROTOCOLS (2021)

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Article Multidisciplinary Sciences

Structure based pharmacophore modeling, virtual screening, molecular docking and ADMET approaches for identification of natural anti-cancer agents targeting XIAP protein

Firoz A. Dain Md Opo et al.

Summary: The study aimed to identify new natural compounds that can induce apoptosis with low toxicity to fight against XIAP related cancer treatment. Through virtual screening, molecular docking, and molecular dynamics simulation, three potential anti-cancer compounds were identified, which require further wet lab evaluation of their efficacy.

SCIENTIFIC REPORTS (2021)

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Article Multidisciplinary Sciences

New machine learning and physics-based scoring functions for drug discovery

Isabella A. Guedes et al.

Summary: Scoring functions are crucial for in silico drug discovery, but accurate prediction of binding affinity remains a challenge. Developing scoring functions based on precise physics-based descriptors is necessary to improve prediction accuracy.

SCIENTIFIC REPORTS (2021)

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Article Chemistry, Medicinal

FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening

Hongyi Zhou et al.

Summary: In modern drug discovery, virtual ligand screening (VLS) is commonly used to reduce time and cost before experimental ligand screening. A new approach called FRAGSITE improves VLS precision and recall by integrating ligand fragment scores with global ligand similarity scores, outperforming state-of-the-art methods and showing better performance on challenging sets.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Chemistry, Physical

Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding

Edward B. Miller et al.

Summary: This study presents a reliable and accurate solution for protein-ligand binding by combining different docking methods, achieving a low root-mean-square deviation in over 90% of cases. The predicted ligand-receptor structures were accurate enough to enable predictive structure-based drug discovery for challenging targets, expanding the applicability of such methods.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Article Chemistry, Physical

Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory

Lieyang Chen et al.

Summary: PME-GIST is a new computational method that can more accurately estimate free energies at a faster speed. By comparing with experimental data from 32 small molecules, the results of PME-GIST are highly consistent with TI calculations. Through a simple correction for high-order entropy terms, the results of PME-GIST are also highly consistent with experimental results.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)

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Review Biochemistry & Molecular Biology

SARS-CoV-2 Mpro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors

Andrea Citarella et al.

Summary: The uncontrolled spread of COVID-19 caused by SARS-CoV-2 in 2020-2021 had devastating impacts on health, economy, and daily life globally. Despite approved vaccines, their long-term efficacy and safety are debated, prompting the search for new target-based drugs. Strategies targeting the coronavirus's main protease, M-pro, show promise for anti-coronavirus drug development.

BIOMOLECULES (2021)

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Article Biochemical Research Methods

A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2

Shiwei Wang et al.

Summary: This study utilized a neural network model to predict potential anti-SARS-CoV-2 compounds and identified a novel compound through experimental testing. The model is highly efficient and can be used for large-scale screening of compound databases to expedite the drug discovery process for treating COVID-19.

BRIEFINGS IN BIOINFORMATICS (2021)

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Article Chemistry, Medicinal

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

Jerome Eberhardt et al.

Summary: AutoDock Vina is a widely used open-source program for molecular docking with new features such as support for macrocycles and explicit water molecules. The latest version also includes support for AutoDock4.2 scoring function, simultaneous docking of multiple ligands, and a batch mode for docking a large number of ligands. Python bindings have been implemented to facilitate scripting and workflow development.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Chemistry, Medicinal

Pharmacophore Model for SARS-CoV-2 3CLpro Small-Molecule Inhibitors and in Vitro Experimental Validation of Computationally Screened Inhibitors

Enrico Glaab et al.

Summary: This study explores pharmacological strategies and small-molecule inhibitors against COVID-19, identifying micromolar activity inhibitors of 3CLpro through virtual screening, MD simulations, and machine learning, and establishing a pharmacophore model for molecular recognition. These experimentally validated inhibitors offer resources for subsequent computational screening and optimization efforts.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)

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Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

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Article Multidisciplinary Sciences

Accurate prediction of protein structures and interactions using a three-track neural network

Minkyung Baek et al.

