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Zixin Deng, Mingyu Li, Zeyu Zhang, Chao Chen, Xia Qu, Zhenyu Wang, Dequan Zhang, Chunjiang Zhang, Boxian Wu, Xueyu Sang

Silong Zhai, Huifeng Zhao, Jike Wang, Shaolong Lin, Tiantao Liu, Shukai Gu, Dejun Jiang, Huanxiang Liu, Yu Kang, Xiaojun Yao, Tingjun Hou

Huifeng Zhao, Odin Zhang, Dejun Jiang, Zhenxing Wu, Hongyan Du, Xiaorui Wang, Yihao Zhao, Yuansheng Huang, Jingxuan Ge, Tingjun Hou, Yu Kang

Pritam V. Bagwe, Shivangi P. Sawant, Shreerang V. Joshi

Taras Voitsitskyi, Volodymyr Bdzhola, Roman Stratiichuk, Ihor Koleiev, Zakhar Ostrovsky, Volodymyr Vozniak, Ivan Khropachov, Pavlo Henitsoi, Leonid Popryho, Roman Zhytar, Semen Yesylevskyy, Alan Nafiiev, Serhii Starosyla

William H. Brown, Davit A. Potoyan

Yuhong Ouyang, Yang Yue, Ning Wu, Jing Wang, Lihua Geng, Quanbin Zhang

David Bickel, Wim Vranken

Alex Berlaga, Kaylyn Torkelson, Aniruddha Seal, Jim Pfaendtner, Andrew L. Ferguson

Dominique A. Ramirez, Loren E. Hough, Michael R. Shirts

Rajarshi Samajdar, Moeen Meigooni, Hao Yang, Jialing Li, Xiaolin Liu, Nicholas E. Jackson, Martín A. Mosquera, Emad Tajkhorshid, Charles M. Schroeder

Vysakh Ramachandran, William Brown, Christopher Gayvert, Davit A. Potoyan

Xiaoyu Chai, Fulu Pan, Qianqian Wang, Xinyu Wang, Xueyan Li, Dongying Qi, Zirong Yi, Huan Liu, Jing Zhang, Yiming Zhang, Yanli Pan, Yang Liu, Guopeng Wang

Eric G. Fuemmeler, Anil Damle, Robert A. DiStasio

Xiaowei Lin, Nan Xu, Chen Li, Zhiyu Wu, Shengfu Chen, Yao Shi, Yi He

Niek van Hilten, Jeroen Methorst, Nino Verwei, Herre Jelger Risselada

Cheikh Cambel Dieng, Colby T. Ford, Anita Lerch, Dickson Doniou, Kovidh Vegesna, Daniel Janies, Liwang Cui, Linda Amoah, Yaw Afrane, Eugenia Lo

Chengxin Zhang, Anna Marie Pyle

Jacob J. Graham, Sinan Keten

Raphael J. Eberle, Marc Sevenich, Ian Gering, Lara Scharbert, Birgit Strodel, Nils A. Lakomek, Karoline Santur, Jeannine Mohrlüder, Mônika A. Coronado, Dieter Willbold

Jaka Kragelj, Rania Dumarieh, Yiling Xiao, Kendra K. Frederick

Alfonso Cabezón, Martin Calvelo, Juan R. Granja, Ángel Piñeiro, Rebeca Garcia-Fandino

Mingming Li, Xin Zhang, Jiapeng Li, Linggao Liu, Qiujin Zhu, Chao Qu, Yunhan Zhang, Shouwei Wang

Seren Hamsici, Andrew D. White, Handan Acar

Xingyu Li, Xue Lin, Xueyin Mei, Pin Chen, Anna Liu, Weicheng Liang, Shan Chang, Jian Li

Jiale Liu, Changsheng Zhang, Luhua Lai

Osita Sunday Nnyigide, Tochukwu Olunna Nnyigide, Sun-Gu Lee, Kyu Hyun

Arup Mondal, Liwei Chang, Alberto Perez

Lijuan Yang, Guanghui Yang, Zhitong Bing, Yuan Tian, Liang Huang, Yuzhen Niu, Lei Yang

