杨建益｜山东大学｜学者主页

2026

COACH-D 2.0: A Server for Template-based Modeling of Protein−ligand Interactions

Xiaoyu An, Hong Wei, Wenkai Wang, Qiuyi Lyu, Jianyi Yang, Zhenling Peng

Genomics Proteomics & Bioinformatics

DOI

2026

Generating Dynamic Structures Through Physics‐Based Sampling of Predicted Inter‐Residue Geometries

Chenxiao Xiang, Wenkai Wang, Zhenling Peng, Jianyi Yang

Advanced Science

DOI

2026

Protein language models for structural biology

Chenxiao Xiang, Bin Cheng, Zhenling Peng, Jianyi Yang

Nature Computational Science

DOI

2026

Integrated experimental and AI innovations for RNA structure determination

Wenkai Wang, Baoquan Su, Zhenling Peng, Jianyi Yang

Nature Biotechnology

DOI

2026

Predicting RNA 3D structure and conformers using a pre-trained secondary structure model and structure-aware attention

Wenkai Wang, Zhenling Peng, Jianyi Yang

Nature Machine Intelligence

DOI

2026

The trRosettaRNA server for RNA structure prediction

Wenkai Wang, Xiaocheng Liu, Zhenling Peng, Jianyi Yang

Nature Protocols

DOI

2026

Opportunities and challenges in protein structure prediction

Wenkai Wang, Baoquan Su, Chenxiao Xiang, Jianyi Yang

Quantitative Biology

DOI

2026

Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps

Xiaocheng Liu, Wenkai Wang, Zongyang Du, Ziyi Wang, Zhenling Peng, Jianyi Yang

Communications Biology

DOI

2025

Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning

Qiuyi Lyu, Hong Wei, Shuaishuai Chen, Zhenling Peng, Jianyi Yang

Journal of Chemical Information and Modeling

DOI

2025

Democratizing protein language model training, sharing and collaboration

Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Qingyan Yuan, Yuan Gao, Tong Si, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Xing Chang, Shiyu Jiang, Dacheng Ma, The OPMC, Anthony Gitter, Milot Mirdita, Kevin Yang, Pascal Notin, Debora S. Marks, Pranam Chatterjee, Rohit Singh, Philip A. Romero, Michael Heinzinger, Jianming Liu, Jia Zheng, Stan Ziqing Li, An‐Ping Zeng, Huaizong Shen, Jijie Chai, Feng Ju, Noelia Ferruz, Anum Azam Glasgow, Philip M. Kim, Christopher Davis Snow, Vasilis Ntranos, Jianyi Yang, Liang Hong, Caixia Gao, Tong Si, Michael M. Bronstein, Xing Chang, Fajie Yuan, Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Shiyu Jiang, Yuan Gao, Jiawei Zhang, Yuliang Fan, Yuyang Tao, Linqi Cheng, Xinzhe Zheng, Lei Chen, Rui Long, Lingjie Kong, Zhongji Pu, Jiaming Guan, Tianyuan Zhang, Cheng Li, Martin Steinegger, Sergey Ovchinnikov, Fajie Yuan

Nature Biotechnology

DOI

2025

RNA language model and graph attention network for RNA and small molecule binding sites prediction

Saisai Sun, Jianyi Yang, Lin Gao, Pengyong Li, Yumeng Liu

Bioinformatics

DOI

2025

Accurate Biomolecular Structure Prediction in CASP16 With Optimized Inputs to State‐Of‐The‐Art Predictors

