Improving the Virtual Screening Ability of Target-Specific Scoring Functions Using Deep Learning Methods.


:Scoring functions play an important role in structure-based virtual screening. It has been widely accepted that target-specific scoring functions (TSSFs) may achieve better performance compared with universal scoring functions in actual drug research and development processes. A method that can effectively construct TSSFs will be of great value to drug design and discovery. In this work, we proposed a deep learning-based model named DeepScore to achieve this goal. DeepScore adopted the form of PMF scoring function to calculate protein-ligand binding affinity. However, different from PMF scoring function, in DeepScore, the score for each protein-ligand atom pair was calculated using a feedforward neural network. Our model significantly outperformed Glide Gscore on validation data set DUD-E. The average ROC-AUC on 102 targets was 0.98. We also combined Gscore and DeepScore together using a consensus method and put forward a consensus model named DeepScoreCS. The comparison results showed that DeepScore outperformed other machine learning-based TSSFs building methods. Furthermore, we presented a strategy to visualize the prediction of DeepScore. All of these results clearly demonstrated that DeepScore would be a useful model in constructing TSSFs and represented a novel way incorporating deep learning and drug design.


Front Pharmacol


Wang D,Cui C,Ding X,Xiong Z,Zheng M,Luo X,Jiang H,Chen K




Has Abstract


2019-08-22 00:00:00








  • Phenprocoumon Dose Requirements, Dose Stability and Time in Therapeutic Range in Elderly Patients With CYP2C9 and VKORC1 Polymorphisms.

    abstract:Background:Dose requirements of vitamin K antagonists are associated with CYP2C9 and VKORC1, but, compared to warfarin, less data is available about phenprocoumon. Furthermore, the effects on dose stability and anticoagulation quality are still unclear. Methods:Aim was to scrutinize phenprocoumon dose requirements, do...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Schneider KL,Kunst M,Leuchs AK,Böhme M,Weckbecker K,Kastenmüller K,Bleckwenn M,Holdenrieder S,Coch C,Hartmann G,Stingl JC

    更新日期:2020-01-28 00:00:00

  • Cysteine Proteases: Modes of Activation and Future Prospects as Pharmacological Targets.

    abstract::Proteolytic enzymes are crucial for a variety of biological processes in organisms ranging from lower (virus, bacteria, and parasite) to the higher organisms (mammals). Proteases cleave proteins into smaller fragments by catalyzing peptide bonds hydrolysis. Proteases are classified according to their catalytic site, a...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审


    authors: Verma S,Dixit R,Pandey KC

    更新日期:2016-04-25 00:00:00

  • Ion Fluxes through KCa2 (SK) and Cav1 (L-type) Channels Contribute to Chronoselectivity of Adenosine A1 Receptor-Mediated Actions in Spontaneously Beating Rat Atria.

    abstract::Impulse generation in supraventricular tissue is inhibited by adenosine and acetylcholine via the activation of A1 and M2 receptors coupled to inwardly rectifying GIRK/KIR3.1/3.4 channels, respectively. Unlike M2 receptors, bradycardia produced by A1 receptors activation predominates over negative inotropy. Such diffe...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Bragança B,Oliveira-Monteiro N,Ferreirinha F,Lima PA,Faria M,Fontes-Sousa AP,Correia-de-Sá P

    更新日期:2016-03-07 00:00:00

  • Phytochemical Profile, Pharmacological Attributes and Medicinal Properties of Convolvulus prostratus - A Cognitive Enhancer Herb for the Management of Neurodegenerative Etiologies.

    abstract::Convolvulus prostratus Forssk., a nootropic herb used in traditional medicinal systems, is also frequently known by its taxonomic synonym Convolvulus pluricaulis. In Indian medicinal system - Ayurveda - it is named as Shankhpushpi. According to the ancient literature, this herb has been attributed with several therape...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审


    authors: Balkrishna A,Thakur P,Varshney A

    更新日期:2020-03-03 00:00:00

  • Blocking p38 Signaling Reduces the Activation of Pro-inflammatory Cytokines and the Phosphorylation of p38 in the Habenula and Reverses Depressive-Like Behaviors Induced by Neuroinflammation.

