pypi: propy | Projects | Ecosyste.ms: Papers

10.1186/s13321-018-0270-2

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions
Cited by: 86
Author(s): Jie Dong, Zhi‐Jiang Yao, Lin Zhang, Feijun Luo, Qinlu Lin, Aiping Lu, Alex F. Chen, Dong‐Sheng Cao
Software Mentions: 8
Published: over 6 years ago

10.1186/s13321-016-0146-2

BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions
Cited by: 36
Author(s): Jie Dong, Zhi‐Jiang Yao, Ming Wen, Min Zhu, Ningning Wang, Hongyu Miao, Aiping Lu, Wenbin Zeng, Dong‐Sheng Cao
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0097446

Supervised Learning Classification Models for Prediction of Plant Virus Encoded RNA Silencing Suppressors
Cited by: 13
Author(s): Zeenia Jagga, Dinesh Gupta
Software Mentions: 5
Published: over 10 years ago

10.1515/jib-2019-0091

Use of Chou’s 5-steps rule to predict the subcellular localization of gram-negative and gram-positive bacterial proteins by multi-label learning based on gene ontology annotation and profile alignment
Cited by: 7
Author(s): Hafida Bouziane, Abdallah Chouarfia
Software Mentions: 5
Published: over 4 years ago

10.1038/s41598-017-14945-1

iDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features
Cited by: 66
Author(s): Shahana Yasmin Chowdhury, Swakkhar Shatabda, Abdollah Dehzangi
Software Mentions: 5
Published: about 7 years ago

10.1111/jcmm.15205

Characterization of the relationship between FLI1 and immune infiltrate level in tumour immune microenvironment for breast cancer
Cited by: 14
Author(s): Shiyuan Wang, Yakun Wang, Changhong Yu, Yiyin Cao, Yao Yu, Yi Pan, Dongqing Su, Qianzi Lu, Weihao Yang, Yongchun Zuo, Lei Yang
Software Mentions: 5
Published: over 4 years ago

10.1186/s12859-017-1751-4

Quantiprot - a Python package for quantitative analysis of protein sequences
Cited by: 8
Author(s): Bogumił M. Konopka, Marta Anna Marciniak, Witold Dyrka
Software Mentions: 4
Published: over 7 years ago

10.7717/peerj.11581

iSUMOK-PseAAC: prediction of lysine sumoylation sites using statistical moments and Chou’s PseAAC
Cited by: 20
Author(s): Yaser Daanial Khan, Nabeel Sabir Khan, Sheraz Naseer, Ahmad Hassan Butt
Software Mentions: 4
Published: over 3 years ago

10.1093/database/baz131

RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou’s five-step rule
Cited by: 49
Author(s): Lei Zheng, Shenghui Huang, Nengjiang Mu, Haoyue Zhang, Jiayu Zhang, Yu Chang, Lei Yang, Yongchun Zuo
Software Mentions: 3
Published: almost 6 years ago

10.15252/msb.20188290

Unraveling the hidden universe of small proteins in bacterial genomes
Cited by: 87
Author(s): Samuel Miravet-Verde, Tony Ferrar, Guadalupe Espadas-García, Rocco Mazzolini, Anas Gharrab, Eduard Sabidò, Luís Serrano, María Lluch‐Senar
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-020-07347-7

Identify RNA-associated subcellular localizations based on multi-label learning using Chou’s 5-steps rule
Cited by: 15
Author(s): Hao Wang, Yongsheng Ding, Jijun Tang, Quan Zou, Fei Guo
Software Mentions: 2
Published: almost 4 years ago

10.1371/journal.pone.0253760

Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach
Cited by: 14
Author(s): Gwangho Lee, Gun Hyuk Jang, Ho Young Kang, Giltae Song
Software Mentions: 2
Published: over 3 years ago

10.1186/s13040-019-0196-x

Encodings and models for antimicrobial peptide classification for multi-resistant pathogens
Cited by: 64
Author(s): Sebastian Spänig, Dominik Heider
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0106691

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition
Cited by: 231
Author(s): Bin Liu, Jinghao Xu, Xun Lan, Ruifeng Xu, Jiyun Zhou, Xiaolong Wang, Kuo‐Chen Chou
Software Mentions: 2
Published: about 10 years ago

10.18632/oncotarget.10027

iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC
Cited by: 144
Author(s): Wang-Ren Qiu, Bo Sun, Xuan Xiao, Zhaochun Xu, Kuo‐Chen Chou
Software Mentions: 2
Published: over 8 years ago