Wenkai Wang, Yuxian Luo, Zhenling Peng, Jianyi Yang

Proteins Structure Function and Bioinformatics

DOI

2025

Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods

Yuxian Luo, Haiyan Wu, Hong Wei, Zhenling Peng, Jianyi Yang

Proteins Structure Function and Bioinformatics

DOI

2025

AlphaFold in protein structure and function prediction

Lukasz Kurgan, Jianyi Yang

Computational and Structural Biotechnology Journal

DOI

2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa R. H. de Aquino, Nagendar Goud Badepally, Robert Batey, Eugene F. Baulin, Paweł Boiński, Michal J. Boniecki, Janusz Marek Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi‐Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne Dawson, Frank DiMaio, Feng Ding, Anne‐Catherine Dock‐Brégeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D’Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, Benoı̂t Masquida, Seyed Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory I. Nikolaev, Chandran Nithin, Grace Nye, Iswarya P. N. Pandaranadar Jeyeram, Alberto Pérez, Phillip Pham, Joseph A. Piccirilli, Smita P. Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Łukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzyńska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna Chaitanya Suddala, Marta Szachniuk, Raphael J.L. Townshend, Robert J. Trachman, Jian Wang, Wenkai Wang, Andrew M. Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Żok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Éric Westhof, Zhichao Miao

Nature Methods

DOI

2024

Author Correction: PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu

Nature Communications

DOI

2024

AI accurately predicting the structure of biomolecular interactions

Zhenling Peng, Peilong Lu, Jianyi Yang

Cell Research

DOI

2024

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu

Nature Communications

DOI

2024

RNA threading with secondary structure and sequence profile

Zongyang Du, Zhenling Peng, Jianyi Yang

Bioinformatics

DOI

2024

Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions

Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang

Genomics Proteomics & Bioinformatics

DOI

2023

trRosettaRNA: automated prediction of RNA 3D structure with transformer network

Wenkai Wang, Chenjie Feng, Renmin Han, Ziyi Wang, Lisha Ye, Zongyang Du, Hong Wei, Fa Zhang, Zhenling Peng, Jianyi Yang

Nature Communications

DOI

2023

Challenges and opportunities in macromolecular structure determination

Xiao‐chen Bai, Tamir Gonen, Angela M. Gronenborn, Anastassis Perrakis A, Andrea Thorn, Jianyi Yang

Nature Reviews Molecular Cell Biology

DOI

2023

Improved protein structure prediction with trRosettaX2 , AlphaFold2 , and optimized MSAs in CASP15

Zhenling Peng, Wenkai Wang, Hong Wei, Xiaoge Li, Jianyi Yang

Proteins Structure Function and Bioinformatics

DOI

2023

A unified approach to protein domain parsing with inter-residue distance matrix

Kun Zhu, Hong Lin Su, Zhenling Peng, Jianyi Yang

Bioinformatics

DOI

2022

Single-sequence protein structure prediction using supervised transformer protein language models

Wenkai Wang, Zhenling Peng, Jianyi Yang

Nature Computational Science

DOI

2022

Protein structure prediction in the deep learning era

Zhenling Peng, Wenkai Wang, Renmin Han, Fa Zhang, Jianyi Yang

Current Opinion in Structural Biology

DOI

2021

Improved Protein Structure Prediction Using a New Multi‐Scale Network and Homologous Templates

Hong Su, Wen-Kai Wang, Zongyang Du, Zhenling Peng, Shanghua Gao, Ming-Ming Cheng, Jianyi Yang

Advancement of science

DOI

2021

Accurate Sequence-Based Prediction of Deleterious nsSNPs with Multiple Sequence Profiles and Putative Binding Residues

Ruiyang Song, Baixin Cao, Zhenling Peng, C. Oldfield, Lukasz Kurgan, Ka-Chun Wong, Jianyi Yang

Biomolecules

DOI

2021

Recognition of small molecule–RNA binding sites using RNA sequence and structure

Hong Su, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2021

The trRosetta server for fast and accurate protein structure prediction

Zongyang Du, Hong Su, Wen-Kai Wang, Lisha Ye, Hong Wei, Zhenling Peng, I. Anishchenko, D. Baker, Jianyi Yang

Nature Protocols

DOI

2021

Improved estimation of model quality using predicted inter-residue distance

Lisha Ye, Pei-Lin Wu, Zhenling Peng, Jian-Zhao Gao, Jian Liu, Jianyi Yang

Bioinform.

