Research graph
References from Exploring the computational methods for protein-ligand binding site prediction. Local targets link to admitted publications; unresolved targets remain external evidence.
Unresolved reference
2011 · External reference
Molecular dynamics simulations and drug discovery
10.1186/1741-7007-9-71 · 2011 · External reference
10.1093/bioinformatics/bty593
10.1093/bioinformatics/bty593 · External reference
A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
10.1093/bioinformatics/btq112 · 2010 · External reference
Binding site detection and druggability index from first principles
10.1021/jm801385d · 2009 · External reference
GalaxySite: ligand-binding-site prediction by using molecular docking
10.1093/nar/gku321 · 2014 · External reference
10.1016/s0022-2836(05)80360-2
10.1016/s0022-2836(05)80360-2 · External reference
Characterization of protein-ligand interaction sites using experimental and computational methods
2006 · External reference
10.1146/annurev.pharmtox.37.1.71
10.1146/annurev.pharmtox.37.1.71 · External reference
Combinatorial and computational approaches in structure-based drug design
1998 · External reference
Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction
10.1093/bioinformatics/btr331 · 2011 · External reference
10.1126/science.1064987
10.1126/science.1064987 · External reference
10.1002/jmr.984
10.1002/jmr.984 · External reference
10.1002/prot.340230303
10.1002/prot.340230303 · External reference
(2013) The Protein Model Portal—a comprehensive resource for protein structure and model information
2013 · External reference
10.1038/nmeth.2340
10.1038/nmeth.2340 · External reference
The Protein Data Bank: a computer-based archival file for macromolecular structures
10.1016/s0022-2836(77)80200-3 · 1977 · External reference
Unresolved reference
2003 · External reference
BioLiP: a semi-manually curated database for biologically relevant ligand–protein interactions
10.1093/nar/gks966 · 2012 · External reference
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
10.1016/0005-2795(75)90109-9 · 1975 · External reference
Computed tomography angiography-based analysis of high-risk intracerebral haemorrhage patients by employing a mathematical model
10.1186/s12859-019-2741-5 · 2019 · External reference
CpG-Island-based annotation and analysis of human house-keeping genes
2019 · External reference
An overview of scoring functions used for protein-ligand interactions in molecular docking
10.1007/s12539-019-00327-w · 2019 · External reference
Building up a robust risk mathematical platform to predict colorectal cancer
10.1155/2017/8917258 · 2017 · External reference
Exploring the key genes and signaling transduction pathways related to the survival time of glioblastoma multiforme patients by a novel survival analysis model
10.1186/s12864-016-3256-3 · 2017 · External reference
10.1016/s1093-3263(98)00002-3
10.1016/s1093-3263(98)00002-3 · External reference
10.1016/0263-7855(92)80074-n
10.1016/0263-7855(92)80074-n · External reference
SITEHOUND-web: a server for ligand binding site identification in protein structures
10.1093/nar/gkp281 · 2009 · External reference
3DLigandSite: predicting ligand-binding sites using similar structures
10.1093/nar/gkq406 · 2010 · External reference
L1pred: a sequence-based prediction tool for catalytic residues in enzymes with the L1-logreg classifier
10.1371/journal.pone.0035666 · 2012 · External reference
Protein–ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment
10.1093/bioinformatics/btt447 · 2013 · External reference
Deep learning in bioinformatics
2017 · External reference
DANN: a deep learning approach for annotating the pathogenicity of genetic variants
10.1093/bioinformatics/btu703 · 2014 · External reference
10.1093/bioinformatics/btx431
10.1093/bioinformatics/btx431 · External reference
10.1371/journal.pcbi.1006718
10.1371/journal.pcbi.1006718 · External reference
DeepSite: protein-binding site predictor using 3D-convolutional neural networks
10.1093/bioinformatics/btx350 · 2017 · External reference
10.1016/s0014-827x(02)01211-9
10.1016/s0014-827x(02)01211-9 · External reference