10.1038/s41598-018-19752-w

AmPEP: Sequence-based prediction of antimicrobial peptides using distribution patterns of amino acid properties and random forest
Cited by: 154
Author(s): Pratiti Bhadra, Jielu Yan, Jinyan Li, Simon Fong, Shirley W. I. Siu
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13040-020-00231-w

ISLAND: in-silico proteins binding affinity prediction using sequence information
Cited by: 27
Author(s): Wajid Arshad Abbasi, Adiba Yaseen, Fahad Hassan, Saiqa Andleeb, Fayyaz Minhas
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12859-018-2249-4

Detecting Succinylation sites from protein sequences using ensemble support vector machine
Cited by: 36
Author(s): Ning Qiao, Xiaosa Zhao, Lingling Bao, Zhiqiang Ma, Xiaowei Zhao
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-49430-4

csDMA: an improved bioinformatics tool for identifying DNA 6 mA modifications via Chou’s 5-step rule
Cited by: 24
Author(s): Ze Liu, Wei Dong, Wei Jiang, Zhi Min He
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-016-1337-6

Prediction of HIV-1 protease cleavage site using a combination of sequence, structural, and physicochemical features
Cited by: 23
Author(s): Onkar Singh, Emily Chia-Yu Su
Software Mentions: 1
Published: almost 8 years ago

10.3390/ijms15021746

iRSpot-TNCPseAAC: Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Acid Components
Cited by: 219
Author(s): Wang Qiu, Xuan Xiao, Kuo Chen Chou
Software Mentions: 1
Published: almost 11 years ago

10.3390/ijms15033495

PseAAC-General: Fast Building Various Modes of General Form of Chou’s Pseudo-Amino Acid Composition for Large-Scale Protein Datasets
Cited by: 252
Author(s): Pu-Feng Du, Shuwang Gu, Ya-Sen Jiao
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms15034915

iNR-Drug: Predicting the Interaction of Drugs with Nuclear Receptors in Cellular Networking
Cited by: 70
Author(s): Yue-Nong Fan, Xuan Xiao, Jianliang Min, Kuo‐Chen Chou
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms150610410

Prediction of Protein S-Nitrosylation Sites Based on Adapted Normal Distribution Bi-Profile Bayes and Chou’s Pseudo Amino Acid Composition
Cited by: 85
Author(s): Cangzhi Jia, Xin Lin, Zhiping Wang
Software Mentions: 1
Published: over 10 years ago

10.3390/ijms22094435

Deep Learning in Virtual Screening: Recent Applications and Developments
Cited by: 71
Author(s): Talia B. Kimber, Yonghui Chen, Andrea Volkamer
Software Mentions: 1
Published: over 3 years ago

10.18632/oncotarget.9148

iCar-PseCp: identify carbonylation sites in proteins by Monte Carlo sampling and incorporating sequence coupled effects into general PseAAC
Cited by: 161
Author(s): Jianhua Jia, Zi Li, Xuan Xiao, Bingxiang Liu, Kuo‐Chen Chou
Software Mentions: 1
Published: over 8 years ago

10.1155/2014/286419

iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels
Cited by: 166
Author(s): Hui Ding, En-Ze Deng, Lufeng Yuan, Li Liu, Hao Lin, Wei Chen, Kuo‐Chen Chou
Software Mentions: 1
Published: almost 11 years ago

10.1155/2014/623149

iSS-PseDNC: Identifying Splicing Sites Using Pseudo Dinucleotide Composition
Cited by: 111
Author(s): Wei Chen, Pengmian Feng, Hao Lin, Kuo‐Chen Chou
Software Mentions: 1
Published: almost 11 years ago

10.3390/molecules21010095

iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets
Cited by: 140
Author(s): Jianhua Jia, Zi Liu, Xuan Xiao, Bingxiang Liu, Kuo‐Chen Chou
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.9987

iPhos-PseEn: Identifying phosphorylation sites in proteins by fusing different pseudo components into an ensemble classifier
Cited by: 131
Author(s): Wang-Ren Qiu, Xuan Xiao, Zhaochun Xu, Kuo‐Chen Chou
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0105018

iNitro-Tyr: Prediction of Nitrotyrosine Sites in Proteins with General Pseudo Amino Acid Composition
Cited by: 173
Author(s): Yan Xu, Xin Wen, Lu Wen, Lingyun Wu, Ning Deng, Kuo‐Chen Chou
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0191900

Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams
Cited by: 49
Author(s): Abdollah Dehzangi, Yosvany López, Sunder Lal, Ghazaleh Taherzadeh, Abdul Sattar, Tatsuhiko Tsunoda, Alok Sharma
Software Mentions: 1
Published: almost 7 years ago

Ecosyste.ms: Papers

Projects: pypi: propy

Papers Mentioning propy 35