Ruth Nussinov

Also affiliated with Cancer Institute (WIA), Frederick National Laboratory for Cancer Research

Biochemistry, Genetics and Molecular BiologyMaterials ScienceComputer Science

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 4%percentile

0.803Author DataRank

Indexed papers

3in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 3 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype

Genome biology(2021)10.1186/s13059-021-02269-3

Top 25%

0.803DataRank

Top 25%22 citations

Junfei Zhao, Jiansong Fang, William R. Martin, Lang Li, Ruth Nussinov +4 more

Papers

Driven by 144 papers — median percentile 75. Top paper: “Artificial intelligence in COVID-19 drug repurposing”.

Artificial intelligence in COVID-19 drug repurposing

The Lancet Digital Health(2020)10.1016/s2589-7500(20)30192-8

N/A

9.8DataRank · unranked

643 citations

Fei Wang, Jian Tang, Ruth Nussinov, Feixiong Cheng, Yadi Zhou

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis

Chemical Reviews(2021)10.1021/acs.chemrev.0c01122

N/A

7.3DataRank · unranked

672 citations

Ayyalusamy Ramamoorthy, Bikash R. Sahoo, Jie Zheng, Peter Faller, John E. Straub +29 more

Novel Approach for Efficient Pharmacophore-Based Virtual Screening: Method and Applications

Journal of Chemical Information and Modeling(2009)10.1021/ci900263d

N/A

5.5DataRank · unranked

140 citations

Dina Schneidman-Duhovny, Yuval Inbar, Ruth Nussinov, Haim J. Wolfson, Oranit Dror

Conserved quartets near 5′ intron junctions in primate nuclear pre-mRNA

Journal of Theoretical Biology(1988)10.1016/s0022-5193(88)80025-0

N/A

1.9DataRank · unranked

28 citations

Ruth Nussinov

My personal mutanome: a computational genomic medicine platform for searching network perturbing alleles linking genotype to phenotype

Genome biology(2021)10.1186/s13059-021-02269-3

Top 25%

0.803DataRank

Top 25%22 citations

Junfei Zhao, Jiansong Fang, William R. Martin, Lang Li, Ruth Nussinov +4 more

The Structural Basis of ATP as an Allosteric Modulator

PLoS Computational Biology(2014)10.1371/journal.pcbi.1003831

N/A

0.672DataRank · unranked

87 citations

Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov +2 more

Temperature-Dependent Molecular Adaptation Features in Proteins

Physiology and Biochemistry of Extremophiles(2014)10.1128/9781555815813.ch6

N/A

0.512DataRank · unranked

7 citations

Sunil Arya, Ruth Nussinov, Sandeep Kumar

The Structural Basis of ATP as an Allosteric Modulator

Biophysical Journal(2015)10.1016/j.bpj.2014.11.2894

N/A

0.483DataRank · unranked

24 citations

Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov +2 more

Tumor-derived RHOA mutants interact with effectors in the GDP-bound state

Nature Communications(2024)10.1038/s41467-024-51445-z

N/A

0.402DataRank · unranked

7 citations

Theresa A. Ramelot, Simge Senyuz, Attila Gürsoy, Hyunbum Jang, Ruth Nussinov +3 more

Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment

Protein Structure Prediction(2008)10.1007/978-1-59745-574-9_5

N/A

0.384DataRank · unranked

4 citations

Ruth Nussinov, Haim J. Wolfson, Maxim Shatsky

Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family

Familial Cancer(2021)10.1007/s10689-021-00267-9

N/A

0.241DataRank · unranked

4 citations

Mai Xu, Michael R. Sargen, Hyunbum Jang, Mingzhen Zhang, Tongwu Zhang +24 more

A Quantum Framework for Protein Binding‐Site Structure Prediction on Utility‐Level Quantum Processors

Advanced Science(2025)10.1002/advs.202513641

N/A

0.165DataRank · unranked

2 citations

Yuxin Yang, W T Martin, Ko-Chow Lin, Zixu Wang, Cheng‐Chang Lu +6 more

Nucleotide-Specific Autoinhibition of Full-Length K-Ras4B Identified by Extensive Conformational Sampling

Frontiers in Molecular Biosciences(2020)10.3389/fmolb.2020.00145

N/A

0DataRank · unranked

16 citations

Franci Merzel, Hyunbum Jang, Ruth Nussinov, David Pérahia, Erika Balog +1 more

RAS Signaling in the PI3K/AKT/MTOR Pathway

Biophysical Journal(2020)10.1016/j.bpj.2019.11.458

N/A

0DataRank · unranked

5 citations

Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov

Ras assemblies and signaling at the membrane

Current Opinion in Structural Biology(2020)10.1016/j.sbi.2020.01.009

N/A

0DataRank · unranked

46 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Phosphorylation and Driver Mutations in PI3Kα and PTEN Autoinhibition