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education
10.1093/nar/gku1214 · 2014 · External reference
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
10.1021/jm00145a002 · 1985 · External reference
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
10.1016/0263-7855(95)00073-9 · 1995 · External reference
10.1002/pro.5560070905
10.1002/pro.5560070905 · External reference
10.1093/nar/gkl282
10.1093/nar/gkl282 · External reference
CASTp: computed atlas of surface topography of proteins
10.1093/nar/gkg512 · 2003 · External reference
10.1016/s0166-218x(98)00067-5
10.1016/s0166-218x(98)00067-5 · External reference
Q-SiteFinder: an energy-based method for the prediction of protein–ligand binding sites
10.1093/bioinformatics/bti315 · 2005 · External reference
LIGSITE csc: predicting ligand binding sites using the Connolly surface and degree of conservation
10.1186/1472-6807-6-19 · 2006 · External reference
VISCANA: visualized cluster analysis of protein− ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
10.1021/ci050262q · 2006 · External reference
Fpocket: an open source platform for ligand pocket detection
10.1186/1471-2105-10-168 · 2009 · External reference
Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites
10.1002/prot.22154 · 2009 · External reference
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets
10.1093/bioinformatics/btq672 · 2010 · External reference
FTSite: high accuracy detection of ligand binding sites on unbound protein structures
10.1093/bioinformatics/btr651 · 2011 · External reference
10.1093/bioinformatics/bts095
10.1093/bioinformatics/bts095 · External reference
LISE: a server using ligand-interacting and site-enriched protein triangles for prediction of ligand-binding sites
10.1093/nar/gkt300 · 2013 · External reference
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2. 0
10.1093/bioinformatics/btu724 · 2014 · External reference
CB-Dock: a web server for cavity detection-guided protein–ligand blind docking
2019 · External reference
10.1093/bioinformatics/19.1.163
10.1093/bioinformatics/19.1.163 · External reference
10.1093/bioinformatics/btm270
10.1093/bioinformatics/btm270 · External reference
10.1073/pnas.0707684105
10.1073/pnas.0707684105 · External reference
Protein-binding site prediction based on three-dimensional protein modeling
10.1002/prot.22572 · 2009 · External reference
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
10.1186/1471-2105-12-160 · 2011 · External reference
Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement
10.1016/j.str.2012.03.009 · 2012 · External reference
webPDBinder: a server for the identification of ligand binding sites on protein structures
10.1093/nar/gkt457 · 2013 · External reference
10.1002/prot.20106
10.1002/prot.20106 · External reference
10.1002/1097-0134(20010215)42:3<319::aid-prot30>3.0.co;2-a
10.1002/1097-0134(20010215)42:3<319::aid-prot30>3.0.co;2-a · External reference
10.1093/nar/gki524
10.1093/nar/gki524 · External reference
10.1110/ps.0215902
10.1110/ps.0215902 · External reference
Assessment of ligand binding residue predictions in CASP8
10.1002/prot.22557 · 2009 · External reference
10.1016/0022-2836(70)90057-4
10.1016/0022-2836(70)90057-4 · External reference
Predicting protein− ligand binding affinities using novel geometrical descriptors and machine-learning methods
10.1021/ci034246+ · 2004 · External reference
Kernel partial least squares regression in reproducing kernel hilbert space
2001 · External reference
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
10.1093/bioinformatics/btm537 · 2007 · External reference
Unresolved reference
1994 · External reference
SFCscore: scoring functions for affinity prediction of protein–ligand complexes
10.1002/prot.22058 · 2008 · External reference
Identification of ATP binding residues of a protein from its primary sequence
10.1186/1471-2105-10-434 · 2009 · External reference
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
10.1371/journal.pcbi.1000585 · 2009 · External reference
MetaPocket: a meta approach to improve protein ligand binding site prediction
10.1089/omi.2009.0045 · 2009 · External reference
Unresolved reference
2003 · External reference
