Description
Book SynopsisThis third edition details new and updated methods and protocols on important databases and data mining tools. Chapters guides readers through archives of macromolecular sequences and three-dimensional structures, databases of protein-protein interactions, methods for prediction conformational disorder, mutant thermodynamic stability, aggregation, and drug response. Quality of structural data and their release, soft mechanics applications in biology, and protein flexibility are considered, too, together with pan-genome analyses, rational drug combination screening and Omics Deep Mining. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials, includes step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Data Mining Techniques for the Life Sciences, Third Edition aims to be a practical guide to researches to help furthertheir study in this field.
Table of ContentsPart I: DATABASES
1 EBI data resources
Rolf Apweiler and Amonida Zadissa
2 IMEx databases: displaying molecular interactions into a single, standards-compliant dataset
Pablo Porras, Sandra Orchard and Luana Licata
3 Protein Three-dimensional Structure Databases
Vaishali P. Waman, Christine Orengo, Gerard J. Kleywegt and Arthur M. Lesk
Part II: PREDICTION METHODS
4 Predicting protein conformational disorder and disordered binding sites
Ketty Tamburrini, Giulia Pesce, Juliet Nilsson, Frank Gondelaud, Andrey V. Kajava, Jean-Guy Berrin and Sonia Longhi
5 Profiles of natural and designed protein-like sequences effectively bridge protein sequence gaps: Implications in distant homology detection
Gayatri Kumar, Narayanaswamy Srinivasa and Sankaran Sandhya
6 Turning failures into applications: the problem of protein ΔΔG prediction
Rita Casadio, Castrense Savojardo, Piero Fariselli, Emidio Capriotti and Pier Luigi Martelli
7 Dissecting the genome for drug response prediction
Gerardo Pepe, Chiara Carrino, Luca Parca, Manuela Helmer-Citterich
8 Prediction of the effect of pH on the aggregation and conditional folding of intrinsically disordered proteins with SolupHred and DispHred
Valentín Iglesias, Carlos Pintado-Grima, Jaime Santos, Marc Fornt and Salvador Ventura
9 Extracting the dynamic motion of proteins using Normal Mode Analysis
Jacob A. Bauer and Vladena Bauerová
Part III: DATA QUALITY
10 Pre- and Post- Publication Verification for Reproducible Data Mining in Macromolecular Crystallography
John R Helliwell
11 Soft Statistical Mechanics for Biology
Mariano Bizzarri, Alessandro Giuliani
12 Uses and abuses of the atomic displacement parameters in structural biology
Oliviero Carugo
13 Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes
Erwin Tantoso, Birgit Eisenhaber and Frank Eisenhaber
Part VI: BIG DATA
14 Computational pipeline for rational drug combination screening in patient-derived cells
Paschalis Athanasiadis, Aleksandr Ianevski, Sigrid Skånland and Tero Aittokallio
15 Deep Mining from Omics Data
Abeer Alzubaidi and Jonathan Tepper