Molecular Cancer Research(2020)10.1158/1541-7786.mcr-20-0818

N/A

0DataRank · unranked

45 citations

Mingzhen Zhang, Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.01.025

N/A

0DataRank · unranked

44 citations

Asma Hakouz, Sukejna Valjevac, Özlem Keskin, Chung‐Jung Tsai, Attila Gürsoy +2 more

PI3K Driver Mutations: A Biophysical Membrane-Centric Perspective

Cancer Research(2020)10.1158/0008-5472.can-20-0911

N/A

0DataRank · unranked

42 citations

Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

The Mystery of Rap1 Suppression of Oncogenic Ras

Trends in cancer(2020)10.1016/j.trecan.2020.02.002

N/A

0DataRank · unranked

39 citations

Hyunbum Jang, Mingzhen Zhang, Chung‐Jung Tsai, Anna Sablina, Ruth Nussinov

High-Affinity Interactions of the nSH3/cSH3 Domains of Grb2 with the C-Terminal Proline-Rich Domain of SOS1

Journal of the American Chemical Society(2020)10.1021/jacs.9b10710

N/A

0DataRank · unranked

37 citations

Hyunbum Jang, Ruth Nussinov, David Fushman, Tsung-Jen Liao

Are Parallel Proliferation Pathways Redundant?

Trends in Biochemical Sciences(2020)10.1016/j.tibs.2020.03.013

N/A

0DataRank · unranked

33 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Active and Inactive Cdc42 Differ in Their Insert Region Conformational Dynamics

Biophysical Journal(2020)10.1016/j.bpj.2020.12.007

N/A

0DataRank · unranked

31 citations

Hyunbum Jang, Ruth Nussinov, Nurit Haspel

A network-based deep learning methodology for stratification of tumor mutations

Bioinformatics(2020)10.1093/bioinformatics/btaa1099

N/A

0DataRank · unranked

27 citations

Zhen Han, Zi‐Ke Zhang, Ruth Nussinov, Feixiong Cheng, Chuang Liu

Computational Investigation of Gantenerumab and Crenezumab Recognition of Aβ Fibrils in Alzheimer’s Disease Brain Tissue

ACS Chemical Neuroscience(2020)10.1021/acschemneuro.0c00364

N/A

0DataRank · unranked

25 citations

Guanghong Wei, Jun Zhao, Ruth Nussinov, Buyong Ma, Yujie Chen

A deep learning framework for elucidating whole-genome chemical interaction space

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.10.08.332346

N/A

0DataRank · unranked

3 citations

Hansaim Lim, Kyra Alyssa Abbu, Yue Qiu, Ruth Nussinov, Lei Xie +1 more

The structural basis of the oncogenic mutant K-Ras4B homodimers

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.09.07.285783

N/A

0DataRank · unranked

2 citations

Meltem Eda Omur, Hyunbum Jang, Ruth Nussinov, Özlem Keskin, Attila Gürsoy +1 more

Anticancer drug resistance: An update and perspective

Drug Resistance Updates(2021)10.1016/j.drup.2021.100796

N/A

0DataRank · unranked

377 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

The mechanism of activation of monomeric B-Raf V600E

Computational and Structural Biotechnology Journal(2021)10.1016/j.csbj.2021.06.007

N/A

0DataRank · unranked

83 citations

Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov, Ryan Maloney

The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane

iScience(2021)10.1016/j.isci.2021.102438

N/A

0DataRank · unranked

64 citations

Iris Nira Smith, Charis Eng, Ruth Nussinov, Hyunbum Jang

The mechanism of Raf activation through dimerization

Chemical Science(2021)10.1039/d1sc03444h

N/A

0DataRank · unranked

57 citations

Ryan Maloney, Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

B-Raf autoinhibition in the presence and absence of 14-3-3

Structure(2021)10.1016/j.str.2021.02.005

N/A

0DataRank · unranked

54 citations

Hyunbum Jang, Zhigang Li, David B. Sacks, Ruth Nussinov, Mingzhen Zhang

Mechanistic Differences of Activation of Rac1P29S and Rac1A159V

The Journal of Physical Chemistry B(2021)10.1021/acs.jpcb.1c00883

N/A

0DataRank · unranked

34 citations

Hyunbum Jang, Ruth Nussinov, Özlem Keskin, Attila Gürsoy, Simge Senyuz

Trastuzumab Blocks the Receiver Function of HER2 Leading to the Population Shifts of HER2-Containing Homodimers and Heterodimers

