End-to-End Learning Based Compound Activity Prediction Using Binding Pocket Information

2019 ◽  
pp. 226-234
Author(s):  
Toshitaka Tanebe ◽  
Takashi Ishida
Keyword(s):  
Binding Pocket ◽  
Activity Prediction ◽  
End To End

scholarly journals End-to-end learning for compound activity prediction based on binding pocket information

2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Toshitaka Tanebe ◽  
Takashi Ishida
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Docking Simulation ◽  
Binding Pocket ◽  
Target Protein ◽  
Sequence Information ◽  
Activity Prediction ◽  
End To End ◽  
Novel Target ◽  
Amino Acid Sequence Information

Abstract Background Recently, machine learning-based ligand activity prediction methods have been greatly improved. However, if known active compounds of a target protein are unavailable, the machine learning-based method cannot be applied. In such cases, docking simulation is generally applied because it only requires a tertiary structure of the target protein. However, the conformation search and the evaluation of binding energy of docking simulation are computationally heavy and thus docking simulation needs huge computational resources. Thus, if we can apply a machine learning-based activity prediction method for a novel target protein, such methods would be highly useful. Recently, Tsubaki et al. proposed an end-to-end learning method to predict the activity of compounds for novel target proteins. However, the prediction accuracy of the method was still insufficient because it only used amino acid sequence information of a protein as the input. Results In this research, we proposed an end-to-end learning-based compound activity prediction using structure information of a binding pocket of a target protein. The proposed method learns the important features by end-to-end learning using a graph neural network both for a compound structure and a protein binding pocket structure. As a result of the evaluation experiments, the proposed method has shown higher accuracy than an existing method using amino acid sequence information. Conclusions The proposed method achieved equivalent accuracy to docking simulation using AutoDock Vina with much shorter computing time. This indicated that a machine learning-based approach would be promising even for novel target proteins in activity prediction.

Surgical management of extracranial carotid artery aneurysms

VASA ◽  
2016 ◽  
Vol 45 (3) ◽  
pp. 223-228 ◽  
Author(s):  
Jan Paweł Skóra ◽  
Jacek Kurcz ◽  
Krzysztof Korta ◽  
Przemysław Szyber ◽  
Tadeusz Andrzej Dorobisz ◽  
...  
Keyword(s):  
Carotid Artery ◽  
Surgical Management ◽  
Minor Stroke ◽  
Stroke Rate ◽  
Extracranial Carotid Artery ◽  
Long Term Follow Up ◽  
End To End ◽  
Dacron Patch ◽  
Major Stroke

Abstract. Background: We present the methods and results of the surgical management of extracranial carotid artery aneurysms (ECCA). Postoperative complications including early and late neurological events were analysed. Correlation between reconstruction techniques and morphology of ECCA was assessed in this retrospective study. Patients and methods: In total, 32 reconstructions of ECCA were performed in 31 symptomatic patients with a mean age of 59.2 (range 33 - 84) years. The causes of ECCA were divided among atherosclerosis (n = 25; 78.1 %), previous carotid endarterectomy with Dacron patch (n = 4; 12.5 %), iatrogenic injury (n = 2; 6.3 %) and infection (n = 1; 3.1 %). In 23 cases, intervention consisted of carotid bypass. Aneurysmectomy with end-to-end suture was performed in 4 cases. Aneurysmal resection with patching was done in 2 cases and aneurysmorrhaphy without patching in another 2 cases. In 1 case, ligature of the internal carotid artery (ICA) was required. Results: Technical success defined as the preservation of ICA patency was achieved in 31 cases (96.9 %). There was one perioperative death due to major stroke (3.1 %). Two cases of minor stroke occurred in the 30-day observation period (6.3 %). Three patients had a transient hypoglossal nerve palsy that subsided spontaneously (9.4 %). At a mean long-term follow-up of 68 months, there were no major or minor ipsilateral strokes or surgery-related deaths reported. In all 30 surviving patients (96.9 %), long-term clinical outcomes were free from ipsilateral neurological symptoms. Conclusions: Open surgery is a relatively safe method in the therapy of ECCA. Surgical repair of ECCAs can be associated with an acceptable major stroke rate and moderate minor stroke rate. Complication-free long-term outcomes can be achieved in as many as 96.9 % of patients. Aneurysmectomy with end-to-end anastomosis or bypass surgery can be implemented during open repair of ECCA.

