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Binding Sites

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ClusterTAD: an unsupervised machine learning approach to detecting topologically associated domains of chromosomes from Hi-C data.

BMC bioinformatics Nov 14, 2017
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-...
Binding Sites Enhancer Elements, Genetic Chromosomes Chromatin Immunoprecipitation Cluster Analysis Unsupervised Machine Learning Promoter Regions, Genetic Histone Code CCCTC-Binding Factor Genomics Sequence Analysis, DNA Animals Mice
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Modern drug design: the implication of using artificial neuronal networks and multiple molecular dynamic simulations.

Journal of computer-aided molecular design Nov 13, 2017
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org...
Neural Networks, Computer Machine Learning Molecular Docking Simulation Computer-Aided Design Humans Binding Sites Ligands Drug Design Protein Conformation Protein Binding Receptors, Cytoplasmic and Nuclear Molecular Dynamics Simulation
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Glypre: In Silico Prediction of Protein Glycation Sites by Fusing Multiple Features and Support Vector Machine.

Molecules (Basel, Switzerland) Nov 3, 2017
Glycation is a non-enzymatic process occurring inside or outside the host body by attaching a sugar molecule to a protein or lipid molecule. It is an important form of post-translational modification (PTM), which impairs the function and changes the ...
Lysine Binding Sites Proteins Area Under Curve Amino Acids Algorithms Glycosylation Sensitivity and Specificity Support Vector Machine ROC Curve Computer Simulation
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Specific and intrinsic sequence patterns extracted by deep learning from intra-protein binding and non-binding peptide fragments.

Scientific reports Nov 2, 2017
The key finding in the DNA double helix model is the specific pairing or binding between nucleotides A-T and C-G, and the pairing rules are the molecule basis of genetic code. Unfortunately, no such rules have been discovered for proteins. Here we sh...
Algorithms Deep Learning Peptide Fragments Amino Acid Sequence Protein Conformation Binding Sites Protein Binding Proteins Databases, Protein
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MoRFPred-plus: Computational Identification of MoRFs in Protein Sequences using Physicochemical Properties and HMM profiles.

Journal of theoretical biology Oct 16, 2017
MOTIVATION: Intrinsically Disordered Proteins (IDPs) lack stable tertiary structure and they actively participate in performing various biological functions. These IDPs expose short binding regions called Molecular Recognition Features (MoRFs) that p...
Amino Acid Sequence Intrinsically Disordered Proteins Binding Sites Models, Theoretical Support Vector Machine Protein Domains Algorithms Protein Binding Computational Biology
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The folded k-spectrum kernel: A machine learning approach to detecting transcription factor binding sites with gapped nucleotide dependencies.

PloS one Oct 5, 2017
Understanding the molecular machinery involved in transcriptional regulation is central to improving our knowledge of an organism's development, disease, and evolution. The building blocks of this complex molecular machinery are an organism's genomic...
Machine Learning Nucleotides Transcription Factors Binding Sites Support Vector Machine
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modeling of the cryptic E2∼ubiquitin-binding site of E6-associated protein (E6AP)/UBE3A reveals the mechanism of polyubiquitin chain assembly.

The Journal of biological chemistry Sep 18, 2017
To understand the mechanism for assembly of Lys-linked polyubiquitin degradation signals, we previously demonstrated that the E6AP/UBE3A ligase harbors two functionally distinct E2∼ubiquitin-binding sites: a high-affinity Site 1 required for E6AP Cys...
Point Mutation Ubiquitin-Conjugating Enzymes Cattle Ubiquitination Computational Biology Protein Multimerization Models, Molecular Humans Isoenzymes Iodine Radioisotopes Expert Systems Cysteine Animals Binding Sites Biocatalysis Ubiquitin-Protein Ligases Mutagenesis, Site-Directed Amino Acid Substitution Protein Conformation Molecular Docking Simulation Ubiquitin Recombinant Fusion Proteins
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Convex-PL: a novel knowledge-based potential for protein-ligand interactions deduced from structural databases using convex optimization.

Journal of computer-aided molecular design Sep 18, 2017
We present a novel optimization approach to train a free-shape distance-dependent protein-ligand scoring function called Convex-PL. We do not impose any functional form of the scoring function. Instead, we decompose it into a polynomial basis and ded...
Humans Molecular Docking Simulation Drug Design Machine Learning Algorithms Protein Conformation Binding Sites Structure-Activity Relationship Molecular Structure Protein Binding Proteins Databases, Protein Knowledge Bases Ligands
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Protein-protein interaction site predictions with minimum covariance determinant and Mahalanobis distance.

Journal of theoretical biology Sep 1, 2017
Protein-protein interaction site (PPIS) prediction must deal with the diversity of interaction sites that limits their prediction accuracy. Use of proteins with unknown or unidentified interactions can also lead to missing interfaces. Such data error...
Artificial Intelligence Binding Sites Protein Interaction Domains and Motifs Support Vector Machine Supervised Machine Learning
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Predicting the helix-helix interactions from correlated residue mutations.

Proteins Aug 24, 2017
Helix-helix interactions are crucial in the structure assembly, stability and function of helix-rich proteins including many membrane proteins. In spite of remarkable progresses over the past decades, the accuracy of predicting protein structures fro...
Machine Learning Protein Binding Amino Acid Sequence Computational Biology Binding Sites Membrane Proteins Protein Interaction Domains and Motifs Protein Conformation, alpha-Helical
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