DOI

2021

Toward the assessment of predicted inter-residue distance

Zongyang Du, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2020

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

Kui Wang, Gang Hu, Zhonghua Wu, Hong Su, Jianyi Yang, Lukasz Kurgan

International Journal of Molecular Sciences

DOI

2020

On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions

Ya-Jun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2020

RNA inter-nucleotide 3D closeness prediction by deep residual neural networks

Saisai Sun, Wen-Kai Wang, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2019

Improved protein structure prediction using predicted interresidue orientations

Jianyi Yang, I. Anishchenko, Hahnbeom Park, Zhenling Peng, S. Ovchinnikov, D. Baker

Proceedings of the National Academy of Sciences of the United States of America

DOI

2019

RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility

Hong Wei, Boling Wang, Jianyi Yang, Jian-Zhao Gao

IEEE/ACM Transactions on Computational Biology & Bioinformatics

DOI

2019

Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions

Akila Katuwawala, Zhenling Peng, Jianyi Yang, Lukasz Kurgan

Computational and Structural Biotechnology Journal

DOI

2019

Protein contact prediction using metagenome sequence data and residual neural networks

Qi Wu, Zhenling Peng, I. Anishchenko, Qian Cong, D. Baker, Jianyi Yang

Bioinform.

DOI

2019

CATHER: a novel threading algorithm with predicted contacts

Zongyang Du, Shuo Pan, Qi Wu, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2018

Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method

Zijuan Zhao, Zhenling Peng, Jianyi Yang

Journal of Chemical Information and Modeling

DOI

2018

mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Runze Dong, Shuo Pan, Zhenling Peng, Yang Zhang, Jianyi Yang

Nucleic Acids Res.

DOI

2018

Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles

Saisai Sun, Qi Wu, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2018

mTM‐align: an algorithm for fast and accurate multiple protein structure alignment

Runze Dong, Zhenling Peng, Yang Zhang, Jianyi Yang

Bioinform.

DOI

2018

Improving the prediction of protein‐nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

Hong Su, Mengchen Liu, Saisai Sun, Zhenling Peng, Jianyi Yang

Bioinform.

DOI

2018

CoABind: a novel algorithm for Coenzyme A (CoA)‐ and CoA derivatives‐binding residues prediction

Qiao-Zhen Meng, Zhenling Peng, Jianyi Yang, A. Valencia

Bioinform.

DOI

2018

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

Qi Wu, Zhenling Peng, Yang Zhang, Jianyi Yang

Nucleic Acids Res.

DOI

2017

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions

Y. Li, Jianyi Yang

Journal of Chemical Information and Modeling

DOI

2016

A large-scale comparative assessment of methods for residue–residue contact prediction

Q. Wuyun, Wei Zheng, Zhenling Peng, Jianyi Yang

Briefings Bioinform.

DOI

2016

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals

Xiuzhen Hu, Q. Dong, Jianyi Yang, Yang Zhang

Bioinform.

DOI

2016

An ensemble approach to protein fold classification by integration of template‐based assignment and support vector machine classifier

Jiaqi Xia, Zhenling Peng, Dawei Qi, Hongbo Mu, Jianyi Yang

Bioinform.

DOI

2015

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

Jian Zhang, Jianyi Yang, Richard Jang, Yang Zhang

Structure

DOI

2015

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

Jianyi Yang, Wen-Xuan Zhang, Bao-Ji He, S. Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko J. Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2015

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

Wen-Xuan Zhang, Jianyi Yang, Bao-Ji He, S. Walker, Hongjiu Zhang, Brandon Govindarajoo, Jouko J. Virtanen, Zhidong Xue, Hong-Bin Shen, Yang Zhang

Proteins: Structure, Function, and Bioinformatics

DOI

2015

Protein Structure and Function Prediction Using I-TASSER

Jianyi Yang, Yang Zhang

Current Protocols in Bioinformatics

DOI

2015

ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction

Jianyi Yang, Yan Wang, Yang Zhang

Journal of Molecular Biology

DOI

2015

I-TASSER server: new development for protein structure and function predictions

Jianyi Yang, Yang Zhang

Nucleic Acids Res.