Antibodies(2021)10.3390/antib10010007

N/A

0DataRank · unranked

24 citations

Nishant Mohan, Ruth Nussinov, Buyong Ma, Wen Jin Wu, Jun Zhao

A new precision medicine initiative at the dawn of exascale computing

Signal Transduction and Targeted Therapy(2021)10.1038/s41392-020-00420-3

N/A

0DataRank · unranked

55 citations

Hyunbum Jang, Guy Nir, Chung‐Jung Tsai, Feixiong Cheng, Ruth Nussinov

Inhibition of Nonfunctional Ras

Cell chemical biology(2021)10.1016/j.chembiol.2020.12.012

N/A

0DataRank · unranked

31 citations

Hyunbum Jang, Attila Gürsoy, Özlem Keskin, Vadim Gaponenko, Ruth Nussinov

Mechanism of activation and the rewired network: New drug design concepts

Medicinal Research Reviews(2021)10.1002/med.21863

N/A

0DataRank · unranked

30 citations

Mingzhen Zhang, Ryan Maloney, Chung‐Jung Tsai, Bengi Ruken Yavuz, Nurcan Tunçbağ +2 more

MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization

Journal of Chemical Information and Modeling(2021)10.1021/acs.jcim.0c01285

N/A

0DataRank · unranked

29 citations

Hansaim Lim, Kyra Alyssa Abbu, Yue Qiu, Ruth Nussinov, Lei Xie +1 more

Signaling in the crowded cell

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.05.009

N/A

0DataRank · unranked

27 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics

The Journal of Physical Chemistry B(2021)10.1021/acs.jpcb.1c00891

N/A

0DataRank · unranked

26 citations

Nurcan Tunçbağ, Hyunbum Jang, Ruth Nussinov, Attila Gürsoy, Özlem Keskin +1 more

Ras isoform-specific expression, chromatin accessibility, and signaling

Biophysical Reviews(2021)10.1007/s12551-021-00817-6

N/A

0DataRank · unranked

26 citations

Mingzhen Zhang, Ryan Maloney, Hyunbum Jang, Ruth Nussinov

The structural basis of Akt PH domain interaction with calmodulin

Biophysical Journal(2021)10.1016/j.bpj.2021.03.018

N/A

0DataRank · unranked

23 citations

Hyunbum Jang, Özlem Keskin, Ruth Nussinov, Attila Gürsoy, Jackson Weako

Interpretable artificial intelligence and exascale molecular dynamics simulations to reveal kinetics: Applications to Alzheimer's disease

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.09.001

N/A

0DataRank · unranked

20 citations

Gloria Sheynkman, Felice C. Lightstone, Ruth Nussinov, Feixiong Cheng, William R. Martin

The dynamic nature of the K-Ras/calmodulin complex can be altered by oncogenic mutations

Current Opinion in Structural Biology(2021)10.1016/j.sbi.2021.06.008

N/A

0DataRank · unranked

15 citations

Nicholas Leschinsky, Hyunbum Jang, Avik Banerjee, Ruth Nussinov, Vadim Gaponenko +1 more

Survivin Expression Is Differentially Regulated by a Selective Cross-talk between RBM38 and miRNAs let-7b or miR-203a

Cancer Research(2021)10.1158/0008-5472.can-20-3157

N/A

0DataRank · unranked

7 citations

Jin Zhang, Buyong Ma, Ruth Nussinov, Xinbin Chen, Christopher A. Lucchesi

Conformational Ensemble of TteAdoCbl Riboswitch Provides Stable Structural Elements for Conformation Selection and Population Shift in Cobalamin Recognition

The Journal of Physical Chemistry B(2021)10.1021/acs.jpcb.1c00038

N/A

0DataRank · unranked

7 citations

Ganggang Bai, Ruth Nussinov, Jienyu Ding, Yun‐Xing Wang, Buyong Ma

SARS-CoV-2 Interactome 3D: A Web interface for 3D visualization and analysis of SARS-CoV-2–human mimicry and interactions

Bioinformatics(2021)10.1093/bioinformatics/btab799

N/A

0DataRank · unranked

5 citations

Ameer Taweel, Zeynep Abali, Ece Tezsezen, Yunus Emre Köroğlu, Chung‐Jung Tsai +4 more

Drugging multiple same-allele driver mutations in cancer

Expert Opinion on Drug Discovery(2021)10.1080/17460441.2021.1905628

N/A

0DataRank · unranked

14 citations

Mingzhen Zhang, Ryan Maloney, Hyunbum Jang, Ruth Nussinov

The mechanism of full activation of tumor suppressor PTEN at the phosphoinositide-enriched membrane

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.06.425565

N/A

0DataRank · unranked

2 citations

Iris Nira Smith, Charis Eng, Ruth Nussinov, Hyunbum Jang

Discovery of Latent Drivers from Double Mutations in Pan-Cancer Data Reveal their Clinical Impact

