pdCSM-PPI: Using Graph-Based Signatures to Identify Protein–Protein Interaction Inhibitors

SMMPPI: a machine learning-based approach for prediction of modulators of protein–protein interactions and its application for identification of novel inhibitors for RBD:hACE2 interactions in SARS-CoV-2

(2021) Priya Gupta et al.   BRIEFINGS IN BIOINFORMATICS

mmCSM-AB: guiding rational antibody engineering through multiple point mutations

(2020) Yoochan Myung et al.   NUCLEIC ACIDS RESEARCH

mycoCSM: Using Graph-Based Signatures to Identify Safe Potent Hits against Mycobacteria

(2020) Douglas E. V. Pires et al.   Journal of Chemical Information and Modeling

DynaMut2 : Assessing changes in stability and flexibility upon single and multiple point missense mutations

(2020) Carlos H.M. Rodrigues et al.   PROTEIN SCIENCE

The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators

(2020) Rachel Torchet et al.   BIOINFORMATICS

mCSM-PPI2: predicting the effects of mutations on protein–protein interactions

(2019) Carlos H M Rodrigues et al.   NUCLEIC ACIDS RESEARCH

All-Assay-Max2 pQSAR: Activity Predictions as Accurate as Four-Concentration IC50s for 8558 Novartis Assays

(2019) Eric J. Martin et al.   Journal of Chemical Information and Modeling

mCSM-AB2: guiding rational antibody design using graph-based signatures

(2019) Yoochan Myung et al.   BIOINFORMATICS

dendPoint: a web resource for dendrimer pharmacokinetics investigation and prediction

(2019) Lisa M. Kaminskas et al.   Scientific Reports

SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript

(2018) Daniel Probst et al.   Journal of Chemical Information and Modeling

DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability

(2018) Carlos HM Rodrigues et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: towards direct deposition of bioassay data

(2018) David Mendez et al.   NUCLEIC ACIDS RESEARCH

PPIMpred: a web server for high-throughput screening of small molecules targeting protein–protein interaction

(2017) Tanmoy Jana et al.   Royal Society Open Science

Kekule.js: An Open Source JavaScript Chemoinformatics Toolkit

(2016) Chen Jiang et al.   Journal of Chemical Information and Modeling

mCSM-AB: a web server for predicting antibody–antigen affinity changes upon mutation with graph-based signatures

(2016) Douglas E.V. Pires et al.   NUCLEIC ACIDS RESEARCH

2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein–protein interactions

(2016) Marie-Jeanne Basse et al.   Database-The Journal of Biological Databases and Curation

Structure-Based Analysis Reveals Cancer Missense Mutations Target Protein Interaction Interfaces

(2016) H. Billur Engin et al.   PLoS One

pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures

(2015) Douglas E. V. Pires et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flexibility and small pockets at protein–protein interfaces: New insights into druggability

(2015) Harry Jubb et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Insights into Disease-Associated Mutations in the Human Proteome through Protein Structural Analysis

(2015) Mu Gao et al.   STRUCTURE

Which Three-Dimensional Characteristics Make Efficient Inhibitors of Protein–Protein Interactions?

(2014) Mélaine A. Kuenemann et al.   Journal of Chemical Information and Modeling

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

aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction

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

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

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

2P2IHUNTER: a tool for filtering orthosteric protein-protein interaction modulators via a dedicated support vector machine

(2013) V. Hamon et al.   Journal of the Royal Society Interface

TIMBAL v2: update of a database holding small molecules modulating protein–protein interactions

(2013) Alicia P. Higueruelo et al.   Database-The Journal of Biological Databases and Curation

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

(2011) Douglas EV Pires et al.   BMC GENOMICS

Chemical and structural lessons from recent successes in protein–protein interaction inhibition (2P2I)

(2011) Xavier Morelli et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

(2011) Alessia David et al.   HUMAN MUTATION

Phase I Study of Navitoclax (ABT-263), a Novel Bcl-2 Family Inhibitor, in Patients With Small-Cell Lung Cancer and Other Solid Tumors

(2011) Leena Gandhi et al.   JOURNAL OF CLINICAL ONCOLOGY

Atomic Interactions and Profile of Small Molecules Disrupting Protein-Protein Interfaces: the TIMBAL Database

(2009) Alícia P. Higueruelo et al.   Chemical Biology & Drug Design

A protein–protein interaction network of transcription factors acting during liver cell proliferation

(2008) Jin Gao et al.   GENOMICS