Results for “diffdock”

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Interact with Paddock — AI agent orchestration dashboard. Use when registering agents, managing tasks, syncing skills, or querying agent/task status via Paddock APIs.

Turn a weak/cheap "Flash" model into a "Pro" performer by wrapping HKUDS UpSkill — captures agent session failures, has a strong Teacher model analyze them and draft a skill, then validates it against the weak Student model in a closed Ralph Loop (up to 3 rounds) before storing it for automatic reuse. Use when the user wants to install UpSkill, run `/upskill-init`, `/upskill-configure`, `/upskill-build`, `/upskill-run`, `/upskill-list`, `/upskill-status`, `/upskill-mode`, `/upskill-model`, `/upskill-remove`, or `/upskill-uninstall`, wants a cheap model to perform closer to a Pro model without switching, or wants a good session (success or failure) distilled into a validated skill. Triggers on: upskill, up-skill, flash to pro, teacher student distillation, ralph loop skill validation, distill agent failures into skills. Routes skill-quality ratcheting to `skill-autoresearch`, scaffolding to `write-a-skill`, and spec-compliance rewrites to `skill-standardization`.

Proposes exactly one personal side-project idea per invocation, sized to a 1-3 day MVP. Targets CLI, automation, LLM, DX, productivity, and data-viz angles; avoids clichés like TODO apps, weather apps, and pomodoro timers. Output is an 8-section brief including a ready-to-paste coding-agent prompt. Use for morning/daily idea rituals and weekend-hack ideation. Don't use for existing-product feature proposals (Spark), dialogue brainstorming (Riff), or prototype implementation (Forge).

Validates that a Dynamo deployment's NIXL/UCX/NCCL interconnect is ready for disaggregated serving over RDMA/NVLink. Use after deploying a disagg or multi-node recipe to confirm KV transport is correct, or use troubleshoot for already-failed pods.

Build video analytics pipelines using NVIDIA DeepStream SDK 9.0 with Python pyservicemaker API, including GStreamer-based video processing, TensorRT inference integration, object detection/tracking, and Kafka/message broker integration.

Use kordoc for agent-native HWP/HWPX document parsing, JSON extraction, diffing, form-field extraction, and Markdown→HWPX reverse conversion (read/convert only — for binary editing use rhwp-edit).

Audit specs against codebase — find unimplemented features, diverged implementations, and undocumented code

Clawdex — dual-engine coding agent. Claude Code (reasoning + planning) + OpenAI Codex (fast execution) + Browser Use boxes (web research) + Upstash compute boxes (isolated sandboxes).

Investigates slow responses, tool failures, and guardrail rejections by querying agent trace logs and performance metrics.

Full specialist analysis via parallel agent dispatch. Researcher, Architect, and PM produce a prioritized report of what to build next (30-60s).

Guided first-run that produces a real verified win in under five minutes using the skill library on a seeded offline fixture. Load when a new user asks how to start, run the demo, try agent-loom, or get a quick win. Also triggers on "quickstart", "first run", "demo agent-loom", "try the skills", or onboarding to the library. Zero external credentials required. Idempotent — safe to run multiple times.

DeepClaw - Autonomous Agent Network

PyTorch deep learning development with transformers, diffusion models, and GPU optimization.

Plans and executes complex, multi-step research by decomposing questions, orchestrating subagents, and synthesizing findings into reports.

Use kordoc for agent-native HWP/HWPX document parsing, JSON extraction, diffing, form-field extraction, and Markdown→HWPX reverse conversion (read/convert only — for binary editing use rhwp-edit).

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when predicting an antibody–antigen complex, folding a mixed protein/ligand/nucleic-acid assembly described in one FASTA, or generating a complex with experimental restraints. For binding-affinity prediction or a ligand-focused co-fold prefer alterlab-boltz; for protein-only or protein–protein folding prefer alterlab-alphafold; to dock into a fixed receptor prefer alterlab-diffdock. Part of the AlterLab Academic Skills suite.

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen complexes prefer alterlab-chai; to dock a ligand into a FIXED receptor structure prefer alterlab-diffdock; to look up an existing structure prefer alterlab-pdb. Part of the AlterLab Academic Skills suite.