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.04.02.438239

N/A

0DataRank · unranked

2 citations

Chung‐Jung Tsai, Ruth Nussinov, Nurcan Tunçbağ, Bengi Ruken Yavuz

Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family

medRxiv(2021)10.1101/2021.04.20.21254596

N/A

0DataRank · unranked

1 citations

Mai Xu, Michael R. Sargen, Hyunbum Jang, Mingzhen Zhang, Tongwu Zhang +24 more

Antigen Binding Reshapes Antibody Energy Landscape and Conformation Dynamics

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)(2021)10.1109/bibm52615.2021.9669830

N/A

0DataRank · unranked

1 citations

Ruth Nussinov, Buyong Ma, Amarda Shehu, Kazi Lutful Kabir

Deep generative molecular design reshapes drug discovery

Cell Reports Medicine(2022)10.1016/j.xcrm.2022.100794

N/A

0DataRank · unranked

284 citations

Fei Wang, Yuan Luo, Seung-Gu Kang, Jian Tang, Felice C. Lightstone +5 more

Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework

Nature Machine Intelligence(2022)10.1038/s42256-022-00557-6

N/A

0DataRank · unranked

274 citations

Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov +2 more

Allostery: Allosteric Cancer Drivers and Innovative Allosteric Drugs

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167569

N/A

0DataRank · unranked

69 citations

Mingzhen Zhang, Ryan Maloney, Yonglan Liu, Chung‐Jung Tsai, Hyunbum Jang +1 more

The mechanism of activation of MEK1 by B-Raf and KSR1

Cellular and Molecular Life Sciences(2022)10.1007/s00018-022-04296-0

N/A

0DataRank · unranked

39 citations

Mingzhen Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Ryan Maloney

A New View of Activating Mutations in Cancer

Cancer Research(2022)10.1158/0008-5472.can-22-2125

N/A

0DataRank · unranked

39 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Artificial intelligence approaches to human-microbiome protein–protein interactions

Current Opinion in Structural Biology(2022)10.1016/j.sbi.2022.102328

N/A

0DataRank · unranked

38 citations

Fatma Cankara, Chung‐Jung Tsai, Özlem Keskin, Ruth Nussinov, Attila Gürsoy +1 more

Multiscale Allostery: Basic Mechanisms and Versatility in Diagnostics and Drug Design

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167751

N/A

0DataRank · unranked

33 citations

Ruth Nussinov, Igor N. Berezovsky

Allosteric regulation of autoinhibition and activation of c-Abl

Computational and Structural Biotechnology Journal(2022)10.1016/j.csbj.2022.08.014

N/A

0DataRank · unranked

32 citations

Mingzhen Zhang, Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov, Yonglan Liu

Allostery, and how to define and measure signal transduction

Biophysical Chemistry(2022)10.1016/j.bpc.2022.106766

N/A

0DataRank · unranked

46 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Markov State Models and Molecular Dynamics Simulations Reveal the Conformational Transition of the Intrinsically Disordered Hypervariable Region of K-Ras4B to the Ordered Conformation

Journal of Chemical Information and Modeling(2022)10.1021/acs.jcim.2c00591

N/A

0DataRank · unranked

36 citations

Duan Ni, Jigang Fan, Min-Yu Li, Jian Zhang, Hua Chen +3 more

Neurodevelopmental disorders, immunity, and cancer are connected

iScience(2022)10.1016/j.isci.2022.104492

N/A

0DataRank · unranked

35 citations

Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov

Conformational Dynamics Allows Sampling of an “Active-like” State by Oncogenic K-Ras-GDP

Journal of Molecular Biology(2022)10.1016/j.jmb.2022.167695

N/A

0DataRank · unranked

30 citations

Hyunbum Jang, Nicholas Leschinsky, Ruth Nussinov, Vadim Gaponenko, Patrick Grudzien

The structural basis of BCR-ABL recruitment of GRB2 in chronic myelogenous leukemia

Biophysical Journal(2022)10.1016/j.bpj.2022.05.030

N/A

0DataRank · unranked

23 citations

Hyunbum Jang, Mingzhen Zhang, Chung‐Jung Tsai, Ryan Maloney, Ruth Nussinov +1 more

Host-pathogen protein-nucleic acid interactions: A comprehensive review

Computational and Structural Biotechnology Journal(2022)10.1016/j.csbj.2022.08.001

N/A

0DataRank · unranked

21 citations

Shikha Mittal, Lokesh P. Tripathi, Ruth Nussinov, Shandar Ahmad, Anuja Jain

Higher‐order interactions of Bcr‐Abl can broaden chronic myeloid leukemia (CML) drug repertoire

Protein Science(2022)10.1002/pro.4504

N/A

0DataRank · unranked

20 citations

Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov, Yonglan Liu

Activation of orphan receptor GPR132 induces cell differentiation in acute myeloid leukemia

