PremPS: Predicting the impact of missense mutations on protein stability

DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations

(2019) Ludovica Montanucci et al.   BMC BIOINFORMATICS

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation

(2019) Castrense Savojardo et al.   BRIEFINGS IN BIOINFORMATICS

Quantification of biases in predictions of protein stability changes upon mutations

(2018) Fabrizio Pucci et al.   BIOINFORMATICS

Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation

(2018) Dinara R Usmanova et al.   BIOINFORMATICS

PON-tstab: Protein Variant Stability Predictor. Importance of Training Data Quality

(2018) Yang Yang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Dynamics and structural stability effects of germline PTEN mutations associated with cancer versus autism phenotypes

(2018) Iris Nira Smith et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

On the biases in predictions of protein stability changes upon variations: the INPS test case

(2018) Ludovica Montanucci et al.   BIOINFORMATICS

PremPDI estimates and interprets the effects of missense mutations on protein-DNA interactions

(2018) Ning Zhang et al.   PLoS Computational Biology

Computational tools help improve protein stability but with a solubility tradeoff

(2017) Aron Broom et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Arpeggio: A Web Server for Calculating and Visualising Interatomic Interactions in Protein Structures

(2017) Harry C Jubb et al.   JOURNAL OF MOLECULAR BIOLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

SDM: a server for predicting effects of mutations on protein stability

(2017) Arun Prasad Pandurangan et al.   NUCLEIC ACIDS RESEARCH

Computing disease-linked SOD1 mutations: deciphering protein stability and patient-phenotype relations

(2017) Vijay Kumar et al.   Scientific Reports

INPS-MD: a web server to predict stability of protein variants from sequence and structure: Table 1.

(2016) Castrense Savojardo et al.   BIOINFORMATICS

STRUM: structure-based prediction of protein stability changes upon single-point mutation

(2016) Lijun Quan et al.   BIOINFORMATICS

SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach

(2016) Ivan Getov et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability

(2016) Adi Goldenzweig et al.   MOLECULAR CELL

MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions

(2016) Minghui Li et al.   NUCLEIC ACIDS RESEARCH

Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding

(2016) Yunhui Peng et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation

(2016) Chien-Hao Chiang et al.   Scientific Reports

Towards a “Golden Standard” for computing globin stability: Stability and structure sensitivity of myoglobin mutants

(2015) Kasper P. Kepp   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

INPS: predicting the impact of non-synonymous variations on protein stability from sequence

(2015) Piero Fariselli et al.   BIOINFORMATICS

MAESTRO - multi agent stability prediction upon point mutations

(2015) Josef Laimer et al.   BMC BIOINFORMATICS

cocor: A Comprehensive Solution for the Statistical Comparison of Correlations

(2015) Birk Diedenhofen et al.   PLoS One

NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation

(2014) Manuel Giollo et al.   BMC GENOMICS

Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity

(2014) Minghui Li et al.   Journal of Chemical Theory and Computation

Computing Stability Effects of Mutations in Human Superoxide Dismutase 1

(2014) Kasper P. Kepp   JOURNAL OF PHYSICAL CHEMISTRY B

Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations

(2014) C. Kiel et al.   Molecular Systems Biology

DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach

(2014) D. E. V. Pires et al.   NUCLEIC ACIDS RESEARCH

mCSM: predicting the effects of mutations in proteins using graph-based signatures

(2013) Douglas E. V. Pires et al.   BIOINFORMATICS

Predicting folding free energy changes upon single point mutations

(2012) Zhe Zhang et al.   BIOINFORMATICS

Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases

(2012) Kosuke Hashimoto et al.   HUMAN MUTATION

Structure-based mutant stability predictions on proteins of unknown structure

(2012) Giulia Gonnelli et al.   JOURNAL OF BIOTECHNOLOGY

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

Correlating disease-related mutations to their effect on protein stability: A large-scale analysis of the human proteome

(2011) Rita Casadio et al.   HUMAN MUTATION

SDM--a server for predicting effects of mutations on protein stability and malfunction

(2011) C. L. Worth et al.   NUCLEIC ACIDS RESEARCH

Performance of protein stability predictors

(2010) Sofia Khan et al.   HUMAN MUTATION

A series of PDB related databases for everyday needs

(2010) R. P. Joosten et al.   NUCLEIC ACIDS RESEARCH

Role of conformational sampling in computing mutation-induced changes in protein structure and stability

(2010) Elizabeth H. Kellogg et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0

(2009) Yves Dehouck et al.   BIOINFORMATICS

Correlating protein function and stability through the analysis of single amino acid substitutions

(2009) Yana Bromberg et al.   BMC BIOINFORMATICS

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details

(2009) V. Potapov et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Four Distances between Pairs of Amino Acids Provide a Precise Description of their Interaction

(2009) Mati Cohen et al.   PLoS Computational Biology

Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis

(2008) M. Masso et al.   BIOINFORMATICS

A three-state prediction of single point mutations on protein stability changes

(2008) Emidio Capriotti et al.   BMC BIOINFORMATICS

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

Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction

(2002) Hongyi Zhou et al.   PROTEIN SCIENCE