    abstract::Increasing evidence has demonstrated that neuroinflammation contributes to the development of depressive-like behaviors, in both animal models and human patients; however, the brain areas and signaling pathways involved are still elusive. Recent studies have suggested novel roles of the habenula in the onset of depres...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Zhao YW,Pan YQ,Tang MM,Lin WJ

    更新日期:2018-05-15 00:00:00

  • International Perception of Competence, Education, and Training Needs Among Biomedical Professionals Involved in Medicines Development.

    abstract::The development of new medicines today, requires a multi-professional workforce, both in industry and the clinical research arena. Pharmaceutical physicians (PPs) and medicines development scientists (MDS) need a certain level of competence, achieved through on-the-job experience, with a postgraduate education foundat...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Imamura K,Criscuolo D,Jurczynska A,Kesselring G,Stonier P,Tsuda T,Silva H

    更新日期:2019-03-05 00:00:00

  • Computational Analysis of Therapeutic Neuroadaptation to Chronic Antidepressant in a Model of the Monoaminergic Neurotransmitter and Stress Hormone Systems.

    abstract::The clinical practice of selective serotonin reuptake inhibitor (SSRI) augmentation relies heavily on trial-and-error. Unfortunately, the drug combinations prescribed today fail to provide relief for many depressed patients. In order to identify potentially more effective treatments, we developed a computational model...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Camacho MB,Vijitbenjaronk WD,Anastasio TJ

    更新日期:2019-10-25 00:00:00

  • Sweroside Alleviated Aconitine-Induced Cardiac Toxicity in H9c2 Cardiomyoblast Cell Line.

    abstract::Aconitine is the main bioactive ingredient of Aconitum plants, which are well-known botanical herbs in China. Aconitine is also notorious for its high cardiotoxicity, as it can induce life-threatening ventricular arrhythmias. Unfortunately, there are few effective antidotes to aconitine toxicity. This study aimed to e...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Ma LQ,Yu Y,Chen H,Li M,Ihsan A,Tong HY,Huang XJ,Gao Y

    更新日期:2018-10-25 00:00:00

  • Visceral Fat Dysfunctions in the Rat Social Isolation Model of Psychosis.

    abstract::Medication with neuroleptics has been associated with adipose tissue dysfunctions and, in particular, with increased visceral fat amount. However, several studies suggested that antipsychotic treatment might not be the main responsible of fat mass accumulation, as this has been also described in not treated psychotic ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Schiavone S,Camerino GM,Mhillaj E,Zotti M,Colaianna M,De Giorgi A,Trotta A,Cantatore FP,Conte E,Bove M,Tucci P,Morgese MG,Trabace L

    更新日期:2017-11-08 00:00:00

  • Biocompatible Colloidal Suspensions Based on Magnetic Iron Oxide Nanoparticles: Synthesis, Characterization and Toxicological Profile.

    abstract::The use of magnetic iron oxide nanoparticles in biomedicine has evolved intensely in the recent years due to the multiple applications of these nanomaterials, mainly in domains like cancer. The aim of the present study was: (i) to develop biocompatible colloidal suspensions based on magnetic iron oxide nanoparticles a...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Coricovac DE,Moacă EA,Pinzaru I,Cîtu C,Soica C,Mihali CV,Păcurariu C,Tutelyan VA,Tsatsakis A,Dehelean CA

    更新日期:2017-03-28 00:00:00

  • Ophiopogonin D', a Natural Product From Radix Ophiopogonis, Induces in Vitro and in Vivo RIPK1-Dependent and Caspase-Independent Apoptotic Death in Androgen-Independent Human Prostate Cancer Cells.

    abstract::Objective: The purpose of this study was to evaluate the anticancer effects of Ophiopogonin D' (OPD', a natural product extracted from a traditional Chinese medicine (Radix Ophiopogonis) against androgen-independent prostate cancer cells and to explore the underlying molecular mechanism(s) of action. Methods: The CCK-...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Lu Z,Wang H,Zhu M,Song W,Wang J,Wu C,Kong Y,Guo J,Li N,Liu J,Li Y,Xu H