Cell Death and Disease(2022)10.1038/s41419-022-05434-z

N/A

0DataRank · unranked

20 citations

Jiacheng He, Dan Huang, Yumiao Zhao, Chan Zhang, Xiyun Ye +6 more

IKKα-deficient lung adenocarcinomas generate an immunosuppressive microenvironment by overproducing Treg-inducing cytokines

Proceedings of the National Academy of Sciences(2022)10.1073/pnas.2120956119

N/A

0DataRank · unranked

19 citations

Xin Li, Buyong Ma, Jami Willette‐Brown, Feng Zhu, Chengfei Jiang +11 more

Activation mechanisms of clinically distinct B‐Raf V600E and V600K mutants

Cancer Communications(2022)10.1002/cac2.12395

N/A

0DataRank · unranked

13 citations

Ryan Maloney, Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

Predictive modeling of moonlighting DNA-binding proteins

NAR Genomics and Bioinformatics(2022)10.1093/nargab/lqac091

N/A

0DataRank · unranked

9 citations

Ruth Nussinov, Shandar Ahmad, Dana Mary Varghese

Development of ultra-high affinity bivalent ligands targeting the polo-like kinase 1

RSC Chemical Biology(2022)10.1039/d2cb00153e

N/A

0DataRank · unranked

12 citations

David Hymel, Buyong Ma, Hirokazu Tamamura, Ruth Nussinov, Terrence R. Burke +1 more

Fewer Dimensions, More Structures for Improved Discrete Models of Dynamics of Free versus Antigen-Bound Antibody

Biomolecules(2022)10.3390/biom12071011

N/A

0DataRank · unranked

5 citations

Buyong Ma, Ruth Nussinov, Amarda Shehu, Kazi Lutful Kabir

Accurate prediction of molecular targets using a self-supervised image representation learning framework

Research Square(2022)10.21203/rs.3.rs-1477870/v1

N/A

0DataRank · unranked

11 citations

Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov +2 more

Deep learning for drug repurposing: methods, databases, and applications

arXiv (Cornell University)(2022)10.48550/arxiv.2202.05145

N/A

0DataRank · unranked

11 citations

Xuan Lin, Dongsheng Cao, Xiangxiang Zeng, Philip S. Yu, Lifang He +3 more

Visualizing RNA conformational and architectural heterogeneity in solution

Research Square(2022)10.21203/rs.3.rs-1506923/v1

N/A

0DataRank · unranked

10 citations

Yun-Tzai Lee, Yukti Bhandari, Lixin Fan, Charles D. Schwieters, Ping Yu +8 more

The Mechanism of Activation of MEK1 by B-Raf and KSR1

Research Square(2022)10.21203/rs.3.rs-1412459/v1

N/A

0DataRank · unranked

0 citations

Mingzhen Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Ryan Maloney

Semipres: an Integrated Deep Learning Method of Sequence and 3d Object Detection Models for Host-microbe Interactions by Identification of Protein-protein Contact Residues

Research Square(2022)10.21203/rs.3.rs-2035249/v1

N/A

0DataRank · unranked

0 citations

Özlem Keskin, Ruth Nussinov, Attila Gürsoy, Hansaim Lim

Protein conformational ensembles in function: roles and mechanisms

RSC Chemical Biology(2023)10.1039/d3cb00114h

N/A

0DataRank · unranked

101 citations

Yonglan Liu, Wengang Zhang, Hyunbum Jang, Ruth Nussinov

Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data

Cell Reports Methods(2023)10.1016/j.crmeth.2022.100382

N/A

0DataRank · unranked

98 citations

Jielin Xu, Yajie Meng, Changcheng Lu, Lijun Cai, Xiangxiang Zeng +3 more

AlphaFold, allosteric, and orthosteric drug discovery: Ways forward

Drug Discovery Today(2023)10.1016/j.drudis.2023.103551

N/A

0DataRank · unranked

93 citations

Mingzhen Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov

Visualizing RNA conformational and architectural heterogeneity in solution

Nature Communications(2023)10.1038/s41467-023-36184-x

N/A

0DataRank · unranked

61 citations

Yun-Tzai Lee, Yuba R. Bhandari, Charles D. Schwieters, Lixin Fan, Ping Yu +8 more

Neurodevelopmental disorders, like cancer, are connected to impaired chromatin remodelers, PI3K/mTOR, and PAK1-regulated MAPK

Biophysical Reviews(2023)10.1007/s12551-023-01054-9

N/A

0DataRank · unranked

52 citations

Bengi Ruken Yavuz, M. Kaan Arici, Habibe Cansu Demirel, Mingzhen Zhang, Yonglan Liu +4 more

