BetaCitation Atlas

RESEARCH PAPER · Science · 2020

Protein storytelling through physics

Emiliano Brini, Carlos L. Simmerling, Ken A. Dill

Read original paper ↗

See where this research leads.

80 direct citing papers in this saved network. Explore the next layer with second-order citations.

Open in your workspace →Saved 2026-10-14 · complete coverage
Filter Citing Papers
Press Enter or comma to add · × to remove · searches titles and available abstracts
Journals
All journals
Most represented first · select one or more
Explore Terms In These PapersHide SuggestionsShow Suggestions

Original and current center papers stay visible as anchors.
Numbers show citations received
42 direct citing works

Protein storytelling through physicsOriginalFrom crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain18Quantum States in Templated Biological Processes0Protein Unfolding and Aggregation near a Hydrophobic Interface55Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis678Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field70Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations43Fighting viruses with computers, right now20Biomolecular modeling thrives in the age of technology109Principled Mechanistic Explanations in Biology: A Case Study of Alzheimer's Disease0Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis18Quantitative predictions from molecular simulations using explicit or implicit interactions33The Protein Folding Problem: The Role of Theory108A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure–function relationships of matrix metalloproteinase collagenolysis21Highly accurate protein structure prediction with AlphaFold43269Protein structure prediction by AlphaFold 2: are attention and symmetries all you need?67Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.0Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.0The Proteome Folding Problem and Cellular Proteostasis37Contemporary biomedical engineering perspective on volitional evolution for human radiotolerance enhancement beyond low-earth orbit4Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins29Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure5Deep learning opens up protein science’s next frontiers12Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation1Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins5An Examination of Mechanisms by which Synonymous Mutations may Alter Protein Levels, Structure and Functions4New Horizons in Studying the Cellular Mechanisms of Alzheimer’s Disease1Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins13Stability and Conformational Memory of Electrosprayed and Rehydrated Bacteriophage Ms2 Virus Coat Proteins0An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation11Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers20Computational Studies of Lipid Droplets45Heterogeneity in Protein Folding and Unfolding Reactions75Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir9Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions14SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK19Accurate and efficient constrained molecular dynamics of polymers through Newton’s method and special purpose code0Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation25Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide13Back and forth modeling through biological scales1Enabling technology and core theory of synthetic biology65Protein structure prediction using the evolutionary algorithm USPEX9Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations3Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code6MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands5The nucleotide excision repair proteins through the lens of molecular dynamics simulations8ProtCool 2.0: um gerador de protocolo para ancoragem e simulações de dinâmica molecular em complexos proteína-ligante em versão web0AI 2 BMD: efficient characterization of protein dynamics with ab initio accuracy2Manifold learning in atomistic simulations: a conceptual review19Biochemist Investigates Protein Folding1Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir3Accelerating Kinetics with Time-Reversal Path Sampling5Trends Innovations Challenges in Employing Interdisciplinary Approaches to Biomedical Sciences4An integrative approach to understand structural dynamics of protein molecular machines across spatiotemporal scales0Advancing Molecular Dynamics: Toward Standardization, Integration, and Data Accessibility in Structural Biology8Multi-scale Simulation of Complex Systems: A Perspective of Integrating Knowledge and Data43CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention7Assessing pH-Dependent Conformational Changes in the Fusion Peptide Proximal Region of the SARS-CoV-2 Spike Glycoprotein5Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices12Multi-method analysis revealed the mechanism of substrate selectivity in NHase: A gatekeeper residue at the activity center7Decomposition of Forces in Protein: Methodology and General Properties4Machine learning-assisted investigations toward polymer synthesis2Pouring SIRAH on NAMD6Self-organizing maps of unbiased ligand–target binding pathways and kinetics4Computational approach based on freely accessible tools for antimicrobial drug design2Ab initio characterization of protein molecular dynamics with AI2BMD162The protein universe in 3D2Enzymes can activate and mobilize the cytoplasmic environment across scales8Characterization of the activity of the IRT1 transporter involved in metal uptake in the hyperaccumulator species Noccaea caerulescens0DeepUSPS : Deep Learning‐Empowered Unconstrained‐Structural Protein Sequence Design0Biomolecule-functionalized dental implant surfaces: Towards augmenting soft tissue integration15Branched DNA for disease diagnosis and therapy3Unfolded to Folded: Unraveling the Secrets of Protein Folding with ProteusFold0Challenging AlphaFold in predicting proteins with large-scale allosteric transitions11Announcement: Journal of Structural Biology: Paper of the year0Deep Learning Meets Synthetic Biology: Applications Across Molecular, Cellular, and Metabolic Scales0Scalable Generative Modeling of Protein Ligand Trajectories via Graph Neural Diffusion Networks0Seeking Biology's Physics Stories: Simplify, Simplify0Navigating the uncharted: AI-driven advances in protein structure, dynamics, interactions and ligand interactions for understudied families1Oleuropein aglycone aldehyde as a SARS-CoV-2 main protease inhibitor3Engineered Injectable Hydrogel Platform for Tailoring the Osteoarthritis Microenvironment0

Arrows point to the paper being cited. Selecting a paper shows its incoming citations and its known path back to the original paper.