    更新日期:2018-04-30 00:00:00

  • A Significant Association Between Rhein and Diabetic Nephropathy in Animals: A Systematic Review and Meta-Analysis.

    abstract::Background: Rhein is considered to have beneficial influence on diabetic nephropathy. Animal experiments suggested that the mechanisms of rhein against diabetic nephropathy may involve many processes, but the credibility of the evidence is unclear. Therefore, we conducted systematic review and meta-analysis of pre-cli...

    journal_title:Frontiers in pharmacology



    authors: Hu HC,Zheng LT,Yin HY,Tao Y,Luo XQ,Wei KS,Yin LP

    更新日期:2019-12-13 00:00:00

  • Amifostine Analog, DRDE-30, Attenuates Bleomycin-Induced Pulmonary Fibrosis in Mice.

    abstract::Bleomycin (BLM) is an effective curative option in the management of several malignancies including pleural effusions; but pulmonary toxicity, comprising of pneumonitis and fibrosis, poses challenge in its use as a front-line chemotherapeutic. Although Amifostine has been found to protect lungs from the toxic effects ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Arora A,Bhuria V,Hazari PP,Pathak U,Mathur S,Roy BG,Sandhir R,Soni R,Dwarakanath BS,Bhatt AN

    更新日期:2018-04-24 00:00:00

  • Calcium Handling Defects and Cardiac Arrhythmia Syndromes.

    abstract::Calcium ions (Ca2+) play a major role in the cardiac excitation-contraction coupling. Intracellular Ca2+ concentration increases during systole and falls in diastole thereby determining cardiac contraction and relaxation. Normal cardiac function also requires perfect organization of the ion currents at the cellular le...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审


    authors: Kistamás K,Veress R,Horváth B,Bányász T,Nánási PP,Eisner DA

    更新日期:2020-02-25 00:00:00

  • Aromatic Bromination Abolishes the Psychomotor Features and Pro-social Responses of MDMA ("Ecstasy") in Rats and Preserves Affinity for the Serotonin Transporter (SERT).

    abstract::The entactogen MDMA (3,4-methylenedioxy-methamphetamine, "Ecstasy") exerts its psychotropic effects acting primarily as a substrate of the serotonin transporter (SERT) to induce a non-exocytotic release of serotonin. Nevertheless, the roles of specific positions of the aromatic ring of MDMA associated with the modulat...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Sáez-Briones P,Castro-Castillo V,Díaz-Véliz G,Valladares L,Barra R,Hernández A,Cassels BK

    更新日期:2019-02-28 00:00:00

  • Cannabinoids and Pain: New Insights From Old Molecules.

    abstract::Cannabis has been used for medicinal purposes for thousands of years. The prohibition of cannabis in the middle of the 20th century has arrested cannabis research. In recent years there is a growing debate about the use of cannabis for medical purposes. The term 'medical cannabis' refers to physician-recommended use o...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审


    authors: Vučković S,Srebro D,Vujović KS,Vučetić Č,Prostran M

    更新日期:2018-11-13 00:00:00

  • Gyejibongnyeong-Hwan (Gui Zhi Fu Ling Wan) Ameliorates Human Uterine Myomas via Apoptosis.

    abstract::Uterine leiomyomas are the most common benign neoplasms in women of reproductive age. However, non-surgical treatments for uterine myomas have not been fully evaluated. In Korea and China, Gyejibongnyeong-hwan (GBH) is widely used to treat gynecological diseases. Thus, we investigated the effects of GBH in human uteri...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Lee SM,Choi ES,Ha E,Ji KY,Shin SJ,Jung J

    更新日期:2019-09-25 00:00:00

  • Triptriolide Alleviates Lipopolysaccharide-Induced Liver Injury by Nrf2 and NF-κB Signaling Pathways.