Neurodevelopmental disorders and cancer networks share pathways, but differ in mechanisms, signaling strength, and outcome

npj Genomic Medicine(2023)10.1038/s41525-023-00377-6

N/A

0DataRank · unranked

39 citations

M. Kaan Arici, Habibe Cansu Demirel, Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov +2 more

Cell phenotypes can be predicted from propensities of protein conformations

Current Opinion in Structural Biology(2023)10.1016/j.sbi.2023.102722

N/A

0DataRank · unranked

33 citations

Yonglan Liu, Wengang Zhang, Hyunbum Jang, Ruth Nussinov

Strategy toward Kinase-Selective Drug Discovery

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.2c01171

N/A

0DataRank · unranked

32 citations

Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance

The Annual Review of Pharmacology and Toxicology(2023)10.1146/annurev-pharmtox-022823-113946

N/A

0DataRank · unranked

30 citations

Hyunbum Jang, Ruth Nussinov

SHP2 clinical phenotype, cancer, or RASopathies, can be predicted by mutant conformational propensities

Cellular and Molecular Life Sciences(2023)10.1007/s00018-023-05052-8

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25 citations

Wengang Zhang, Hyunbum Jang, Ruth Nussinov, Yonglan Liu

The allosteric mechanism of mTOR activation can inform bitopic inhibitor optimization

Chemical Science(2023)10.1039/d3sc04690g

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24 citations

Mingzhen Zhang, Hyunbum Jang, Ruth Nussinov, Yonglan Liu

Pan-cancer clinical impact of latent drivers from double mutations

Communications Biology(2023)10.1038/s42003-023-04519-5

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21 citations

Chung‐Jung Tsai, Ruth Nussinov, Nurcan Tunçbağ, Bengi Ruken Yavuz

Cancer and Autism: How PTEN Mutations Degrade Function at the Membrane and Isoform Expression in the Human Brain

Journal of Molecular Biology(2023)10.1016/j.jmb.2023.168354

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21 citations

Jiaye Chen, Lilia M. Iakoucheva, Ruth Nussinov, Hyunbum Jang

Spatial Mechano‐Signaling Regulation of GTPases through Non‐Degradative Ubiquitination

Advanced Science(2023)10.1002/advs.202303367

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21 citations

Paolo Carai, Tonči Ivanišević, Mingzhen Zhang, Hyunbum Jang, Benoit Lechat +6 more

Molecular mechanism of regulation of RhoA GTPase by phosphorylation of RhoGDI

Biophysical Journal(2023)10.1016/j.bpj.2023.11.018

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12 citations

Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty, Krishnendu Sinha

Small GTPase Ran: Depicting the nucleotide-specific conformational landscape of the functionally important C-terminus

Frontiers in Molecular Biosciences(2023)10.3389/fmolb.2023.1111574

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6 citations

Pedro T. Resende-Lara, Bálint Dudás, Hyunbum Jang, David Pérahia, Ruth Nussinov +2 more

Architectural basis for cylindrical self-assembly governing Plk4-mediated centriole duplication in human cells

Communications Biology(2023)10.1038/s42003-023-05067-8

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4 citations

Liang Zhang, H. Ravishankar, Lixin Fan, Klára Kirsch, Yan Zeng +15 more

Pathogen-driven cancers from a structural perspective: Targeting host-pathogen protein-protein interactions

Frontiers in Oncology(2023)10.3389/fonc.2023.1061595

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3 citations

Ruth Nussinov, Emine Sila Ozdemir

Cell cycle progression mechanisms: slower cyclin-D/CDK4 activation and faster cyclin-E/CDK2

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.08.16.553605

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11 citations

Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Wengang Zhang

How PTEN mutations degrade function at the membrane and life expectancy of carriers of mutations in the human brain

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.26.525746

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7 citations

Jiaye Chen, Lilia M. Iakoucheva, Ruth Nussinov, Hyunbum Jang

Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.16.536718

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2 citations

M. Kaan Arici, Habibe Cansu Demirel, Chung‐Jung Tsai, Hyunbum Jang, Ruth Nussinov +2 more

Molecular Mechanism of Regulation of RhoA GTPase by Phosphorylation of RhoGDI

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.10.540210

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0 citations

Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty, Krishnendu Sinha

A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection

Nature Communications(2024)10.1038/s41467-024-51933-2

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0DataRank · unranked

105 citations

Xuanbai Ren, Xiaoli Luo, Zhuole Wang, Zhen‐lu Li, Xiaoyan Luo +8 more

Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer’s disease

Cell Reports(2024)10.1016/j.celrep.2024.114128

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34 citations

Yuan Hou, Dhruv Gohel, Yadi Zhou, Jielin Xu, Marina Bykova +8 more

A molecular video-derived foundation model for scientific drug discovery

Nature Communications(2024)10.1038/s41467-024-53742-z

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33 citations

Li Zeng, Linlin Hou, Kenli Li, Zhimin Fu, Yunguang Qiu +6 more

Anticancer drugs: How to select small molecule combinations?