Niek van Hilten, Kai Steffen Stroh, Herre Jelger Risselada

Fabián Suarez-Leston, Martin Calvelo, Gideon F. Tolufashe, Alicia Muñoz, Uxía Veleiro, César Porto, Margarida Bastos, Ángel Piñeiro, Rebeca Garcia-Fandino

Lisbeth R. Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt

Joe G. Greener, David T. Jones

Raffaele Iannuzzi, Grazisa Rossetti, Andrea Spitaleri, Raoul J. P. Bonnal, Massimiliano Pagani, Luca Mollica

Glen van den Bergen, Martin Stroet, Bertrand Caron, David Poger, Alan E. Mark

Gaoqi Weng, Junbo Gao, Zhe Wang, Ercheng Wang, Xueping Hu, Xiaojun Yao, Dongsheng Cao, Tingjun Hou

Dilnoza B. Amirkulova, Maghesree Chakraborty, Andrew D. White

Gang Xu, Qinghua Wang, Jianpeng Ma

Gang Xu, Tianqi Ma, Junqing Du, Qinghua Wang, Jianpeng Ma

Arthur O. Zalevsky, Alexander S. Zlobin, Vasilina R. Gedzun, Roman V. Reshetnikov, Maxim L. Lovat, Anton V. Malyshev, Igor I. Doronin, Gennady A. Babkin, Andrey V. Golovin

Carl Mensch, Christian Johannessen

Yi He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor Muñoz

Carl Mensch, Patrick Bultinck, Christian Johannessen

Carl Mensch, Christian Johannessen

Oinam Romesh Meitei, Andreas Heßelmann

Rashmi R. Hazarika, Nikolina Sostaric, Yifeng Sun, Vera van Noort

Carl Mensch, Patrick Bultinck, Christian Johannessen

A Di Matteo, M Franceschini, A Paiardini, A Grottesi, S Chiarella, S Rocchio, C Di Natale, D Marasco, L Vitagliano, C Travaglini-Allocatelli, L Federici

Sjoerd J. de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tuffery

Yankai Fu, Tingxuan Yan, Xia Xu

Carl Mensch, Laurence D. Barron, Christian Johannessen

Christina Schindler, Sjoerd de Vries, Martin Zacharias

Oinam Romesh Meitei, Andreas Heßelmann

Ranjan V. Mannige, Joyjit Kundu, Stephen Whitelam

Andrew E. Brereton, P. Andrew Karplus

R. Rentzsch, B. Y. Renard

Christina E.M. Schindler, Sjoerd J. de Vries, Martin Zacharias

Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen

Matthew Z. Tien, Austin G. Meyer, Dariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke

Konrad Hinsen, Shuangwei Hu, Gerald R. Kneller, Antti J. Niemi

2025	Identification and In Silico Characterization of the Novel Inhibitory Peptides of Angiotensin Converting Enzyme from Donkey Meat International Journal of Peptide Research and Therapeutics Zixin Deng, Mingyu Li, Zeyu Zhang, Chao Chen, Xia Qu, Zhenyu Wang, Dequan Zhang, Chunjiang Zhang, Boxian Wu, Xueyu Sang
2025	PepPCBench is a Comprehensive Benchmarking Framework for Protein–Peptide Complex Structure Prediction Journal of Chemical Information and Modeling Silong Zhai, Huifeng Zhao, Jike Wang, Shaolong Lin, Tiantao Liu, Shukai Gu, Dejun Jiang, Huanxiang Liu, Yu Kang, Xiaojun Yao, Tingjun Hou
2025	Protein–peptide docking with a rational and accurate diffusion generative model Nature Machine Intelligence Huifeng Zhao, Odin Zhang, Dejun Jiang, Zhenxing Wu, Hongyan Du, Xiaorui Wang, Yihao Zhao, Yuansheng Huang, Jingxuan Ge, Tingjun Hou, Yu Kang
2025	Peptides Unplugged: Small Chains Tackling Big Challenges—One Life-Saving Sequence at a Time! International Journal of Peptide Research and Therapeutics Pritam V. Bagwe, Shivangi P. Sawant, Shreerang V. Joshi
2024	Augmenting a training dataset of the generative diffusion model for molecular docking with artificial binding pockets RSC Advances Taras Voitsitskyi, Volodymyr Bdzhola, Roman Stratiichuk, Ihor Koleiev, Zakhar Ostrovsky, Volodymyr Vozniak, Ivan Khropachov, Pavlo Henitsoi, Leonid Popryho, Roman Zhytar, Semen Yesylevskyy, Alan Nafiiev, Serhii Starosyla
2024	Phase separation of multicomponent peptide mixtures into dehydrated clusters with hydrophilic cores Biophysical Journal William H. Brown, Davit A. Potoyan
2024	Identification and anticoagulant mechanisms of novel factor XIa inhibitory peptides by virtual screening of a in silico generated deep-sea peptide database Food Research International Yuhong Ouyang, Yang Yue, Ning Wu, Jing Wang, Lihua Geng, Quanbin Zhang
2024	Effects of Phosphorylation on Protein Backbone Dynamics and Conformational Preferences Journal of Chemical Theory and Computation David Bickel, Wim Vranken
2024	A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids The Journal of Chemical Physics Alex Berlaga, Kaylyn Torkelson, Aniruddha Seal, Jim Pfaendtner, Andrew L. Ferguson
2024	Coiled-coil domains are sufficient to drive liquid-liquid phase separation in protein models Biophysical Journal Dominique A. Ramirez, Loren E. Hough, Michael R. Shirts
2024	Secondary structure determines electron transport in peptides Proceedings of the National Academy of Sciences Rajarshi Samajdar, Moeen Meigooni, Hao Yang, Jialing Li, Xiaolin Liu, Nicholas E. Jackson, Martín A. Mosquera, Emad Tajkhorshid, Charles M. Schroeder
2024	Nucleoprotein Phase-Separation Affinities Revealed via Atomistic Simulations of Short Peptide and RNA Fragments The Journal of Physical Chemistry Letters Vysakh Ramachandran, William Brown, Christopher Gayvert, Davit A. Potoyan
2024	Identification, screening, and comprehensive evaluation of novel thrombin inhibitory peptides from the hirudo produced using pepsin Frontiers in Pharmacology Xiaoyu Chai, Fulu Pan, Qianqian Wang, Xinyu Wang, Xueyan Li, Dongying Qi, Zirong Yi, Huan Liu, Jing Zhang, Yiming Zhang, Yanli Pan, Yang Liu, Guopeng Wang
2023	Selected Columns of the Density Matrix in an Atomic Orbital Basis I: An Intrinsic and Non-iterative Orbital Localization Scheme for the Occupied Space Journal of Chemical Theory and Computation Eric G. Fuemmeler, Anil Damle, Robert A. DiStasio
2023	Molecular simulation studies on a zwitterionic peptide-dendrimer conjugate for integrin αvβ3 binding Biointerphases Xiaowei Lin, Nan Xu, Chen Li, Zhiyu Wu, Shengfu Chen, Yao Shi, Yi He
2023	Pepfun 2.0: Improved Protocols for the Analysis of Natural and Modified Peptides Future Drug Discovery Rodrigo Ochoa
2023	Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders Science Advances Niek van Hilten, Jeroen Methorst, Nino Verwei, Herre Jelger Risselada
2023	Genetic variations of Plasmodium falciparum circumsporozoite protein and the impact on interactions with human immunoproteins and malaria vaccine efficacy Infection, Genetics and Evolution Cheikh Cambel Dieng, Colby T. Ford, Anita Lerch, Dickson Doniou, Kovidh Vegesna, Daniel Janies, Liwang Cui, Linda Amoah, Yaw Afrane, Eugenia Lo