Drag to pan · Use + / − to zoom · Escape to close43 nodes / 53 citation links
Browse Matching Papers

Papers that cite this work

80 direct citing papers saved. Showing the first 50 here; use Browse Matching Papers in the map for all loaded papers.

  1. From crystallographic data to the solution structure of photoreceptors: the case of the AppA BLUF domain

    Chemical Science · 2021-01-01

    Shaima Hashem, Veronica Macaluso, Michele Nottoli, Filippo Lipparini, Lorenzo Cupellini, Benedetta Mennucci

    Read original paper ↗ ·

  2. Quantum States in Templated Biological Processes

    Open Journal of Biophysics · 2021-01-01

    R. Englman

    Read original paper ↗ ·

  3. Protein Unfolding and Aggregation near a Hydrophobic Interface

    Polymers · 2021-01-03

    David March, Valentino Bianco, Giancarlo Franzese

    Read original paper ↗ ·

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

    Chemical Reviews · 2021-02-05

    Phuong Hoang Nguyen, Ayyalusamy Ramamoorthy, Bikash Ranjan Sahoo, Jie Zheng, Peter Faller, John E. Straub, Laura Domı́nguez, Joan‐Emma Shea, Nikolay V. Dokholyan, Alfonso De Simone, Buyong Ma, Ruth Nussinov, Saeed Najafi, Sơn Tùng Ngô, Antoine Loquet, Mara Chiricotto, Pritam Ganguly, James McCarty, Mai Suan Li, Carol K. Hall, Yiming Wang, Yifat Miller, Simone Melchionna, Birgit Habenstein, Štěpán Timr, Jiaxing Chen, Brianna Hnath, Birgit Strodel, Rakez Kayed, Sylvain Lesné, Guanghong Wei, Fabio Sterpone, Andrew J. Doig, Philippe Derreumaux

    Read original paper ↗ ·

  5. Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field

    Annual Review of Biophysics · 2021-02-19

    Tamar Schlick A, Stephanie Portillo‐Ledesma, Christopher G. Myers, Lauren Beljak, Justin B. Chen, Sami Dakhel, Daniel Darling, Sayak Ghosh, Joseph W. Hall, Mikaeel Jan, Emily Liang, Sera Saju, Mackenzie Vohr, Chris Wu, Yifan Xu, Eva Xue

    Read original paper ↗ ·

  6. Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations

    The Journal of Physical Chemistry B · 2021-04-29

    Kiyoshi Yagi, Shingo Ito, Yuji Sugita

    Read original paper ↗ ·

  7. Fighting viruses with computers, right now

    Current Opinion in Virology · 2021-05-08

    Matías Rodrigo Machado, Sergio Pantano

    Read original paper ↗ ·

  8. Biomolecular modeling thrives in the age of technology

    Nature Computational Science · 2021-05-20

    Tamar Schlick A, Stephanie Portillo‐Ledesma

    Read original paper ↗ ·

  9. Principled Mechanistic Explanations in Biology: A Case Study of Alzheimer's Disease

    PhilSci-Archive (University of Pittsburgh) · 2021-05-29

    Sepehr Ehsani

    Read original paper ↗ ·

  10. Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis

    The Journal of Physical Chemistry B · 2021-06-18

    Siyoung Kim, Gregory A. Voth

    Read original paper ↗ ·

  11. Quantitative predictions from molecular simulations using explicit or implicit interactions

    Wiley Interdisciplinary Reviews Computational Molecular Science · 2021-06-22

    David van der Spoel, Jin Zhang, Haiyang Zhang

    Read original paper ↗ ·

  12. The Protein Folding Problem: The Role of Theory

    Journal of Molecular Biology · 2021-07-02

    Roy Nassar, Gregory L. Dignon, Rostam M. Razban, Ken A. Dill

    Read original paper ↗ ·

  13. A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure–function relationships of matrix metalloproteinase collagenolysis

    JBIC Journal of Biological Inorganic Chemistry · 2021-07-06

    Ann Varghese, Shobhit S. Chaturvedi, Gregg Fields, Tatyana G. Karabencheva‐Christova

    Read original paper ↗ ·

  14. Highly accurate protein structure prediction with AlphaFold

    Nature · 2021-07-15

    John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, Alex Bridgland, Clemens Meyer, Simon Köhl, Andrew J. Ballard, Andrew Cowie, Bernardino Romera‐Paredes, Stanislav Nikolov, Rishub Jain, Jonas Adler, Trevor Back, Stig Petersen, David Reiman, Ellen Clancy, Michał Zieliński, Martin Steinegger, Michalina Pacholska, Tamas Berghammer, Sebastian W. Bodenstein, David Silver, Oriol Vinyals, Andrew Senior, Koray Kavukcuoglu, Pushmeet Kohli, Demis Hassabis

    Read original paper ↗ ·

  15. Protein structure prediction by AlphaFold 2: are attention and symmetries all you need?

    Acta Crystallographica Section D Structural Biology · 2021-07-29

    Nazim Bouatta, Peter Karl Sorger, Mohammed AlQuraishi

    Read original paper ↗ ·

  16. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.

    Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2021-07-31

    Sutirtha Chakraborty

    Read original paper ↗ ·

  17. Faculty Opinions recommendation of Highly accurate protein structure prediction with AlphaFold.

    Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · 2021-08-01

    Arockia Jeyaprakash Arulanandam

    Read original paper ↗ ·

  18. The Proteome Folding Problem and Cellular Proteostasis

    Journal of Molecular Biology · 2021-08-13

    Evan T. Powers, Lila M. Gierasch

    Read original paper ↗ ·

  19. Contemporary biomedical engineering perspective on volitional evolution for human radiotolerance enhancement beyond low-earth orbit

    Synthetic Biology · 2021-09-01

    Alexander M. Borg, John E. Baker

    Read original paper ↗ ·

  20. Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins

    PLoS ONE · 2021-09-02

    Joe G. Greener, David T. Jones

    Read original paper ↗ ·

  21. Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure

    Journal of Chemical Theory and Computation · 2021-09-08

    Christopher C. Walker, Garrett A. Meek, Theodore L. Fobe, Michael R. Shirts

    Read original paper ↗ ·

  22. Deep learning opens up protein science’s next frontiers

    Physics Today · 2021-09-24

    Johanna L. Miller

    Read original paper ↗ ·

  23. Water Contribution to the Protein Folding and Its Relevance in Protein Design and Protein Aggregation

    Springer proceedings in physics · 2021-09-27

    Giancarlo Franzese, Joan Àguila Rojas, Valentino Bianco, Ivan Coluzza B

    Read original paper ↗ ·

  24. Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins

    Journal of Chemical Theory and Computation · 2021-12-08

    Cong Liu, Emiliano Brini, Ken A. Dill

    Read original paper ↗ ·

  25. An Examination of Mechanisms by which Synonymous Mutations may Alter Protein Levels, Structure and Functions

    Springer eBooks · 2022-01-01

    Yiming J. Zhang, Zsuzsa Bebők

    Read original paper ↗ ·

  26. New Horizons in Studying the Cellular Mechanisms of Alzheimer’s Disease

    Future of business and finance · 2022-01-01

    Sepehr Ehsani

    Read original paper ↗ ·

  27. Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins

    Current Research in Structural Biology · 2022-01-01

    Maxim N. Brodmerkel, Emiliano De Santis, Charlotte Uetrecht, Carl Caleman, Erik G. Marklund

    Read original paper ↗ ·

  28. Stability and Conformational Memory of Electrosprayed and Rehydrated Bacteriophage Ms2 Virus Coat Proteins

    SSRN Electronic Journal · 2022-01-01

    Maxim N. Brodmerkel, Emiliano De Santis, Carl Caleman, Charlotte Uetrecht, Erik G. Marklund

    Read original paper ↗ ·

  29. An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation

    eLife · 2022-01-20

    Rui Fang, Jason Hon, Mengying Zhou, Ying Lu

    Read original paper ↗ ·

  30. Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers

    Journal of Chemical Theory and Computation · 2022-02-08

    Roy Nassar, Emiliano Brini, Sridip Parui, Cong Liu, Gregory L. Dignon, Ken A. Dill

    Read original paper ↗ ·

  31. Computational Studies of Lipid Droplets

    The Journal of Physical Chemistry B · 2022-03-09

    Siyoung Kim, Jessica M. J. Swanson, Gregory A. Voth

    Read original paper ↗ ·

  32. Heterogeneity in Protein Folding and Unfolding Reactions

    Chemical Reviews · 2022-03-11

    Sandhya Bhatia, Jayant B. Udgaonkar

    Read original paper ↗ ·

  33. Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir

    Journal of Chemical Theory and Computation · 2022-05-03

    kenneth lam, Koushik Kasavajhala, Sarah Gunasekera, Carlos L. Simmerling

    Read original paper ↗ ·

  34. Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

    Molecules · 2022-09-05

    Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita

    Read original paper ↗ ·

  35. SP-A binding to the SARS-CoV-2 spike protein using hybrid quantum and classical in silico modeling and molecular pruning by Quantum Approximate Optimization Algorithm (QAOA) Based MaxCut with ZDOCK

