Copertina

BEER: Biochemical Estimator and Explorer of Residues -- A Comprehensive Software Suite for Protein Sequence Analysis

Fuente: arXiv

Salvato in:

Dettagli Bibliografici
Autore principale:	Mukherjee, Saumyak
Natura:	Preprint
Pubblicazione:	2025
Soggetti:	Biomolecules
Accesso online:	Acceder al recurso
Tags:	Aggiungi Tag Nessun Tag, puoi essere il primo ad aggiungerne!!

Documenti analoghi

Surface Induced Frustration of Inherent Dipolar Order in Nanoconfined Water
di: Mondal, Sayantan, et al.
Pubblicazione: (2025)

A Comprehensive System for Secondary Structure Analysis of Protein Models
di: Kannan, Vedh
Pubblicazione: (2024)

A Comprehensive Review of Protein Language Models
di: Wang, Lei, et al.
Pubblicazione: (2025)

Diffusion Sequence Models for Enhanced Protein Representation and Generation
di: Hallee, Logan, et al.
Pubblicazione: (2025)

Advances of Deep Learning in Protein Science: A Comprehensive Survey
di: Hu, Bozhen, et al.
Pubblicazione: (2024)

SCOP: A Sequence-Structure Contrast-Aware Framework for Protein Function Prediction
di: Ma, Runze, et al.
Pubblicazione: (2024)

STELLA: A Multimodal LLM for Protein Functional Annotation via Unified Sequence-Structure Encoding
di: Xiao, Hongwang, et al.
Pubblicazione: (2025)

MAP Format for Representing Chemical Modifications, Annotations, and Mutations in Protein Sequences: An Extension of the FASTA Format
di: Shendre, Akshay, et al.
Pubblicazione: (2025)

Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design
di: Reidenbach, Danny, et al.
Pubblicazione: (2025)

Integrating Protein Sequence and Expression Level to Analysis Molecular Characterization of Breast Cancer Subtypes
di: Sholehrasa, Hossein, et al.
Pubblicazione: (2024)

Bridging Classical Molecular Dynamics and Quantum Foundations for Comprehensive Protein Structural Analysis
di: Roosan, Don, et al.
Pubblicazione: (2025)

Peptide Sequencing Via Protein Language Models
di: Pham, Thuong Le Hoai, et al.
Pubblicazione: (2024)

MP2D: Constrained Monte Carlo Tree-Guided Diffusion for Multi-Objective Protein Sequence Design
di: Kong, Zitai, et al.
Pubblicazione: (2026)

Single-Sequence-Based Protein Secondary Structure Prediction using One-Hot and Chemical Encodings of Amino Acids
di: Trinh, Hoa, et al.
Pubblicazione: (2024)

QMProt: A Comprehensive Dataset of Quantum Properties for Proteins
di: Sala, Laia Coronas, et al.
Pubblicazione: (2025)

Importance Weighted Expectation-Maximization for Protein Sequence Design
di: Song, Zhenqiao, et al.
Pubblicazione: (2023)

Differential Effects of Sequence-Local versus Nonlocal Charge Patterns on Phase Separation and Conformational Dimensions of Polyampholytes as Model Intrinsically Disordered Proteins
di: Pal, Tanmoy, et al.
Pubblicazione: (2024)

Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
di: Qiu, Jiahao, et al.
Pubblicazione: (2024)

Compact Artificial Neural Network Models for Predicting Protein Residue -- RNA Base Binding
di: Selitskiy, Stanislav
Pubblicazione: (2025)

Pseudo-perplexity in One Fell Swoop for Protein Fitness Estimation
di: Kantroo, Pranav, et al.
Pubblicazione: (2024)

Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
di: Wei, Chen, et al.
Pubblicazione: (2026)

Frequency-Space Mechanics: A Sequence and Coordinate-Free Representation for Protein Function Prediction
di: Reilly, Charles B
Pubblicazione: (2026)

Scoring-Assisted Generative Exploration for Proteins (SAGE-Prot): A Framework for Multi-Objective Protein Optimization via Iterative Sequence Generation and Evaluation
di: Lim, Hocheol, et al.
Pubblicazione: (2025)

Protein FID: Improved Evaluation of Protein Structure Generative Models
di: Faltings, Felix, et al.
Pubblicazione: (2025)

Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation
di: Huguet, Guillaume, et al.
Pubblicazione: (2024)

Beyond ESM2: Graph-Enhanced Protein Sequence Modeling with Efficient Clustering
di: Jiao, Shujian, et al.
Pubblicazione: (2024)

CARE: a Benchmark Suite for the Classification and Retrieval of Enzymes
di: Yang, Jason, et al.
Pubblicazione: (2024)

Fold-switching Proteins
di: Chakravarty, Devlina, et al.
Pubblicazione: (2025)

Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
di: Ko, Eunji, et al.
Pubblicazione: (2024)

Speak to a Protein: An Interactive Multimodal Co-Scientist for Protein Analysis
di: Navarro, Carles, et al.
Pubblicazione: (2025)

A New Route for the Determination of Protein Structure and Function
di: Mejias, S. H., et al.
Pubblicazione: (2024)

Decoding How Proteins Fold
di: Vila, Jorge
Pubblicazione: (2025)

PLD-Tree: Persistent Laplacian Decision Tree for Protein-Protein Binding Free Energy Prediction
di: Xu, Xingjian, et al.
Pubblicazione: (2024)

Generative AI for Controllable Protein Sequence Design: A Survey
di: Zhu, Yiheng, et al.
Pubblicazione: (2024)

Toward the Explainability of Protein Language Models
di: Hunklinger, Andrea, et al.
Pubblicazione: (2025)

Topological Enhancement of Protein Kinetic Stability
di: Especial, João NC, et al.
Pubblicazione: (2026)

Protein Evolution as a Complex System
di: Gall, Barnabas, et al.
Pubblicazione: (2024)

SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins
di: Jing, Bowen, et al.
Pubblicazione: (2026)

Implicitly and Differentiably Representing Protein Surfaces and Interfaces
di: Scott, Cory B., et al.
Pubblicazione: (2025)

Probing the Dark Energy in the Functional Protein Universe
di: Galpern, Ezequiel A., et al.
Pubblicazione: (2025)