2023	PDC: a highly compact file format to store protein 3D coordinates Database Chengxin Zhang, Anna Marie Pyle
2023	Increase in Charge and Density Improves the Strength and Toughness of Mussel Foot Protein 5 Inspired Protein Materials ACS Biomaterials Science & Engineering Jacob J. Graham, Sinan Keten
2023	Discovery of All-d-Peptide Inhibitors of SARS-CoV-2 3C-like Protease ACS Chemical Biology Raphael J. Eberle, Marc Sevenich, Ian Gering, Lara Scharbert, Birgit Strodel, Nils A. Lakomek, Karoline Santur, Jeannine Mohrlüder, Mônika A. Coronado, Dieter Willbold
2023	Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins Protein Science Jaka Kragelj, Rania Dumarieh, Yiling Xiao, Kendra K. Frederick
2023	Uncovering the mechanisms of cyclic peptide self-assembly in membranes with the chirality-aware MA(R/S)TINI forcefield Journal of Colloid and Interface Science Alfonso Cabezón, Martin Calvelo, Juan R. Granja, Ángel Piñeiro, Rebeca Garcia-Fandino
2023	Identification and In Silico Simulation on Inhibitory Platelet-Activating Factor Acetyl Hydrolase Peptides from Dry-Cured Pork Coppa Foods Mingming Li, Xin Zhang, Jiapeng Li, Linggao Liu, Qiujin Zhu, Chao Qu, Yunhan Zhang, Shouwei Wang
2022	Peptide framework for screening the effects of amino acids on assembly Science Advances Seren Hamsici, Andrew D. White, Handan Acar
2022	HLA3D: an integrated structure-based computational toolkit for immunotherapy Briefings in Bioinformatics Xingyu Li, Xue Lin, Xueyin Mei, Pin Chen, Anna Liu, Weicheng Liang, Shan Chang, Jian Li
2022	GeoPacker: A novel deep learning framework for protein side‐chain modeling Protein Science Jiale Liu, Changsheng Zhang, Luhua Lai
2022	Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions Journal of Chemical Information and Modeling Osita Sunday Nnyigide, Tochukwu Olunna Nnyigide, Sun-Gu Lee, Kyu Hyun
2022	Modelling peptide–protein complexes: docking, simulations and machine learning QRB Discovery Arup Mondal, Liwei Chang, Alberto Perez
2022	Accelerating the discovery of anticancer peptides targeting lung and breast cancers with the Wasserstein autoencoder model and PSO algorithm Briefings in Bioinformatics Lijuan Yang, Guanghui Yang, Zhitong Bing, Yuan Tian, Liang Huang, Yuzhen Niu, Lei Yang
2022	Efficient Quantification of Lipid Packing Defect Sensing by Amphipathic Peptides: Comparing Martini 2 and 3 with CHARMM36 Journal of Chemical Theory and Computation Niek van Hilten, Kai Steffen Stroh, Herre Jelger Risselada
2022	SuPepMem: A database of innate immune system peptides and their cell membrane interactions Computational and Structural Biotechnology Journal Fabián Suarez-Leston, Martin Calvelo, Gideon F. Tolufashe, Alicia Muñoz, Uxía Veleiro, César Porto, Margarida Bastos, Ángel Piñeiro, Rebeca Garcia-Fandino
2021	General Protocol for Constructing Molecular Models of Nanodiscs Journal of Chemical Information and Modeling Lisbeth R. Kjølbye, Leonardo De Maria, Tsjerk A. Wassenaar, Haleh Abdizadeh, Siewert J. Marrink, Jesper Ferkinghoff-Borg, Birgit Schiøtt
2021	Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins PLOS ONE Joe G. Greener, David T. Jones
2021	A Simplified Amino Acidic Alphabet to Unveil the T-Cells Receptors Antigens: A Computational Perspective Frontiers in Chemistry Raffaele Iannuzzi, Grazisa Rossetti, Andrea Spitaleri, Raoul J. P. Bonnal, Massimiliano Pagani, Luca Mollica
2020	Curved or linear? Predicting the 3‐dimensional structure of α‐helical antimicrobial peptides in an amphipathic environment FEBS Letters Glen van den Bergen, Martin Stroet, Bertrand Caron, David Poger, Alan E. Mark
2020	Comprehensive Evaluation of Fourteen Docking Programs on Protein–Peptide Complexes Journal of Chemical Theory and Computation Gaoqi Weng, Junbo Gao, Zhe Wang, Ercheng Wang, Xueping Hu, Xiaojun Yao, Dongsheng Cao, Tingjun Hou
2020	Experimentally Consistent Simulation of Aβ21–30 Peptides with a Minimal NMR Bias The Journal of Physical Chemistry B Dilnoza B. Amirkulova, Maghesree Chakraborty, Andrew D. White