    Frontiers in Immunology · 2022-09-13

    Sona Aramyan, Kirk McGregor, Samarth Sandeep, Angela Haczku

    Read original paper ↗ ·

  36. Accurate and efficient constrained molecular dynamics of polymers through Newton’s method and special purpose code

    bioRxiv (Cold Spring Harbor Laboratory) · 2022-09-28

    Lorién López‐Villellas, Carl Christian Kjelgaard Mikkelsen, Juan José Galano‐Frutos, Santiago Marco‐Sola, Jesús Alastruey-Benedé, Pablo Ibáñez, Miquel Moretó, Javier Sancho, Pablo García‐Risueño

    Read original paper ↗ ·

  37. Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation

    Proceedings of the National Academy of Sciences · 2022-10-03

    Tae-Eun Kim, Kotaro Tsuboyama, Scott Houliston, Cydney M. Martell, Claire M. Phoumyvong, Alexander S. Lemak, Hugh K. Haddox, C.H. Arrowsmith, Gabriel J. Rocklin

    Read original paper ↗ ·

  38. Mechanistic basis of the increased methylation activity of the SETD2 protein lysine methyltransferase towards a designed super-substrate peptide

    Communications Chemistry · 2022-10-28

    Philipp Schnee, Michel Choudalakis, Sara Weirich, Mina S. Khella, Henrique F. Carvalho, Jürgen Pleiss, Albert Jeltsch

    Read original paper ↗ ·

  39. Back and forth modeling through biological scales

    Biochemical and Biophysical Research Communications · 2022-11-04

    Sergio Pantano

    Read original paper ↗ ·

  40. Enabling technology and core theory of synthetic biology

    Science China Life Sciences · 2023-02-06

    Xian‐En Zhang, Chenli Liu, Junbiao Dai, Ying‐Jin Yuan, Caixia Gao, Yan Fang Feng, Bian Wu, Ping Wei, Chun You, Xiaowo Wang, Tong Si

    Read original paper ↗ ·

  41. Protein structure prediction using the evolutionary algorithm USPEX

    Proteins Structure Function and Bioinformatics · 2023-02-13

    Pavel Rachitskii, Ivan A. Kruglov, Alexei V. Finkelstein, Артем Ромаевич Оганов

    Read original paper ↗ ·

  42. Exploring the Transferability of Replica Exchange Structure Reservoirs to Accelerate Generation of Ensembles for Alternate Hamiltonians or Protein Mutations

    Journal of Chemical Theory and Computation · 2023-03-02

    Koushik Kasavajhala, Carlos L. Simmerling

    Read original paper ↗ ·

  43. Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

    Computer Physics Communications · 2023-03-29

    Lorién López‐Villellas, Carl Christian Kjelgaard Mikkelsen, Juan José Galano‐Frutos, Santiago Marco‐Sola, Jesús Alastruey-Benedé, Pablo Ibáñez, Miquel Moretó, Javier Sancho, Pablo García‐Risueño

    Read original paper ↗ ·

  44. MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands

    Journal of Chemical Information and Modeling · 2023-04-24

    Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill

    Read original paper ↗ ·

  45. The nucleotide excision repair proteins through the lens of molecular dynamics simulations

    DNA repair · 2023-04-26

    Éderson Sales Moreira Pinto, Mathias J. Krause, Márcio Dorn, Bruno César Feltes

    Read original paper ↗ ·

  46. ProtCool 2.0: um gerador de protocolo para ancoragem e simulações de dinâmica molecular em complexos proteína-ligante em versão web

    Unknown journal · 2023-06-27

    Moises Pinheiro Souza, Levi Medeiros Magny, Fabiana Costa Guedes, Carlos Henrique da Silveira

    Read original paper ↗ ·

  47. AI 2 BMD: efficient characterization of protein dynamics with ab initio accuracy

    bioRxiv (Cold Spring Harbor Laboratory) · 2023-07-13

    Tong Wang, Xinheng He, Mingyu Li, Yusong Wang, Zun Wang, Shaoning Li, Bin Shao, Tie‐Yan Liu

    Read original paper ↗ ·

  48. Manifold learning in atomistic simulations: a conceptual review

    Machine Learning Science and Technology · 2023-07-17

    Jakub Rydzewski, Ming Chen, Ómar Valsson

    Read original paper ↗ ·

  49. Biochemist Investigates Protein Folding

    Biomedical Materials & Devices · 2023-08-02

    Richard F. Dods

    Read original paper ↗ ·

  50. Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir

    Journal of Chemical Theory and Computation · 2023-10-13

    Juan Alcantara, Kelley Chiu, John D. Bickel, Robert C. Rizzo, Carlos L. Simmerling

    Read original paper ↗ ·
More citing papers →
Citation Atlas · A map of research, not a ranking.