MetaDBSite: a meta approach to improve protein DNA-binding sites prediction
10.1186/1752-0509-5-s1-s7 · 2011 · External reference
Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors
10.1093/bioinformatics/btr657 · 2011 · External reference
NNScore 2.0: a neural-network receptor–ligand scoring function
10.1021/ci2003889 · 2011 · External reference
NNScore: a neural-network-based scoring function for the characterization of protein–ligand complexes
10.1021/ci100244v · 2010 · External reference
Neural computation of arithmetic functions
10.1109/5.58350 · 1990 · External reference
Designing template-free predictor for targeting protein-ligand binding sites with classifier ensemble and spatial clustering
10.1109/tcbb.2013.104 · 2013 · External reference
10.1007/s10822-013-9663-5
10.1007/s10822-013-9663-5 · External reference
Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information
10.1186/1471-2105-14-44 · 2013 · External reference
Unresolved reference
2014 · External reference
Constructing query-driven dynamic machine learning model with application to protein-ligand binding sites prediction
10.1109/tnb.2015.2394328 · 2015 · External reference
A sequence-based dynamic ensemble learning system for protein ligand-binding site prediction
10.1109/tcbb.2015.2505286 · 2015 · External reference
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features
10.1186/s13321-015-0059-5 · 2015 · External reference
Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction
10.1002/cnm.2914 · 2018 · External reference
Scikit-learn: machine learning in Python
2011 · External reference
SAnDReS a computational tool for statistical analysis of docking results and development of scoring functions
2016 · External reference
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
10.1186/s13321-018-0285-8 · 2018 · External reference
COACH-D: improved protein–ligand binding sites prediction with refined ligand-binding poses through molecular docking
10.1093/nar/gky439 · 2018 · External reference
Taba: A tool to analyze the binding affinity
2019 · External reference
Prediction of DNA-binding residues from sequence
10.1093/bioinformatics/btm174 · 2007 · External reference
Predicting DNA-binding sites of proteins from amino acid sequence
10.1186/1471-2105-7-262 · 2006 · External reference
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences
10.1093/nar/gkl298 · 2006 · External reference
Prediction of DNA-binding residues from protein sequence information using random forests
10.1186/1471-2164-10-s1-s1 · 2009 · External reference
DP-Bind: a web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins
10.1093/bioinformatics/btl672 · 2007 · External reference
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
10.1093/bioinformatics/btg432 · 2004 · External reference
10.1101/gr.229202
10.1101/gr.229202 · External reference
Prediction of GTP interacting residues, dipeptides and tripeptides in a protein from its evolutionary information
10.1186/1471-2105-11-301 · 2010 · External reference
10.1093/nar/gks372
10.1093/nar/gks372 · External reference
10.1126/science.1127647
10.1126/science.1127647 · External reference
Unresolved reference
External reference
Unresolved reference
2016 · External reference
Unresolved reference
2015 · External reference
(2018) Deep learning for computer vision: a brief review
10.1155/2018/7068349 · 2018 · External reference
Where does AlphaGo go: From church-turing thesis to AlphaGo thesis and beyond
10.1109/jas.2016.7471613 · 2016 · External reference
Guest editorial deep learning in medical imaging: overview and future promise of an exciting new technique
10.1109/tmi.2016.2553401 · 2016 · External reference
Unresolved reference
2016 · External reference
10.1016/j.drudis.2018.01.039
10.1016/j.drudis.2018.01.039 · External reference
Computer-aided diagnosis with deep learning architecture: applications to breast lesions in US images and pulmonary nodules in CT scans
10.1038/srep24454 · 2016 · External reference
Unresolved reference
External reference
Learning representations by back-propagating errors
1988 · External reference
Unresolved reference
External reference