    abstract::Nrf2 (Nuclear Factor Erythroid 2 Related Factor 2) transcription factor not only regulates oxidative stress response, but also represses inflammation by regulating cytokines production and cross-talking with NF-κB signaling pathways. Nrf2 plays an essential role in liver injury induced by oxidative stress and inflamma...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Yang YQ,Yan XT,Wang K,Tian RM,Lu ZY,Wu LL,Xu HT,Wu YS,Liu XS,Mao W,Xu P,Liu B

    更新日期:2018-08-29 00:00:00

  • Key Clinical Interest Outcomes of Pharmaceutical Administration for Veterans With Post-Traumatic Stress Disorder Based on Pooled Evidences of 36 Randomised Controlled Trials With 2,331 Adults.

    abstract::Background: The effects of drug treatment on veterans, who have a high risk of post-traumatic stress disorder (PTSD), are not clear, and the guidelines are different from the recommendations of the recent meta-analysis. Our goal was to find the efficacy and frequencies of complications of drugs that can treat PTSD in ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章,评审


    authors: Zhao YF,Huang ZD,Gu HY,Guo GL,Yuan RX,Zhang C

    更新日期:2020-12-17 00:00:00

  • Salvinorin A Inhibits Airway Hyperreactivity Induced by Ovalbumin Sensitization.

    abstract::Salvinorin A, a neoclerodane diterpene isolated from Salvia divinorum, exerts a number of pharmacological actions which are not solely limited to the central nervous system. Recently it has been demonstrated that Salvinorin A inhibits acute inflammatory response affecting leukotriene (LT) production. Since LTs are pot...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Rossi A,Caiazzo E,Bilancia R,Riemma MA,Pagano E,Cicala C,Ialenti A,Zjawiony JK,Izzo AA,Capasso R,Roviezzo F

    更新日期:2017-01-13 00:00:00

  • Mitochondrial Fission Is Required for Angiotensin II-Induced Cardiomyocyte Apoptosis Mediated by a Sirt1-p53 Signaling Pathway.

    abstract::Hypertension-induced cardiac apoptosis is a major contributor to early-stage heart-failure. Our previous studies have found that p53-mediated mitochondrial fission is involved in aldosterone-induced podocyte apoptosis. However, it is not clear that whether p53-induced mitochondrial fission is critical for hypertensive...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Qi J,Wang F,Yang P,Wang X,Xu R,Chen J,Yuan Y,Lu Z,Duan J

    更新日期:2018-03-09 00:00:00

  • Anxiolytic and Antiepileptic Properties of the Aqueous Extract of Cissus quadrangularis (Vitaceae) in Mice Pilocarpine Model of Epilepsy.

    abstract::Cissus quadrangularis (C. quadrangularis) is a plant of the Vitaceae family known for its anticonvulsant effects in traditional medicine. The objective of this study was to elucidate the anxiolytic and antiepileptic effects of aqueous extract of C. quadrangularis. The mice were divided into different groups and treate...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Moto FCO,Arsa'a A,Ngoupaye GT,Taiwe GS,Njapdounke JSK,Kandeda AK,Nkantchoua GCN,Omam Omam JP,Pale S,Kouemou NE,Ayissi Mbomo ER,Pahaye DB,Ojong L,Mairara V,Ngo Bum E

    更新日期:2018-07-17 00:00:00

  • PAI-1 Exacerbates White Adipose Tissue Dysfunction and Metabolic Dysregulation in High Fat Diet-Induced Obesity.

    abstract::Background: Plasminogen activator inhibitor (PAI)-1 levels and activity are known to increase during metabolic syndrome and obesity. In addition, previous studies have implicated PAI-1 in adipose tissue (AT) expansion while also contributing to insulin resistance. As inflammation is also known to occur in AT during ob...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Wang L,Chen L,Liu Z,Liu Y,Luo M,Chen N,Deng X,Luo Y,He J,Zhang L,Hill MA,Li R,Wu J

    更新日期:2018-09-26 00:00:00

  • Acute Effects of 2C-E in Humans: An Observational Study.