Summary: Through the three-track network, we achieved accuracies approaching those of DeepMind in CASP14, enabling rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and providing insights into the functions of proteins with currently unknown structure.

SCIENCE (2021)

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Article Chemistry, Medicinal

Recognition of Divergent Viral Substrates by the SARS-CoV-2 Main Protease

Elizabeth A. MacDonald et al.

Summary: The main protease (Mpro) of SARS-CoV-2 plays a key role in viral replication by cleaving viral polyproteins at specific sites, and its interactions with substrates can have significant effects on catalytic efficiency. The study provides insights into potential targets for antiviral drug design and highlights the importance of finely tuned substrate-dependent catalytic parameters in the coronavirus lifecycle.

ACS INFECTIOUS DISEASES (2021)

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Review Biochemistry & Molecular Biology

Recent Developments in Free Energy Calculations for Drug Discovery

Edward King et al.

Summary: The grand challenge of structure-based drug design lies in accurately predicting binding free energies. Molecular dynamics simulations have enabled the modeling of conformational changes in the binding process, leading to the calculation of thermodynamic quantities for estimating binding affinities. Various approaches, including MM-PBSA, LIE, and alchemical methods, have been widely used to model molecular recognition for drug discovery and lead optimization.

FRONTIERS IN MOLECULAR BIOSCIENCES (2021)

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Article Computer Science, Software Engineering

Green Computing Approaches - A Survey

Mahdi Dhaini et al.

Summary: The surge in global warming and greenhouse gas emissions has become increasingly severe in recent years due to the growing use of technological resources. Therefore, advocating for green computing in the technological field is highly recommended. This paper reviews various approaches to green computing in five main areas - software engineering, cloud computing, mobile computing, data centers, and the educational sector.

INFORMATICA-AN INTERNATIONAL JOURNAL OF COMPUTING AND INFORMATICS (2021)

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Article Biochemistry & Molecular Biology

Current approaches to flexible loop modeling

Amelie Barozet et al.

Summary: Loops in protein structures are crucial for various biological functions, but their conformational variability poses a challenge for structural investigation. This paper provides an overview of current computational approaches to flexible loop modeling, emphasizing the difficulty in accurately capturing the conformational variability of long flexible loops. Future advancements in this field are expected to come from a combination of experimental and computational techniques, leading to a better understanding of the relationships between loop sequence, structural flexibility, and functional roles. Accurate loop modeling holds promise for applications in biomedicine and biotechnology.

CURRENT RESEARCH IN STRUCTURAL BIOLOGY (2021)

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Article Chemistry, Multidisciplinary

Automated discovery of noncovalent inhibitors of SARS-CoV-2 main protease by consensus Deep Docking of 40 billion small molecules

Francesco Gentile et al.

Summary: The study presented an artificial intelligence-driven virtual screening pipeline that screened 40 billion molecules against SARS-CoV-2 main protease, identifying numerous experimentally confirmed Mpro enzyme inhibitors and benchmarking the performance of various degrees of automation hit-selecting strategies.

CHEMICAL SCIENCE (2021)

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Article Chemistry, Multidisciplinary

Combination of pose and rank consensus in docking-based virtual screening: the best of both worlds

Valeria Scardino et al.

Summary: The study introduces a new methodology named PRC that combines pose and ranking consensus approaches to overcome the limitations of stand-alone strategies. By combining results from multiple docking programs, this method shows improved performance in drug discovery while reducing computational costs.

RSC ADVANCES (2021)

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Article Chemistry, Multidisciplinary

Alchemical absolute protein-ligand binding free energies for drug design

Y. Khalak et al.

Summary: Recent advances in relative protein-ligand binding free energy calculations have demonstrated the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies remains a challenging task, especially when considering the need to explicitly account for the protein in its apo state. This study presents several approaches for obtaining apo state ensembles to facilitate accurate absolute Delta G calculations and outlines protocols for future application in drug discovery.

CHEMICAL SCIENCE (2021)

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Article Chemistry, Medicinal

Virtual Screening in the Cloud: How Big Is Big Enough?

Christoph Grebner et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

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Review Chemistry, Multidisciplinary

Machine-learning scoring functions for structure-based drug lead optimization

Hongjian Li et al.