DOI

2015

In various protein complexes, disordered protomers have large per‐residue surface areas and area of protein‐, DNA‐ and RNA‐binding interfaces

Zhonghua Wu, Gang Hu, Jianyi Yang, Zhenling Peng, V. Uversky, Lukasz Kurgan

FEBS Letters

DOI

2015

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, J. Brender, J. Hur, Arzucan Özgür, Yang Zhang

Bioinform.

DOI

2014

Super Spy variants implicate flexibility in chaperone action

S. Quan, Lili Wang, E. Petrotchenko, Karl A. T. Makepeace, S. Horowitz, Jianyi Yang, Yang Zhang, C. Borchers, J. Bardwell

eLife

DOI

2014

The I-TASSER Suite: protein structure and function prediction

Jianyi Yang, Renxiang Yan, Ambrish Roy, Dong Xu, Jonathan Poisson, Yang Zhang

Nature Methods

DOI

2013

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Renxiang Yan, Dong Xu, Jianyi Yang, S. Walker, Yang Zhang

Scientific Reports

DOI

2013

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

Jianyi Yang, Ambrish Roy, Yang Zhang

Bioinform.

DOI

2013

CHAPTER 16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURE CLASSES AND FUNCTIONS

Zun-Peng Yu, Jianyi Yang, Shao-Ming Zhu

2012

Enhanced prediction of several protein structural attributes with machine learning algorithms

Jianyi Yang

DOI

2012

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

Ambrish Roy, Jianyi Yang, Yang Zhang

Nucleic Acids Res.

DOI

2012

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

Jianyi Yang, Ambrish Roy, Yang Zhang

Nucleic Acids Res.

DOI

2011

A Consensus Approach to Predicting Protein Contact Map via Logistic Regression

Jianyi Yang, Xin Chen

International Symposium on Bioinformatics Research and Applications

DOI

2011

Improving taxonomy‐based protein fold recognition by using global and local features

Jianyi Yang, Xin Chen

Proteins: Structure, Function, and Bioinformatics

DOI

2010

An improved classification of G-protein-coupled receptors using sequence-derived features

Zhenling Peng, Jianyi Yang, Xin Chen

BMC Bioinformatics

DOI

2009

Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation.

Jianyi Yang, Zhenling Peng, Zu-Guo Yu, Rui Zhang, Anh Vo, De-Sheng Wang

Journal of Theoretical Biology

DOI

2009

Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

Jianyi Yang, Zu-Guo Yu, Anh Vo

DOI

2008

Protein Structure Classification Based on Chaos Game Representation and Multifractal Analysis

Jianyi Yang, Zu-Guo Yu, Anh Vo

2008 Fourth International Conference on Natural Computation

DOI

2007

Correlations between designability and various structural characteristics of protein lattice models.

Jianyi Yang, Zu-Guo Yu, Anh Vo

Journal of Chemical Physics

DOI

精选作品

期刊论文

COACH-D 2.0: A Server for Template-based Modeling of Protein−ligand Interactions

Generating Dynamic Structures Through Physics‐Based Sampling of Predicted Inter‐Residue Geometries

Protein language models for structural biology

Integrated experimental and AI innovations for RNA structure determination

Predicting RNA 3D structure and conformers using a pre-trained secondary structure model and structure-aware attention

The trRosettaRNA server for RNA structure prediction

Opportunities and challenges in protein structure prediction

Quality assessment of RNA 3D structure models using deep learning and intermediate 2D maps

Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning

Democratizing protein language model training, sharing and collaboration

RNA language model and graph attention network for RNA and small molecule binding sites prediction

Accurate Biomolecular Structure Prediction in CASP16 With Optimized Inputs to State‐Of‐The‐Art Predictors

Predicting the Oligomeric State of Proteins Using Multiple Templates Detected by Complementary Alignment Methods