A deep learning framework for modeling structural features of RNA-binding protein targets
2015 · External reference
10.1038/nbt.3300
10.1038/nbt.3300 · External reference
KDEEP: protein-ligand absolute binding affinity prediction via 3D-convolutional neural networks
10.1021/acs.jcim.7b00650 · 2018 · External reference
Predicting protein-ligand binding residues with deep convolutional neural networks
10.1186/s12859-019-2672-1 · 2019 · External reference
DeepConv-DTI: prediction of drug-target interactions via deep learning with convolution on protein sequences
10.1371/journal.pcbi.1007129 · 2019 · External reference
10.1021/acsomega.9b01997
10.1021/acsomega.9b01997 · External reference
10.1371/journal.pcbi.1007069
10.1371/journal.pcbi.1007069 · External reference
Discovery of a ruthenium complex for the theranosis of glioma through targeting the mitochondrial DNA with bioinformatic methods
10.3390/ijms20184643 · 2019 · External reference
Revealing dynamic regulations and the related key proteins of myeloma-initiating cells by integrating experimental data into a systems biological model
2019 · External reference
10.1093/jmcb/mjx056
10.1093/jmcb/mjx056 · External reference
Investigation of mechanism of bone regeneration in a porous biodegradable calcium phosphate (CaP) scaffold by a combination of a multi-scale agent-based model and experimental optimization/validation
10.1039/c6nr01637e · 2016 · External reference
Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA)
10.1093/bioinformatics/bty392 · 2018 · External reference
Using game theory to investigate the epigenetic control mechanisms of embryo development: Comment on: “Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition” by Qian Wang et al
10.1016/j.plrev.2017.01.007 · 2017 · External reference
10.1016/j.bpc.2018.01.004
10.1016/j.bpc.2018.01.004 · External reference
10.1093/nar/gkv342
10.1093/nar/gkv342 · External reference
10.1038/nmeth.3213
10.1038/nmeth.3213 · External reference
Target M6A: identifying N 6-methyladenosine sites from RNA sequences via position-specific nucleotide propensities and a support vector machine
10.1109/tnb.2016.2599115 · 2016 · External reference
A cascade random forests algorithm for predicting protein-protein interaction sites
10.1109/tnb.2015.2475359 · 2015 · External reference
Protein–protein interaction sites prediction by ensembling SVM and sample-weighted random forests
10.1016/j.neucom.2016.02.022 · 2016 · External reference
CombFunc: predicting protein function using heterogeneous data sources
10.1093/nar/gks489 · 2012 · External reference
Designing new kinase inhibitor derivatives as therapeutics against common complex diseases: structural basis of microtubule affinity-regulating kinase 4 (MARK4) inhibition
10.1089/omi.2015.0111 · 2015 · External reference
KinasepKipred: a predictive model for estimating ligand-kinase inhibitor constant (pKi)
2019 · External reference
Unresolved reference
2016 · External reference
10.1038/nature14539
10.1038/nature14539 · External reference
Structural basis for inhibition of enoyl-[acyl carrier protein] reductase (InhA) from Mycobacterium tuberculosis
2019 · External reference
10.2174/1389450120666181204165344
10.2174/1389450120666181204165344 · External reference
Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2
10.1016/j.bbrc.2017.10.035 · 2017 · External reference
10.1016/j.jmb.2016.01.029
10.1016/j.jmb.2016.01.029 · External reference
Ligand-binding-site structure refinement using molecular dynamics with restraints derived from predicted binding site templates
10.1021/acs.jctc.9b00751 · 2019 · External reference
10.1073/pnas.1417811112
10.1073/pnas.1417811112 · External reference
10.1016/j.jmb.2013.04.009
10.1016/j.jmb.2013.04.009 · External reference
10.1073/pnas.1209309109
10.1073/pnas.1209309109 · External reference
Computational allosteric ligand binding site identification on Ras proteins
10.1093/abbs/gmv100 · 2015 · External reference
10.1002/prot.24786
10.1002/prot.24786 · External reference
10.1371/journal.pcbi.1004469
10.1371/journal.pcbi.1004469 · External reference
10.1016/j.bpj.2016.01.019
10.1016/j.bpj.2016.01.019 · External reference