Trends in Pharmacological Sciences(2024)10.1016/j.tips.2024.04.012

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29 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

The value of protein allostery in rational anticancer drug design: an update

Expert Opinion on Drug Discovery(2024)10.1080/17460441.2024.2384467

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25 citations

Hyunbum Jang, Ruth Nussinov

Slower CDK4 and faster CDK2 activation in the cell cycle

Structure(2024)10.1016/j.str.2024.04.012

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21 citations

Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Wengang Zhang

K128 ubiquitination constrains RAS activity by expanding its binding interface with GAP proteins

The EMBO Journal(2024)10.1038/s44318-024-00146-w

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17 citations

Mikhail Steklov, Hyunbum Jang, Raj Nayan Sewduth, Amir Florentin, Benoit Lechat +7 more

Review: Cancer and neurodevelopmental disorders: multi-scale reasoning and computational guide

Frontiers in Cell and Developmental Biology(2024)10.3389/fcell.2024.1376639

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15 citations

Bengi Ruken Yavuz, Habibe Cansu Demirel, M. Kaan Arici, Hyunbum Jang, Nurcan Tunçbağ +1 more

Single cell spatial biology over developmental time can decipher pediatric brain pathologies

Neurobiology of Disease(2024)10.1016/j.nbd.2024.106597

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12 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Binding Modalities and Phase-Specific Regulation of Cyclin/Cyclin-Dependent Kinase Complexes in the Cell Cycle

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c03243

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12 citations

Wengang Zhang, Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Michael T. Bergman

Ras, RhoA, and vascular pharmacology in neurodevelopment and aging

Neurochemistry International(2024)10.1016/j.neuint.2024.105883

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3 citations

Hyunbum Jang, Feixiong Cheng, Ruth Nussinov

Disruption of Ca 2+ /calmodulin: KSR1 interaction lowers ERK activation

Protein Science(2024)10.1002/pro.4982

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4 citations

Hyunbum Jang, Zhigang Li, Samar Sayedyahossein, Ryan Maloney, Ruth Nussinov +2 more

A Molecular Video-derived Foundation Model Streamlines Scientific Drug Discovery

Research Square(2024)10.21203/rs.3.rs-3773235/v1

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3 citations

Hongxin Xiang, Li Zeng, Linlin Hou, Kenli Li, Zhimin Fu +6 more

Co-occurring Mutations in Different Genes Can Fuel Oncogenic Signaling and Serve as Metastatic Tumor Markers

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.05.01.592039

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1 citations

Uğur Şahin, Hyunbum Jang, Ruth Nussinov, Nurcan Tunçbağ, Bengi Ruken Yavuz

Molecular principles underlying aggressive cancers

Signal Transduction and Targeted Therapy(2025)10.1038/s41392-025-02129-7

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69 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data

Nucleic Acids Research(2025)10.1093/nar/gkaf138

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38 citations

Changcheng Lu, Shuting Jin, Yajie Meng, Xiangzheng Fu, Xiangxiang Zeng +3 more

Pioneer in Molecular Biology: Conformational Ensembles in Molecular Recognition, Allostery, and Cell Function

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169044

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20 citations

Ruth Nussinov

A Review of 2011 for PLoS Computational Biology

PLoS Computational Biology(2012)10.1371/journal.pcbi.1002387

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0 citations

Chris James Hall, Laura K. Taylor, Ruth Nussinov, Philip E. Bourne, Andy Collings +1 more

Allostery in Disease: Anticancer Drugs, Pockets, and the Tumor Heterogeneity Challenge

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169050

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15 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Allostery: allosteric networks and allosteric signaling bias

Quarterly Reviews of Biophysics(2025)10.1017/s0033583525100061

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14 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Drug resistance and tumor heterogeneity: cells and ensembles

Biophysical Reviews(2025)10.1007/s12551-025-01320-y

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13 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Discovering anticancer drug target combinations via network-informed signaling-based approach

Communications Medicine(2025)10.1038/s43856-025-01150-9

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7 citations

Hyunbum Jang, Ruth Nussinov, Bengi Ruken Yavuz

How residence time works in allosteric drugs

Current Opinion in Structural Biology(2025)10.1016/j.sbi.2025.103149

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6 citations

Hyunbum Jang, Ruth Nussinov

ERK Allosteric Activation: The Importance of Two Ordered Phosphorylation Events

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169130

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8 citations

Hyunbum Jang, Ruth Nussinov, Clil Regev

Allostery in Disease: From Mutations, Mechanisms, and Signalling Partners to Diagnostic and Drug Therapies

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169407

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7 citations

Ruth Nussinov, Igor N. Berezovsky

Distinct Allosteric Networks in CDK4 and CDK6 in the Cell Cycle and in Drug Resistance

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169121

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5 citations

Devin Bradburn, Gretchen Heidebrink, Yonglan Liu, Hyunbum Jang, Ruth Nussinov +2 more

