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Introduction to pdb-profiling

预备知识 RefSeq数据资源与Ensembl数据资源 什么是PDB 什么是UniProt-KB 什么是可变剪切(Alternative Splicing) 什么是蛋白质一级结构 (序列) 什么是蛋白质三级结构 (晶体结构) 从中心法则谈起: 基因位点到蛋白质位点 ...

Exercise of Markov Chain

Q1 Suppose you repeatedly does toss a fair coin and denote $T$ the first time you get three consecutive heads. Compute $E[T]$ Verify your answer in [1] via simulation. You may use any progra...

Implement KDTree in PDB Coordinates

Concept K-D Tree In computer science, a k-d tree (short for k-dimensional tree) is a space-partitioning data structure for organizing points in a k-dimensional space. k-d trees are a useful da...

Record for PDBe API Issues

Basic Information This Gist is a personal note that recording those issues encountered during my use cases. API References PDBe REST API https://www.ebi.ac.uk/pdbe/api/doc/pdb.html htt...

Generation of Biological Assembly and related information

Get Info from mmCIF assg_cols = ('_pdbx_struct_assembly_gen.asym_id_list', '_pdbx_struct_assembly_gen.oper_expression', '_pdbx_struct_assembly_gen.assembly_id') oper_cols = ('_pdbx_...

Cluster Interface / Interface Similarity

Data Resource (2007) PISA (2011, 2020) ProtCID (2012) InterEvol (2014) PIFACE (2014) EPPIC (2017) ❌QSbio Method (2004) MultiProt (2005) TM-Align (2009) MM-align (2010) iAl...

Summary of Proteomics Informatics (Course ver.2020)

Basic Information Note: This blog is a personal note of the Proteomics Informatics Course and most of the content is non-original. 8 蛋白质结构与功能分析 蛋白质结构相关软件 蛋白质结构比对 蛋白质功能 蛋白质结构与功能分析方法 ...

Predicting Protein-Protein Interactions from the Molecular to the Proteome Level

Basic Information This blog is a personal note of the following review. Keskin O, Tuncbag N, Gursoy A. Predicting Protein-Protein Interactions from the Molecular to the Proteome Level. Che...

Illuminating biology at the nanoscale and systems scale by imaging

Basic Information 2018 Emilio Segrè Lecture with Xiaowei Zhuang Novermeber 7, 2018 Howard Hughes Medical Insititue Investigator David B. Arnold Jr. Professor of Science of Chemistry an...

Knowledge of Variant Annotation

Minor Allele Frequency Minor allele frequency (MAF) is the frequency at which the second most common allele occurs in a given population. They play a surprising role in heritability since MAF v...