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Publication search results
found 98 matches
- 2024
- Anna Carbery, Martin Buttenschoen, Rachael Skyner, Frank von Delft, Charlotte M. Deane:
Learnt representations of proteins can be used for accurate prediction of small molecule binding sites on experimentally determined and predicted protein structures. J. Cheminformatics 16(1): 32 (2024) - 2023
- Yidong Song, Qianmu Yuan
, Huiying Zhao, Yuedong Yang
:
Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures. Briefings Bioinform. 24(6) (2023) - Yanpeng Zhao
, Jingjing Wang, Fubin Chang, Weikang Gong, Yang Liu, Chunhua Li
:
Identification of metal ion-binding sites in RNA structures using deep learning method. Briefings Bioinform. 24(2) (2023) - Vid Ravnik
, Marko Jukic
, Urban Bren
:
Identifying Metal Binding Sites in Proteins Using Homologous Structures, the MADE Approach. J. Chem. Inf. Model. 63(16): 5204-5219 (2023) - 2022
- Vinícius de Almeida Paiva, Murillo Ventura Mendonça
, Sabrina de Azevedo Silveira, David B. Ascher
, Douglas E. V. Pires
, Sandro C. Izidoro
:
GASS-Metal: identifying metal-binding sites on protein structures using genetic algorithms. Briefings Bioinform. 23(5) (2022) - Swati Adhikari, Parthajit Roy:
A geometry based approach to compare five metal binding sites on biomolecular structures. Int. J. Comput. Biol. Drug Des. 15(1): 1-29 (2022) - Janez Konc
, Dusanka Janezic
:
ProBiS-Fold Approach for Annotation of Human Structures from the AlphaFold Database with No Corresponding Structure in the PDB to Discover New Druggable Binding Sites. J. Chem. Inf. Model. 62(22): 5821-5829 (2022) - Vincenzo Laveglia, Andrea Giachetti
, Davide Sala
, Claudia Andreini, Antonio Rosato
:
Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network. J. Chem. Inf. Model. 62(12): 2951-2960 (2022) - Huiyan Lu, Yuji Komukai, Koto Usami, Yan Guo, Xinyue Qiao, Michiyoshi Nukaga, Tyuji Hoshino
:
Computational and Crystallographic Analysis of Binding Structures of Inhibitory Compounds for HIV-1 RNase H Activity. J. Chem. Inf. Model. 62(24): 6762-6774 (2022) - Jinze Zhang, Hao Li, Xuejun Zhao, Qilong Wu
, Sheng-You Huang
:
Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J. Chem. Inf. Model. 62(22): 5806-5820 (2022) - David Jakubec, Petr Skoda
, Radoslav Krivák, Marian Novotny
, David Hoksza
:
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res. 50(W1): 593-597 (2022) - 2021
- Wajid Arshad Abbasi
, Syed Ali Abbas, Saiqa Andleeb
:
PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures. J. Bioinform. Comput. Biol. 19(4): 2150015:1-2150015:19 (2021) - Hugo Guterres
, Sang-Jun Park
, Wei Jiang
, Wonpil Im
:
Ligand-Binding-Site Refinement to Generate Reliable Holo Protein Structure Conformations from Apo Structures. J. Chem. Inf. Model. 61(1): 535-546 (2021) - 2020
- Rostislav K. Skitchenko
, Dmitrii Usoltsev
, Mayya Uspenskaya, Andrey V. Kajava
, Albert Guskov
:
Census of halide-binding sites in protein structures. Bioinform. 36(10): 3064-3071 (2020) - Takashi Yoshidome
, Mitsunori Ikeguchi
, Masateru Ohta
:
Comprehensive 3D-RISM analysis of the hydration of small molecule binding sites in ligand-free protein structures. J. Comput. Chem. 41(28): 2406-2419 (2020) - Lucia Fusani, David S. Palmer
, Don O. Somers, Ian D. Wall:
Exploring Ligand Stability in Protein Crystal Structures Using Binding Pose Metadynamics. J. Chem. Inf. Model. 60(3): 1528-1539 (2020) - Tomohide Masuda, Matthew Ragoza, David Ryan Koes:
Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models. CoRR abs/2010.14442 (2020) - 2019
- Zhe Wang
, Xuwen Wang, Youyong Li, Tailong Lei, Ercheng Wang
, Dan Li, Yu Kang
, Feng Zhu
, Tingjun Hou:
farPPI: a webserver for accurate prediction of protein-ligand binding structures for small-molecule PPI inhibitors by MM/PB(GB)SA methods. Bioinform. 35(10): 1777-1779 (2019) - Mei Qian Yau
, Abigail L. Emtage
, Nathaniel J. Y. Chan, Stephen W. Doughty
, Jason S. E. Loo
:
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures. J. Comput. Aided Mol. Des. 33(5): 487-496 (2019) - Awatef Hattab, Zoubeida Dhaouadi, Alhadji Malloum
, Jean Jules Fifen
, Souad Lahmar, Nino Russo
, Emilia Sicilia
:
Structures, binding energies, temperature effects, infrared spectroscopy of [Mg(NH3)n = 1-10]+ clusters from DFT and MP2 investigations. J. Comput. Chem. 40(18): 1707-1717 (2019) - François Bonnardel
, Julien Mariethoz
, Sebastian Salentin, Xavier Robin
, Michael Schroeder, Serge Pérez, Frédérique Lisacek, Anne Imberty
:
UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res. 47(Database-Issue): D1236-D1244 (2019) - 2018
- Damiano Piovesan
, Silvio C. E. Tosatto
:
Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures. Bioinform. 34(1): 122-123 (2018) - Claas Strecker
, Bernd Meyer
:
Plasticity of the Binding Site of Renin: Optimized Selection of Protein Structures for Ensemble Docking. J. Chem. Inf. Model. 58(5): 1121-1131 (2018) - 2017
- Xia Lin
, Michael Khoo, Jae-wook Ahn, Douglas Tudhope
, Ceri Binding
, Diane Massam, Hilary Jane Jones
:
Mapping metadata to DDC classification structures for searching and browsing. Int. J. Digit. Libr. 18(1): 25-39 (2017) - 2016
- Xihao Hu, Yang Wu
, Zhi John Lu, Kevin Y. Yip
:
Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations. Briefings Bioinform. 17(6): 1032-1043 (2016) - Hoon Ryu
, Yosang Jeong, Ji Hoon Kang
, Kyunam Cho
:
Time-efficient simulations of tight-binding electronic structures with Intel Xeon PhiTM many-core processors. Comput. Phys. Commun. 209: 79-87 (2016) - Li Rao, Bo Chi, Yanliang Ren, Yongjian Li, Xin Xu, Jian Wan:
DOX: A new computational protocol for accurate prediction of the protein-ligand binding structures. J. Comput. Chem. 37(3): 336-344 (2016) - Joshua Meyers
, Nathan Brown, Julian Blagg
:
Mapping the 3D structures of small molecule binding sites. J. Cheminformatics 8(1): 70:1-70:13 (2016) - David Xu
, Samy O. Meroueh:
Effect of Binding Pose and Modeled Structures on SVMGen and GlideScore Enrichment of Chemical Libraries. J. Chem. Inf. Model. 56(6): 1139-1151 (2016) - Ana Zafra Ruano, Elisa Cilia, José R. Couceiro
, Javier Ruiz Sanz
, Joost Schymkowitz
, Frederic Rousseau, Irene Luque
, Tom Lenaerts
:
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors. PLoS Comput. Biol. 12(5) (2016)
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