Allostery in Biomolecular Condensates

Journal of Molecular Biology(2025)10.1016/j.jmb.2025.169446

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5 citations

Clil Regev, Hyunbum Jang, Ruth Nussinov

M-Ras distinct activation scenarios: A mechanistic outlook and targeting

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.11.025

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4 citations

Yonglan Liu, Hyunbum Jang, Ruth Nussinov, Liang Xu

Reimagining computational macromolecular modeling: AI-driven approaches

Biophysical Journal(2025)10.1016/j.bpj.2025.11.028

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3 citations

Hyunbum Jang, Ruth Nussinov, Özlem Keskin, Attila Gürsoy, E. Sıla Özdemir

Phosphorylation induces altered protonation states and allosterically regulates Rac1– RhoGDI complex

Protein Science(2025)10.1002/pro.70413

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2 citations

Amit Kumawat, Hyunbum Jang, Ruth Nussinov, Suman Chakrabarty, Krishnendu Sinha

The structural heterogeneity of AKT autoinhibition

Protein Science(2025)10.1002/pro.70420

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2 citations

Meryem Eren, Jackson Weako, Hyunbum Jang, Özlem Keskin, Attila Gürsoy +2 more

Tumors and their microenvironments: Learning from pediatric brain pathologies

Biochimica et Biophysica Acta (BBA) - Reviews on Cancer(2025)10.1016/j.bbcan.2025.189328

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3 citations

Bengi Ruken Yavuz, Hyunbum Jang, Ruth Nussinov

Cellular Mechanisms Underlying Melanoma Brain Metastasis

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.24.689301

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1 citations

Hyunbum Jang, Ruth Nussinov, Bengi Ruken Yavuz

Kinase signaling cascades: an updated mechanistic landscape

Chemical Science(2025)10.1039/d5sc04657b

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18 citations

Clil Regev, Hyunbum Jang, Ruth Nussinov

PI3K inhibitors: review and new strategies

Chemical Science(2020)10.1039/d0sc01676d

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189 citations

Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

Network-based prediction of drug–target interactions using an arbitrary-order proximity embedded deep forest

Bioinformatics(2020)10.1093/bioinformatics/btaa010

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152 citations

Siyi Zhu, Yuan Hou, Pengyue Zhang, Lang Li, Jing Li +5 more

Target identification among known drugs by deep learning from heterogeneous networks

Chemical Science(2020)10.1039/c9sc04336e

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354 citations

Siyi Zhu, Weiqiang Lü, Zehui Liu, Jin Huang, Yadi Zhou +10 more

Harnessing endophenotypes and network medicine for Alzheimer's drug repurposing

Medicinal Research Reviews(2020)10.1002/med.21709

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96 citations

Andrew A. Pieper, Ruth Nussinov, Garam Lee, Lynn M. Bekris, James B. Leverenz +3 more

Individualized genetic network analysis reveals new therapeutic vulnerabilities in 6,700 cancer genomes

PLoS Computational Biology(2020)10.1371/journal.pcbi.1007701

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52 citations

Junfei Zhao, Weiqiang Lü, Yao Dai, Jennifer Hockings, Yadi Zhou +4 more

Structural Features that Distinguish Inactive and Active PI3K Lipid Kinases

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.09.002

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47 citations

Hyunbum Jang, Ruth Nussinov, Mingzhen Zhang

Medin Oligomer Membrane Pore Formation: A Potential Mechanism of Vascular Dysfunction

Biophysical Journal(2020)10.1016/j.bpj.2020.04.026

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16 citations

Hyunbum Jang, Hannah A. Davies, Martin Niemiec, Joe G. N. Garcia, Ruth Nussinov +4 more

The Allosteric Effect in Antibody-Antigen Recognition

Methods in molecular biology(2020)10.1007/978-1-0716-1154-8_11

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14 citations

Ruth Nussinov, Buyong Ma, Jun Zhao

Peptide–MHC Binding Reveals Conserved Allosteric Sites in MHC Class I- and Class II-Restricted T Cell Receptors (TCRs)

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.10.031

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25 citations

Pragati Agnihotri, Sneha Rangarajan, Yi-Hong Chen, Melissa C. Kerzic, Buyong Ma +4 more

SOS1 interacts with Grb2 through regions that induce closed nSH3 conformations

The Journal of Chemical Physics(2020)10.1063/5.0013926

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23 citations

Hyunbum Jang, David Fushman, Ruth Nussinov, Tsung-Jen Liao

Oncogenic K-Ras4B Dimerization Enhances Downstream Mitogen-activated Protein Kinase Signaling

Journal of Molecular Biology(2020)10.1016/j.jmb.2020.01.002

N/A

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20 citations

Cihan Aydın, Ezgi Odabasi, E. Sıla Özdemir, Elif Nur Firat‐Karalar, Hyunbum Jang +6 more

Ruth Nussinov

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