AlphaFold in protein structure and function prediction

RNA-Puzzles Round V: blind predictions of 23 RNA structures

Author Correction: PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

AI accurately predicting the structure of biomolecular interactions

PLMSearch: Protein language model powers accurate and fast sequence search for remote homology

RNA threading with secondary structure and sequence profile

Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions

trRosettaRNA: automated prediction of RNA 3D structure with transformer network

Challenges and opportunities in macromolecular structure determination

Improved protein structure prediction with trRosettaX2 , AlphaFold2 , and optimized MSAs in CASP15

A unified approach to protein domain parsing with inter-residue distance matrix

Single-sequence protein structure prediction using supervised transformer protein language models

Protein structure prediction in the deep learning era

Improved Protein Structure Prediction Using a New Multi‐Scale Network and Homologous Templates

Accurate Sequence-Based Prediction of Deleterious nsSNPs with Multiple Sequence Profiles and Putative Binding Residues

Recognition of small molecule–RNA binding sites using RNA sequence and structure

The trRosetta server for fast and accurate protein structure prediction

Improved estimation of model quality using predicted inter-residue distance

Toward the assessment of predicted inter-residue distance

Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type

On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions

RNA inter-nucleotide 3D closeness prediction by deep residual neural networks

Improved protein structure prediction using predicted interresidue orientations

RNA Flexibility Prediction With Sequence Profile and Predicted Solvent Accessibility

Computational Prediction of MoRFs, Short Disorder-to-order Transitioning Protein Binding Regions

Protein contact prediction using metagenome sequence data and residual neural networks

CATHER: a novel threading algorithm with predicted contacts

Improving Sequence-Based Prediction of Protein-Peptide Binding Residues by Introducing Intrinsic Disorder and a Consensus Method

mTM-align: a server for fast protein structure database search and multiple protein structure alignment

Enhanced prediction of RNA solvent accessibility with long short-term memory neural networks and improved sequence profiles

mTM‐align: an algorithm for fast and accurate multiple protein structure alignment

Improving the prediction of protein‐nucleic acids binding residues via multiple sequence profiles and the consensus of complementary methods

CoABind: a novel algorithm for Coenzyme A (CoA)‐ and CoA derivatives‐binding residues prediction

COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking

Structural and Sequence Similarity Makes a Significant Impact on Machine-Learning-Based Scoring Functions for Protein-Ligand Interactions

A large-scale comparative assessment of methods for residue–residue contact prediction

Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals

An ensemble approach to protein fold classification by integration of template‐based assignment and support vector machine classifier

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

Template-based protein structure prediction in CASP11 and retrospect of I-TASSER in the last decade

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

Protein Structure and Function Prediction Using I-TASSER

ResQ: An approach to unified estimation of B-factor and residue-specific error in protein structure prediction

I-TASSER server: new development for protein structure and function predictions

In various protein complexes, disordered protomers have large per‐residue surface areas and area of protein‐, DNA‐ and RNA‐binding interfaces

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations

Super Spy variants implicate flexibility in chaperone action

The I-TASSER Suite: protein structure and function prediction

A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction

Protein-ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment

CHAPTER 16 FRACTAL RELATED METHODS FOR PREDICTING PROTEIN STRUCTURE CLASSES AND FUNCTIONS

Enhanced prediction of several protein structural attributes with machine learning algorithms

COFACTOR: an accurate comparative algorithm for structure-based protein function annotation

BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions

A Consensus Approach to Predicting Protein Contact Map via Logistic Regression

Improving taxonomy‐based protein fold recognition by using global and local features

An improved classification of G-protein-coupled receptors using sequence-derived features

Prediction of protein structural classes by recurrence quantification analysis based on chaos game representation.

Clustering structures of large proteins using multifractal analyses based on a 6-letter model and hydrophobicity scale of amino acids

Protein Structure Classification Based on Chaos Game Representation and Multifractal Analysis

Correlations between designability and various structural characteristics of protein lattice models.

会议论文

Protein Structure Prediction and Structure Comparison

预印本

trFlow: ultrafast all-atom protein conformational ensemble generation via conditional flow matching