    abstract::2,5-Dimethoxy-4-ethylphenethylamine (2C-E) is psychedelic phenylethylamine, with a chemical structure similar to mescaline, used as new psychoactive substance (NPS). It inhibits norepinephrine and serotonin uptake and, more relevant, acts as a partial agonist of the serotonin 2A (5-HT2A), 2B (5-HT2B), and (5-HT2C) rec...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Papaseit E,Olesti E,Pérez-Mañá C,Torrens M,Grifell M,Ventura M,Pozo OJ,de Sousa Fernandes Perna EB,Ramaekers JG,de la Torre R,Farré M

    更新日期:2020-03-18 00:00:00

  • Pharmacological Characterization of Orofacial Nociception in Female Rats Following Nitroglycerin Administration.

    abstract::Rodent models of human disease can be valuable for understanding the mechanisms of a disease and for identifying novel therapies. However, it is critical that these models be vetted prior to committing resources to developing novel therapeutics. Failure to confirm the model can lead to significant losses in time and r...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Caudle RM,Caudle SL,Flenor ND,Rohrs EL,Neubert JK

    更新日期:2020-12-03 00:00:00

  • Serum Concentrations of Cholinesterase Inhibitors in Patients With Alzheimer's Dementia Are Frequently Below the Recommended Levels.

    abstract:Background:Acetylcholinesterase inhibitors (AChE-I) are recommended for the treatment of cognitive symptoms but also of behavioral and psychological symptoms in dementia. They are widely used not only in Alzheimer's disease, but also in other forms of dementia. Efficacy of treatment might depend on serum concentration ...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Ortner M,Stange M,Schneider H,Schroeder C,Buerger K,Müller C,Dorn B,Goldhardt O,Diehl-Schmid J,Förstl H,Steimer W,Grimmer T

    更新日期:2020-05-21 00:00:00

  • Differential Patterns of Adherence to Opioid Therapy in Opioid Naïve and Opioid Existing Patients With Different Age Groups.

    abstract::Limited data are available on the adherence to opioid therapy and the influence of different patient groups on adherence. This study examined the patterns of adherence in opioid naïve and opioid existing patients with varying age and gender. This retrospective cohort study was conducted using the prescription database...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Zin CS,Taufek NH,Ahmad MM

    更新日期:2019-10-29 00:00:00

  • ORY-1001 Suppresses Cell Growth and Induces Apoptosis in Lung Cancer Through Triggering HK2 Mediated Warburg Effect.

    abstract::ORY-1001, an inhibitor of covalent lysine (K)-specific demethylase 1A (KDM1A), has been used as a therapy for the treatment of acute leukemia. However, the underlying mechanisms of anticancer are still not fully elucidated. Here, we report that KDM1A is highly expressed in lung cancers, where it appears to drive aggre...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Lu Z,Guo Y,Zhang X,Li J,Li L,Zhang S,Shan C

    更新日期:2018-12-04 00:00:00

  • Striatal Tyrosine Hydroxylase Is Stimulated via TAAR1 by 3-Iodothyronamine, But Not by Tyramine or β-Phenylethylamine.

    abstract::The trace amine-associated receptor 1 (TAAR1) is expressed by dopaminergic neurons, but the precise influence of trace amines upon their functional activity remains to be fully characterized. Here, we examined the regulation of tyrosine hydroxylase (TH) by tyramine and beta-phenylethylamine (β-PEA) compared to 3-iodot...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Zhang X,Mantas I,Alvarsson A,Yoshitake T,Shariatgorji M,Pereira M,Nilsson A,Kehr J,Andrén PE,Millan MJ,Chergui K,Svenningsson P

    更新日期:2018-03-01 00:00:00

  • Supramammillary serotonin reduction alters place learning and concomitant hippocampal, septal, and supramammillar theta activity in a Morris water maze.

    abstract::Hippocampal theta activity is related to spatial information processing, and high-frequency theta activity, in particular, has been linked to efficient spatial memory performance. Theta activity is regulated by the synchronizing ascending system (SAS), which includes mesencephalic and diencephalic relays. The supramam...

    journal_title:Frontiers in pharmacology

    pub_type: 杂志文章


    authors: Hernández-Pérez JJ,Gutiérrez-Guzmán BE,López-Vázquez MÁ,Olvera-Cortés ME

    更新日期:2015-10-29 00:00:00