Characterization of Recombinant Human Coagulation Factor XFriuli

1996 ◽  
Vol 75 (02) ◽  
pp. 313-317 ◽  
Author(s):  
D J Kim ◽  
A Girolami ◽  
H L James
Keyword(s):  
Catalytic Domain ◽  
Coagulation Factor ◽  
Molecular Size ◽  
Binding Pocket ◽  
Site Directed Mutagenesis ◽  
Bleeding Tendency ◽  
Factor X ◽  
Amino Terminal ◽  
Normal Plasma ◽  
Plasma Factor

SummaryNaturally occurring plasma factor XFriuli (pFXFr) is marginally activated by both the extrinsic and intrinsic coagulation pathways and has impaired catalytic potential. These studies were initiated to obtain confirmation that this molecule is multi-functionally defective due to the substitution of Ser for Pro at position 343 in the catalytic domain. By the Nelson-Long site-directed mutagenesis procedure a construct of cDNA in pRc/CMV was derived for recombinant factor XFriuli (rFXFr) produced in human embryonic (293) kidney cells. The rFXFr was purified and shown to have a molecular size identical to that of normal plasma factor X (pFX) by gel electrophoretic, and amino-terminal sequencing revealed normal processing cleavages. Using recombinant normal plasma factor X (rFXN) as a reference, the post-translational y-carboxy-glutamic acid (Gla) and (β-hydroxy aspartic acid (β-OH-Asp) content of rFXFr was over 85% and close to 100%, respectively, of expected levels. The specific activities of rFXFr in activation and catalytic assays were the same as those of pFXFr. Molecular modeling suggested the involvement of a new H-bond between the side-chains of Ser-343 and Thr-318 as they occur in anti-parallel (3-pleated sheets near the substrate-binding pocket of pFXFr. These results support the conclusion that the observed mutation in pFXFr is responsible for its dysfunctional activation and catalytic potentials, and that it accounts for the moderate bleeding tendency in the homozygous individuals who possess this variant procoagulant.

Reliability of the Mangled Extremity Severity Score in the Management of Peripheral Vascular Injuries in Children: A Retrospective Review

2020 ◽  
Author(s):  
Ahmed Mousa ◽  
Ossama M. Zakaria ◽  
Mai A. Elkalla ◽  
Lotfy A. Abdelsattar ◽  
Hamad Al-Game'a
Keyword(s):  
Severity Score ◽  
Vein Graft ◽  
Bypass Surgery ◽  
Age Groups ◽  
Vascular Injuries ◽  
Peripheral Vascular ◽  
Group Iii ◽  
Mangled Extremity ◽  
Group I ◽  
End To End

AbstractThis study was aimed to evaluate different management modalities for peripheral vascular trauma in children, with the aid of the Mangled Extremity Severity Score (MESS). A single-center retrospective analysis took place between 2010 and 2017 at University Hospitals, having emergencies and critical care centers. Different types of vascular repair were adopted by skillful vascular experts and highly trained pediatric surgeons. Patients were divided into three different age groups. Group I included those children between 5 and 10 years; group II involved pediatrics between 11 and 15 years; while children between 16 and 21 years participated in group III. We recruited 183 children with peripheral vascular injuries. They were 87% males and 13% females, with the mean age of 14.72 ± 04. Arteriorrhaphy was performed in 32%; end-to-end anastomosis and natural vein graft were adopted in 40.5 and 49%, respectively. On the other hand, 10.5% underwent bypass surgery. The age groups I and II are highly susceptible to penetrating trauma (p = 0.001), while patients with an extreme age (i.e., group III) are more susceptible to blunt injury (p = 0.001). The MESS has a significant correlation to both age groups I and II (p = 0.001). Vein patch angioplasty and end-to-end primary repair should be adopted as the main treatment options for the repair of extremity vascular injuries in children. Moreover, other treatment modalities, such as repair with autologous vein graft/bypass surgery, may be adopted whenever possible. They are cost-effective, reliable, and simple techniques with fewer postoperative complication, especially in poor/limited resources.

WS-Security on PRODML

2014 ◽  
Vol 1 (1) ◽  
pp. 9-34
Author(s):  
Bobby Suryajaya
Keyword(s):  
Web Services ◽  
Digital Signature ◽  
Data Transfer ◽  
Web Services Security ◽  
Soap Message ◽  
Simulation Results ◽  
End To End

SKK Migas plans to apply end-to-end security based on Web Services Security (WS-Security) for Sistem Operasi Terpadu (SOT). However, there are no prototype or simulation results that can support the plan that has already been communicated to many parties. This paper proposes an experiment that performs PRODML data transfer using WS-Security by altering the WSDL to include encryption and digital signature. The experiment utilizes SoapUI, and successfully loaded PRODML WSDL that had been altered with WSP-Policy based on X.509 to transfer a SOAP message.