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2020)

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Article Multidisciplinary Sciences

Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors

Linlin Zhang et al.

SCIENCE (2020)

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Article Chemistry, Physical

Ligand-based pharmacophore filtering, atom based 3D-QSAR, virtual screening and ADME studies for the discovery of potential ck2 inhibitors

A. Mohan et al.

JOURNAL OF MOLECULAR STRUCTURE (2020)

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Review Chemistry, Multidisciplinary

Structure-Based Virtual Screening: From Classical to Artificial Intelligence

Eduardo Habib Bechelane Maia et al.

FRONTIERS IN CHEMISTRY (2020)

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Article Chemistry, Medicinal

Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds

Anh-Tien Ton et al.

MOLECULAR INFORMATICS (2020)

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Article Multidisciplinary Sciences

An open-source drug discovery platform enables ultra-large virtual screens

Christoph Gorgulla et al.

NATURE (2020)

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Article Multidisciplinary Sciences

Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors

Zhenming Jin et al.

NATURE (2020)

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Article Medicine, General & Internal

Remdesivir for the Treatment of Covid-19-Final Report

John H. Beigel et al.

NEW ENGLAND JOURNAL OF MEDICINE (2020)

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Review Biochemistry & Molecular Biology

Application of Fragment-Based Drug Discovery to Versatile Targets

Qingxin Li

FRONTIERS IN MOLECULAR BIOSCIENCES (2020)

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Article Medicine, Research & Experimental

Virtual screening and repurposing of FDA approved drugs against COVID-19 main protease

Mahmoud Kandeel et al.

LIFE SCIENCES (2020)

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Article Multidisciplinary Sciences

Generating Multibillion Chemical Space of Readily Accessible Screening Compounds

Oleksandr O. Grygorenko et al.

ISCIENCE (2020)

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Article Chemistry, Medicinal

ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery

John J. Irwin et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)

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Review Chemistry, Multidisciplinary

QSAR without borders

Eugene N. Muratov et al.

CHEMICAL SOCIETY REVIEWS (2020)

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Article Biochemistry & Molecular Biology

QEX: target-specific druglikeness filter enhances ligand-based virtual screening

Masahiro Mochizuki et al.

MOLECULAR DIVERSITY (2019)

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Review Biochemistry & Molecular Biology

The Light and Dark Sides of Virtual Screening: What Is There to Know?

Aleix Gimeno et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

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Article Multidisciplinary Sciences

Ultra-large library docking for discovering new chemotypes

Jiankun Lyu et al.

NATURE (2019)

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Review Mathematical & Computational Biology

An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking

Jin Li et al.

INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES (2019)

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Article Biochemistry & Molecular Biology

Receptor-based pharmacophore modeling, virtual screening, and molecular docking studies for the discovery of novel GSK-3 inhibitors

Ahmed M. El Kerdawy et al.

JOURNAL OF MOLECULAR MODELING (2019)

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Article Chemistry, Medicinal

Fragment-Based Discovery of Novel Potent Sepiapterin Reductase Inhibitors

Jo Alen et al.

JOURNAL OF MEDICINAL CHEMISTRY (2019)

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Article Chemistry, Physical

Replica-Based Protein Structure Sampling Methods II: Advanced Hybrid Solvent TIGER2hs

Norman Geist et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2019)

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Article Multidisciplinary Sciences

A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site

Crystal Nguyen et al.

PLOS ONE (2019)

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Article Biochemistry & Molecular Biology

Electrostatic-field and surface-shape similarity for virtual screening and pose prediction

Ann E. Cleves et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2019)

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Article Biochemistry & Molecular Biology

PubChem 2019 update: improved access to chemical data

Sunghwan Kim et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Multidisciplinary Sciences

Exponential consensus ranking improves the outcome in docking and receptor ensemble docking

Karen Palacio-Rodriguez et al.

SCIENTIFIC REPORTS (2019)

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Article Biochemistry & Molecular Biology

DrugBank 5.0: a major update to the DrugBank database for 2018

David S. Wishart et al.

