Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning

Predicting the functional consequences of cancer-associated amino acid substitutions

(2013) Hashem A. Shihab et al.   BIOINFORMATICS

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions

(2013) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations

(2013) Yves Dehouck et al.   NUCLEIC ACIDS RESEARCH

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions

(2013) Rocco Moretti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies

(2013) Miao-Xin Li et al.   PLoS Genetics

SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models

(2012) Iain H. Moal et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Identification of Novel Type 1 Diabetes Candidate Genes by Integrating Genome-Wide Association Data, Protein-Protein Interactions, and Human Pancreatic Islet Gene Expression

(2012) R. Bergholdt et al.   DIABETES

A Combined Functional Annotation Score for Non-Synonymous Variants

(2012) Margarida C. Lopes et al.   HUMAN HEREDITY

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

(2012) Brian J. O’Roak et al.   NATURE

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

Improving the Assessment of the Outcome of Nonsynonymous SNVs with a Consensus Deleteriousness Score, Condel

(2011) Abel González-Pérez et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GOAP: A Generalized Orientation-Dependent, All-Atom Statistical Potential for Protein Structure Prediction

(2011) Hongyi Zhou et al.   BIOPHYSICAL JOURNAL

Three-dimensional modeling of protein interactions and complexes is going ‘omics

(2011) Amelie Stein et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Protein-protein interaction sites are hot spots for disease-associated nonsynonymous SNPs

(2011) Alessia David et al.   HUMAN MUTATION

DOMMINO: a database of macromolecular interactions

(2011) X. Kuang et al.   NUCLEIC ACIDS RESEARCH

Predicting the functional impact of protein mutations: application to cancer genomics

(2011) Boris Reva et al.   NUCLEIC ACIDS RESEARCH

RAD51C Germline Mutations in Breast and Ovarian Cancer Cases from High-Risk Families

(2011) Jessica Clague et al.   PLoS One

A structure-based benchmark for protein-protein binding affinity

(2011) Panagiotis L. Kastritis et al.   PROTEIN SCIENCE

Feature-based classification of native and non-native protein-protein interactions: Comparing supervised and semi-supervised learning approaches

(2011) Nan Zhao et al.   PROTEOMICS

Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin

(2011) S. J. Fleishman et al.   SCIENCE

Kinetic Stability May Determine the Interaction Dynamics of the Bifunctional Protein DCoH1, the Dimerization Cofactor of the Transcription Factor HNF-1α,

(2010) H. Rho et al.   BIOCHEMISTRY

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins

(2010) Y. Qi et al.   BIOINFORMATICS

DROP: an SVM domain linker predictor trained with optimal features selected by random forest

(2010) Teppei Ebina et al.   BIOINFORMATICS

Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models

(2010) Cornelia Caragea et al.   BMC BIOINFORMATICS

Computational Mutagenesis Studies of Hammerhead Ribozyme Catalysis

(2010) Tai-Sung Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Knowledge-based computational mutagenesis for predicting the disease potential of human non-synonymous single nucleotide polymorphisms

(2010) Majid Masso et al.   JOURNAL OF THEORETICAL BIOLOGY

Protein–protein docking tested in blind predictions: the CAPRI experiment

(2010) Joël Janin   Molecular BioSystems

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Comparing experimental and computational alanine scanning techniques for probing a prototypical protein–protein interaction

(2010) Richard T. Bradshaw et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Accounting for conformational entropy in predicting binding free energies of protein-protein interactions

(2010) Hetunandan Kamisetty et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions

(2009) Shaolei Teng et al.   BIOPHYSICAL JOURNAL

Semi-supervised protein subcellular localization

(2009) Qian Xu et al.   BMC BIOINFORMATICS

XRCC3 Thr241Met polymorphism and breast cancer risk: a meta-analysis

(2009) Konstantinos P. Economopoulos et al.   BREAST CANCER RESEARCH AND TREATMENT

HNF1A gene polymorphisms and cardiovascular risk factors in individuals with late-onset autosomal dominant diabetes: a cross-sectional study

(2009) Fernando MA Giuffrida et al.   Cardiovascular Diabetology

Human genetic variation and its contribution to complex traits

(2009) Kelly A. Frazer et al.   NATURE REVIEWS GENETICS

Functional characterization of the RAD51D E233G genetic variant

(2009) Aditi Nadkarni et al.   Pharmacogenetics and Genomics

Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature

(2008) Jiansheng Wu et al.   BIOINFORMATICS

SNAP predicts effect of mutations on protein function

(2008) Yana Bromberg et al.   BIOINFORMATICS

A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification

(2008) Alexander Statnikov et al.   BMC BIOINFORMATICS

Predicting free energy changes using structural ensembles

(2008) Alexander Benedix et al.   NATURE METHODS

Ab initio folding of terminal segments with secondary structures reveals the fine difference between two closely related all-atom statistical energy functions

(2008) Yuedong Yang et al.   PROTEIN SCIENCE

Statistical geometry based prediction of nonsynonymous SNP functional effects using random forest and neuro-fuzzy classifiers

(2008) Maxim Barenboim et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

OPUS-PSP: An Orientation-dependent Statistical All-atom Potential Derived from Side-chain Packing

(2007) Mingyang Lu et al.   JOURNAL OF MOLECULAR BIOLOGY