List of works - Yang Shen

Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

scientific article

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

scientific article published on 17 August 2019

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

scientific article published on 23 August 2019

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

scientific article published on 25 October 2019

Blind prediction of interfacial water positions in CAPRI

scientific article

Charge Optimization Theory for Induced-Fit Ligands.

scientific article published on 17 June 2012

ClusPro: performance in CAPRI rounds 6-11 and the new server

scientific article published in December 2007

DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks

scientific article published on 01 September 2019

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.

scientific article published on December 2007

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer

scientific article

Engineering a HER2-specific antibody-drug conjugate to increase lysosomal delivery and therapeutic efficacy

scientific article published on 01 April 2019

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

scientific article published on 12 July 2019

Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts

scientific article published on 21 December 2020

Extracellular Domains I and II of cell-surface glycoprotein CD44 mediate its trans-homophilic dimerization and tumor cluster aggregation

scientific article published on 22 January 2020

G protein-coupled receptors in arthropod vectors: omics and pharmacological approaches to elucidate ligand-receptor interactions and novel organismal functions

scientific article published on 26 May 2018

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

scientific article published in April 2018

Homophilic CD44 interactions mediate tumor cell aggregation and polyclonal metastasis in patient-derived breast cancer models

scientific article published on 25 October 2018

Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.

scientific article published on February 2015

Overcoming mutation-based resistance to antiandrogens with rational drug design

scientific article (publication date: 9 April 2013)

Predicting pathogenicity of missense variants with weakly supervised regression

scientific article published on 07 August 2019

Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

scientific article published on 15 November 2016

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

scientific article

Protein docking by the underestimation of free energy funnels in the space of encounter complexes

scientific article

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.

scientific article published on April 2007

Testing the substrate-envelope hypothesis with designed pairs of compounds.

scientific article published on 26 September 2013

The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells.

scientific article published on 29 November 2018

Towards aspirin-inspired self-immolating molecules which target the cyclooxygenases

scientific article

iCFN: an efficient exact algorithm for multistate protein design

scholarly article by Mostafa Karimi published in September 2018

List of works by Yang Shen

Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment

Blind prediction of interfacial water positions in CAPRI

Charge Optimization Theory for Induced-Fit Ligands.

ClusPro: performance in CAPRI rounds 6-11 and the new server

DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks

Docking with PIPER and refinement with SDU in rounds 6-11 of CAPRI.

ESR1 ligand-binding domain mutations in hormone-resistant breast cancer

Engineering a HER2-specific antibody-drug conjugate to increase lysosomal delivery and therapeutic efficacy

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

Explainable Deep Relational Networks for Predicting Compound-Protein Affinities and Contacts

Extracellular Domains I and II of cell-surface glycoprotein CD44 mediate its trans-homophilic dimerization and tumor cluster aggregation

G protein-coupled receptors in arthropod vectors: omics and pharmacological approaches to elucidate ligand-receptor interactions and novel organismal functions

Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

Homophilic CD44 interactions mediate tumor cell aggregation and polyclonal metastasis in patient-derived breast cancer models

Molecular mechanisms and design principles for promiscuous inhibitors to avoid drug resistance: lessons learned from HIV-1 protease inhibition.

Overcoming mutation-based resistance to antiandrogens with rational drug design

Predicting pathogenicity of missense variants with weakly supervised regression

Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility.

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Protein docking by the underestimation of free energy funnels in the space of encounter complexes

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking.

Testing the substrate-envelope hypothesis with designed pairs of compounds.

The SERM/SERD bazedoxifene disrupts ESR1 helix 12 to overcome acquired hormone resistance in breast cancer cells.

Towards aspirin-inspired self-immolating molecules which target the cyclooxygenases

iCFN: an efficient exact algorithm for multistate protein design