NUCLEIC ACIDS RESEARCH (2018)

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Article Biochemistry & Molecular Biology

Spiropyrrolidine/spiroindolizino[6,7-b]indole heterocyclic hybrids: Stereoselective synthesis, cholinesterase inhibitory activity and their molecular docking study

Natarajan Arumugam et al.

BIOORGANIC CHEMISTRY (2018)

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Review Biophysics

Ensemble Docking in Drug Discovery

Rommie E. Amaro et al.

BIOPHYSICAL JOURNAL (2018)

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Article Chemistry, Multidisciplinary

Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules

Rafael Gomez-Bombarelli et al.

ACS CENTRAL SCIENCE (2018)

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Review Chemistry, Medicinal

Structure-Based Drug Design Strategies and Challenges

Xin Wang et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2018)

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Article Biochemistry & Molecular Biology

The Impact of Protein Structure and Sequence Similarity on the Accuracy of Machine-Learning Scoring Functions for Binding Affinity Prediction

Hongjian Li et al.

BIOMOLECULES (2018)

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Article Chemistry, Medicinal

Docking of Macrocycles: Comparing Rigid and Flexible Docking in Glide

Hiba Alogheli et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

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Article Chemistry, Medicinal

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

Zoe Cournia et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2017)

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Review Chemistry, Medicinal

6 Deep Learning in Drug Discovery

Erik Gawehn et al.

MOLECULAR INFORMATICS (2016)

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Article Chemistry, Organic

Microwave-assisted synthesis of functionalized spirohydantoins as 3-D privileged fragments for scouting the chemical space

Hugues Prevet et al.

TETRAHEDRON LETTERS (2016)

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Article Biochemistry & Molecular Biology

Novel spirohydantoin derivative as a potent multireceptor-active antipsychotic and antidepressant agent

Anna Czopek et al.

BIOORGANIC & MEDICINAL CHEMISTRY (2015)

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Review Biochemistry & Molecular Biology

MALT1-a universal soldier: multiple strategies to ensure NF-κB activation and target gene expression

Inna S. Afonina et al.

FEBS JOURNAL (2015)

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Article Chemistry, Medicinal

ZINC 15-Ligand Discovery for Everyone

Teague Sterling et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2015)

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Review Biochemistry & Molecular Biology

Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases

Teresa Kaserer et al.

MOLECULES (2015)

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Article Biochemical Research Methods

Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study

Hongjian Li et al.

BMC BIOINFORMATICS (2014)

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Article Chemistry, Multidisciplinary

Shape-Based Virtual Screening with Volumetric Aligned Molecular Shapes

David Ryan Koes et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2014)

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Editorial Material Pharmacology & Pharmacy

How far can virtual screening take us in drug discovery?

Supratik Kar et al.

EXPERT OPINION ON DRUG DISCOVERY (2013)

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Article Chemistry, Medicinal

Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context

Douglas R. Houston et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2013)

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Article Biochemistry & Molecular Biology

Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments

G. Madhavi Sastry et al.

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN (2013)

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Article Multidisciplinary Sciences

SWEETLEAD: an In Silico Database of Approved Drugs, Regulated Chemicals, and Herbal Isolates for Computer-Aided Drug Discovery

Paul A. Novick et al.

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Adaptation of High-Throughput Screening in Drug Discovery-Toxicological Screening Tests

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Enumeration of 166 Billion Organic Small Molecules in the Chemical Universe Database GDB-17

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Docking and scoring with ICM: the benchmarking results and strategies for improvement

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NNScore 2.0: A Neural-Network Receptor-Ligand Scoring Function

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JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

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WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE (2011)

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NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein-Ligand Complexes

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ACCOUNTS OF CHEMICAL RESEARCH (2009)

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EXPERT OPINION ON DRUG DISCOVERY (2008)

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Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding

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PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

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Origin and evolution of high throughput screening

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BRITISH JOURNAL OF PHARMACOLOGY (2007)

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Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes

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ZINC - A free database of commercially available compounds for virtual screening

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Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy

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JOURNAL OF MEDICINAL CHEMISTRY (2004)

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Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening

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Protein flexibility in ligand docking and virtual screening to protein kinases

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