Mit MindSphere die digitale Transformation vorantreiben

Controlling ◽  
2019 ◽  
Vol 31 (6) ◽  
pp. 63-65
Author(s):  
Carsten Speckmann ◽  
Péter Horváth
Keyword(s):  
Digitale Transformation ◽  
Internet Der Dinge ◽  
End To End

MindSphere ist das cloudbasierte, offene IoT-Betriebssystem von Siemens. Es verbindet Produkte, Anlagen, Systeme und Maschinen und ermöglicht es so, die Fülle von Daten aus dem Internet der Dinge (IoT) mit umfangreichen Analysen zu nutzen. Als eine sichere, skalierbare End-to-End-Lösung für die Industrie sorgt MindSphere für die Konnektivität von Anlagen und liefert somit handlungsrelevante Geschäftserkenntnisse, die zur Steigerung der Produktivität und Effizienz im gesamten Unternehmen nutzbar gemacht werden können. MindSphere ist weltweit verfügbar.

End-to-End Redundancy and Maintenance Condition Design for Nationwide Optical Transport Network

2018 ◽  
Vol E101.B (11) ◽  
pp. 2267-2276 ◽  
Author(s):  
Yoshihiko UEMATSU ◽  
Shohei KAMAMURA ◽  
Hiroshi YAMAMOTO ◽  
Aki FUKUDA ◽  
Rie HAYASHI
Keyword(s):  
Transport Network ◽  
Optical Transport Network ◽  
End To End ◽  
Optical Transport

RANCANG BANGUN KEAMANAN TRANSFER DATA VOIP OVER VPN PADA SISTEM OPENSOURCE TRIXBOX

2014 ◽  
Vol 11 (1) ◽  
Author(s):  
I Wayan Eka Putra Darmawan
Keyword(s):  
Internet Protocol ◽  
Virtual Private Network ◽  
Transfer Data ◽  
Virtual Channels ◽  
End To End ◽  
Private Network

VoIP (Voice over Internet) dikenal juga dengan sebutan IP (Internet Protocol) Telephony saat ini semakin banyak digunakan karena memiliki beberapa keunggulan, salah satu diantaranya yaitu tarif yang jauh lebih murah daripada tarif telepon tradisional sehinggapengguna telepon dapat memilih layanan tersebut sesuai dengan kebutuhannya. VoIP dapat mereduksi biaya percakapan sampai 70%. Selain memiliki beberapa keunggulan di atas,VoIP juga memiliki kelemahan yang sangat vital yaitu dari segi keamanan transfer suarakarena berbasis IP, sehingga siapapun bisa melakukan penyadapan dan perekaman terhadap data VoIP. Ganguan yang terjadi pada sistem VoIP ada berbagai macam diantaranya, transferdata yang lewat pada suatu jaringan seperti misalnya dapat disalahgunakan (abuse), dapatdibajak isi data tersebut (sniffing), dan tidak dapat mengakses server dikarenakan server yang kelebihan muatan (Denial of Services).Ada beberapa cara untuk mengamankan komunikasi data VoIP, antara lain, dengan mengamankan jalur yang digunakan pengguna untuk melakukan komunikasi VoIP denganmenggunakan metode VPN (Virtual Private Network) dan juga dapat dilakukan suatu metode kriptografi pada aplikasi VoIP tersebut sehingga data yang dikirimkan dapat dilindungidengan baik. VPN adalah teknik pengaman jaringan yang bekerja dengan cara membuat suatu tunnel sehingga jaringan yang dipercaya dapat menghubungkan jaringan yang ada diluar melalui internet. Titik akhir dari VPN adalah tersambungnya Virtual Channels (VCs)dengan cara pemisahan. Kenyataannya koneksi sebuah end-to-end VPN tergantung dari sebuah nilai dari hubungan daripada titik-titiknya. VPN mempunyai dua metode dalampengamanan yakni IPSec dan Crypto IP Encapsulation (CIPE). Selain itu dapat dipergunakan teknik Kriptografi (cryptography) yang merupakan ilmu dan seni penyimpanan pesan, data,atau informasi secara aman.Sistem VoIP menggunakan VPN ini diharapkan dapat memberikan keamanan transfer data pada jaringan internet maupun intranet.

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