2020	OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation Journal of Chemical Theory and Computation Gang Xu, Qinghua Wang, Jianpeng Ma
2019	OPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method Journal of Chemical Theory and Computation Gang Xu, Tianqi Ma, Junqing Du, Qinghua Wang, Jianpeng Ma
2019	PeptoGrid—Rescoring Function for AutoDock Vina to Identify New Bioactive Molecules from Short Peptide Libraries Molecules Arthur O. Zalevsky, Alexander S. Zlobin, Vasilina R. Gedzun, Roman V. Reshetnikov, Maxim L. Lovat, Anton V. Malyshev, Igor I. Doronin, Gennady A. Babkin, Andrey V. Golovin
2019	The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins ChemPhysChem Carl Mensch, Christian Johannessen
2019	Glutton: a tool for generating structural ensembles of partly disordered proteins from chemical shifts Bioinformatics Yi He, Suhani Nagpal, Mourad Sadqi, Eva de Alba, Victor Muñoz
2019	The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra Physical Chemistry Chemical Physics Carl Mensch, Patrick Bultinck, Christian Johannessen
2018	Is Raman Optical Activity Spectroscopy Sensitive to β‐Turns in Proteins? Secondary Structure and Side‐Chain Dependence ChemPhysChem Carl Mensch, Christian Johannessen
2018	Geometry optimizations with the incremental molecular fragmentation method Journal of Theoretical and Computational Chemistry Oinam Romesh Meitei, Andreas Heßelmann
2018	The BackMAP Python module: how a simpler Ramachandran number can simplify the life of a protein simulator PeerJ Ranjan Mannige
2018	Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana PLOS ONE Rashmi R. Hazarika, Nikolina Sostaric, Yifeng Sun, Vera van Noort
2018	Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity ACS Omega Carl Mensch, Patrick Bultinck, Christian Johannessen
2017	Structural investigation of nucleophosmin interaction with the tumor suppressor Fbw7γ Oncogenesis A Di Matteo, M Franceschini, A Paiardini, A Grottesi, S Chiarella, S Rocchio, C Di Natale, D Marasco, L Vitagliano, C Travaglini-Allocatelli, L Federici
2017	An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h) PeerJ Ranjan V. Mannige
2017	The pepATTRACT web server for blind, large-scale peptide–protein docking Nucleic Acids Research Sjoerd J. de Vries, Julien Rey, Christina E. M. Schindler, Martin Zacharias, Pierre Tuffery
2017	Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation The Journal of Physical Chemistry B Yankai Fu, Tingxuan Yan, Xia Xu
2016	Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra Physical Chemistry Chemical Physics Carl Mensch, Laurence D. Barron, Christian Johannessen
2016	Development and Application of a Fully Blind Flexible Peptide-protein Docking Protocol, pepATTRACT BIO-PROTOCOL Christina Schindler, Sjoerd de Vries, Martin Zacharias
2016	Molecular energies from an incremental fragmentation method The Journal of Chemical Physics Oinam Romesh Meitei, Andreas Heßelmann
2016	The Ramachandran Number: An Order Parameter for Protein Geometry PLOS ONE Ranjan V. Mannige, Joyjit Kundu, Stephen Whitelam
2016	Local Molecular Orbitals from a Projection onto Localized Centers Journal of Chemical Theory and Computation Andreas Heßelmann
2015	Native proteins trap high-energy transit conformations Science Advances Andrew E. Brereton, P. Andrew Karplus
2015	Docking small peptides remains a great challenge: an assessment using AutoDock Vina Briefings in Bioinformatics R. Rentzsch, B. Y. Renard
2015	Fully Blind Peptide-Protein Docking with pepATTRACT Structure Christina E.M. Schindler, Sjoerd J. de Vries, Martin Zacharias
2014	FragBuilder: an efficient Python library to setup quantum chemistry calculations on peptides models PeerJ Anders S. Christensen, Thomas Hamelryck, Jan H. Jensen
2013	Maximum Allowed Solvent Accessibilites of Residues in Proteins PLoS ONE Matthew Z. Tien, Austin G. Meyer, Dariya K. Sydykova, Stephanie J. Spielman, Claus O. Wilke
2013	A comparison of reduced coordinate sets for describing protein structure The Journal of Chemical Physics Konrad Hinsen, Shuangwei Hu, Gerald R. Kneller, Antti J. Niemi
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